Contacts of the helix formed by residues 78 - 107 (chain A) in PDB entry 4KPD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ARG 5.1 2.4 + - - +
76A LYS* 3.4 10.1 + - - +
77A GLN* 1.4 77.2 - - - +
79A ALA* 1.3 59.3 + - - +
80A ASP* 3.3 14.1 + - - +
81A SER* 2.9 35.6 + - - -
82A LEU* 2.9 28.6 + - - +
84A ARG* 4.2 4.6 + - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 1.3 72.2 - - - +
80A ASP* 1.3 61.8 + - - +
82A LEU* 3.5 11.1 + - - +
83A GLN* 3.0 28.9 + - - +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 3.3 10.3 + - - +
79A ALA* 1.3 79.7 - - - +
81A SER* 1.3 56.1 + - - +
83A GLN* 3.3 17.6 + - - +
84A ARG* 3.0 50.6 + - - +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.7 24.2 - - - -
72A VAL* 5.6 0.2 - - - +
76A LYS 3.7 10.6 + - - -
77A GLN 4.4 1.3 - - - -
78A ASP* 2.9 38.3 + - - -
80A ASP* 1.3 75.1 - - - +
82A LEU* 1.4 56.5 + - - +
84A ARG* 3.4 24.1 + - - +
85A ALA* 3.1 25.5 + - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 4.5 8.7 - - + -
69A ARG* 3.8 42.6 - - + +
77A GLN* 3.4 41.1 - - + +
78A ASP 2.9 17.9 + - - +
79A ALA* 3.9 8.7 - - - +
81A SER* 1.4 72.1 - - - +
83A GLN* 1.4 65.2 + - - +
85A ALA* 3.2 8.2 + - + +
86A TRP* 3.1 34.7 + - + +
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 4.2 9.3 - - - +
79A ALA 3.0 18.4 + - - +
80A ASP* 3.3 18.3 + - - +
82A LEU* 1.4 75.6 - - - +
84A ARG* 1.4 53.1 + - - +
86A TRP* 3.5 40.2 + - + +
87A THR* 2.8 35.7 + - - -
146A TYR* 3.6 36.8 + - + -
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 4.2 5.7 + - - -
80A ASP* 3.0 32.8 + - - +
81A SER* 3.5 36.6 + - - +
82A LEU 3.3 0.2 - - - -
83A GLN* 1.4 75.4 - - - +
85A ALA* 1.3 56.6 + - - +
87A THR* 3.3 7.3 + - - -
88A VAL* 2.9 34.1 + - - +
146A TYR* 3.2 36.4 + - + +
147A CYS* 4.2 7.6 - - - -
150A GLN* 3.5 34.0 + - - +
152A TYR* 3.4 19.7 + - - -
216A MET* 3.6 13.0 - - + -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.5 12.9 - - + +
65A VAL* 4.2 10.6 - - + +
68A PHE* 3.6 42.0 - - + -
81A SER 3.1 10.0 + - - +
82A LEU* 3.2 11.8 + - + +
84A ARG* 1.3 74.2 - - - +
86A TRP* 1.4 58.7 + - + +
88A VAL 3.4 1.2 + - - -
89A GLY* 3.0 21.8 + - - -
216A MET* 3.6 11.8 - - - +
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.7 12.5 - - + -
20A HIS* 3.1 65.3 + + + -
23A GLN* 3.4 29.6 - - + -
24A ILE* 4.4 9.9 - - + -
65A VAL* 3.6 27.8 - - + +
69A ARG* 6.3 0.7 - - - -
82A LEU* 3.1 29.2 + - + +
83A GLN* 3.5 35.9 - - + +
85A ALA* 1.4 73.1 - - - +
87A THR* 1.4 76.9 + - - +
89A GLY 4.2 0.2 - - - +
90A TRP* 2.9 33.1 + + + -
146A TYR* 5.6 2.7 - - - -
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.9 16.6 - - + +
83A GLN 2.8 22.4 + - - -
84A ARG* 3.3 8.3 + - - -
86A TRP* 1.4 88.3 - - - +
88A VAL* 1.3 59.5 + - + +
90A TRP* 3.1 5.5 + - - +
91A CYS* 2.9 28.7 + - - -
142A LEU* 4.0 22.3 - - + +
143A LEU* 5.9 0.7 - - + -
146A TYR* 3.6 42.2 - - + -
147A CYS* 5.8 0.9 - - - -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.9 10.5 - - + -
84A ARG 2.9 20.8 + - - +
85A ALA 3.8 4.5 - - - +
87A THR* 1.3 72.7 - - + +
89A GLY* 1.3 64.1 + - - +
91A CYS* 3.0 18.3 + - - +
92A VAL* 3.1 13.3 + - - +
143A LEU* 4.0 8.5 - - + -
147A CYS* 4.0 12.1 - - - -
156A LEU* 3.8 18.8 - - + -
160A PHE* 4.3 13.7 - - + -
212A ALA* 3.9 27.8 - - + -
216A MET* 3.7 22.7 - - + -
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.8 3.1 - - - -
61A GLY* 3.2 41.4 - - - -
64A VAL* 3.7 11.4 - - - +
85A ALA 3.0 13.4 + - - -
86A TRP 3.4 4.0 + - - -
87A THR 3.3 0.2 - - - -
88A VAL* 1.3 75.1 - - - +
90A TRP* 1.3 59.0 + - - +
92A VAL* 3.2 4.2 + - - -
93A GLU* 3.1 16.6 + - - +
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Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 2.9 51.9 + + - -
18A VAL* 4.1 7.2 - - - -
20A HIS* 4.2 6.0 - - + +
21A PHE* 3.5 49.1 - + + +
24A ILE* 3.9 33.7 - - + -
53A ALA* 3.5 21.3 - - + -
54A ILE* 3.7 15.7 - - + -
58A TYR* 3.8 13.7 - + - -
86A TRP 2.9 23.9 + - - +
87A THR 3.1 8.9 + - - +
89A GLY* 1.3 75.1 - - - +
91A CYS* 1.4 54.9 + - - +
93A GLU* 3.1 24.1 + - + +
94A LEU* 2.9 36.7 + - + +
142A LEU* 5.2 1.3 - - + -
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 2.9 19.6 + - - -
88A VAL* 3.0 12.3 + - - +
90A TRP* 1.4 71.9 - - - +
92A VAL* 1.3 60.6 + - - +
94A LEU* 3.3 4.4 + - - -
95A LEU 3.0 22.0 + - - -
139A ILE* 3.4 45.0 - - + +
142A LEU* 3.8 22.0 - - - -
143A LEU* 4.1 15.0 - - - -
160A PHE* 3.7 21.0 - - + -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG* 3.6 30.2 - - + -
64A VAL* 3.9 20.4 - - + -
88A VAL* 3.1 14.8 + - + +
89A GLY 3.2 5.8 + - - +
91A CYS* 1.3 74.4 - - - +
93A GLU* 1.4 57.8 + - - +
95A LEU* 3.2 4.6 + - + +
96A GLN* 3.0 26.5 + - - +
160A PHE* 3.6 21.3 - - + -
204A PHE* 4.1 10.7 - - + +
208A LEU* 3.8 28.5 - - + +
209A PRO* 4.6 6.3 - - + -
212A ALA* 5.3 0.7 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.0 20.6 - - + -
53A ALA* 4.6 8.6 - - - +
56A GLY* 6.0 0.3 - - - -
58A TYR* 3.3 38.9 + - - -
59A ASN 4.0 0.2 + - - -
60A ARG* 3.6 10.2 + - - +
61A GLY 2.9 22.2 + - - -
89A GLY 3.1 16.1 + - - +
90A TRP* 3.1 28.5 + - + +
92A VAL* 1.4 75.7 - - - +
94A LEU* 1.3 56.9 + - - +
96A GLN* 3.4 10.1 - - - +
97A ALA* 3.0 26.5 + - - +
113A ARG* 4.6 13.2 + - - -
404A IPE 4.7 3.6 + - - -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 5.3 4.5 - - + -
24A ILE* 5.2 3.8 - - + -
28A LEU* 4.7 2.5 - - + -
49A LEU* 3.7 28.0 - - + -
53A ALA* 4.3 13.9 - - + -
90A TRP* 2.9 21.2 + - + +
91A CYS* 3.6 9.6 - - - +
92A VAL 3.3 0.2 - - - -
93A GLU* 1.3 72.2 - - - +
95A LEU* 1.4 61.2 + - - +
97A ALA* 3.2 5.8 + - - +
98A PHE* 2.9 28.4 + - - +
135A LEU* 3.8 24.3 - - + +
138A CYS* 3.9 21.1 - - + -
139A ILE* 3.8 11.9 - - + +
142A LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A CYS 3.0 10.1 + - - +
92A VAL* 3.2 10.9 + - + +
94A LEU* 1.4 75.5 - - - +
96A GLN* 1.4 61.1 + - - +
98A PHE* 3.3 16.2 + - + +
99A PHE* 3.1 55.6 + - + -
136A GLU* 5.0 2.5 - - + -
139A ILE* 3.7 23.5 - - + +
140A TYR* 5.5 0.9 - - - +
160A PHE* 4.4 9.4 - - + +
163A SER* 4.6 6.1 - - - -
164A SER* 3.4 26.5 - - - +
204A PHE* 4.3 11.4 - - + -
208A LEU* 3.5 31.2 - - + -
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG* 3.1 29.5 + - - +
92A VAL 3.0 12.1 + - - +
93A GLU* 3.4 15.3 - - - +
95A LEU* 1.4 75.2 - - - +
97A ALA* 1.3 55.5 + - - +
99A PHE* 3.2 3.7 + - - +
100A LEU* 2.9 55.0 + - + +
113A ARG* 3.4 20.2 - - - +
204A PHE* 3.2 30.6 - - - -
404A IPE 2.8 41.6 + - - +
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASN 3.4 28.7 - - - +
53A ALA* 4.4 3.4 - - - -
93A GLU 3.0 14.7 + - - +
94A LEU* 3.2 12.8 + - - +
96A GLN* 1.3 75.8 - - - +
98A PHE* 1.4 62.5 + - - +
100A LEU* 3.4 5.9 + - - +
101A VAL* 3.0 30.7 + - - +
113A ARG* 5.2 1.1 - - - +
135A LEU* 3.8 22.2 - - + -
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU 2.9 13.0 + - - +
95A LEU* 3.5 25.6 - - + +
96A GLN 3.3 0.2 - - - -
97A ALA* 1.4 78.3 - - - +
99A PHE* 1.3 91.8 + + - +
101A VAL 3.6 0.2 + - - -
102A ALA* 3.4 22.6 + - + +
132A ALA* 3.2 40.3 - - + +
133A ASN* 3.9 19.5 - - - -
135A LEU* 4.1 4.9 - - + +
136A GLU* 3.7 42.2 - - + +
164A SER* 5.1 0.4 - - - -
168A GLU* 3.7 17.7 - - - -
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.1 47.4 + - + +
96A GLN* 3.8 3.8 - - - +
98A PHE* 1.3 104.9 - + - +
100A LEU* 1.3 58.9 + - - +
102A ALA* 3.6 5.0 + - + +
103A ASP* 2.8 32.7 + - - +
164A SER* 3.7 18.8 - - - -
167A THR* 3.5 44.9 - - + -
168A GLU* 3.8 19.3 - - + -
171A GLN* 4.8 9.3 + - + -
204A PHE* 4.4 14.4 - + + -
405A RIS 4.1 15.4 - + + -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 2.9 41.2 + - + +
97A ALA* 4.0 5.4 - - - +
99A PHE* 1.3 74.6 - - + +
101A VAL* 1.3 60.8 + - + +
103A ASP* 3.9 2.4 - - - +
104A ASP* 3.0 36.4 + - - +
112A ARG* 3.6 51.4 - - + +
113A ARG* 3.5 32.8 - - - +
404A IPE 4.1 7.0 - - + +
405A RIS 4.0 22.7 - - + -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASN* 3.3 39.5 - - + +
97A ALA 3.0 21.5 + - - +
100A LEU* 1.3 76.9 - - + +
102A ALA* 1.3 61.8 + - - +
104A ASP* 4.0 5.8 - - - +
105A ILE* 3.4 20.8 + - - +
118A TRP* 4.0 13.2 - - + -
119A TYR* 5.0 1.9 - - - +
128A ALA* 3.6 38.6 - - + +
131A ASP* 5.2 0.2 - - + -
132A ALA* 3.9 13.9 - - + +
135A LEU* 4.0 7.9 - - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.4 20.9 + - + +
99A PHE* 4.0 4.0 - - + +
101A VAL* 1.3 78.1 - - - +
103A ASP* 1.3 64.7 + - - +
105A ILE* 3.2 15.2 + - + +
106A MET* 3.1 38.8 + - + +
129A ILE* 6.3 1.3 - - + -
132A ALA* 4.4 9.6 - - + +
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE 2.8 24.1 + - - +
100A LEU* 3.9 4.7 - - - +
102A ALA* 1.3 71.6 - - - +
104A ASP* 1.4 51.6 + - - +
106A MET* 3.3 10.9 + - - +
107A ASP* 2.8 35.7 + - - +
112A ARG* 3.7 4.3 + - - -
171A GLN* 3.0 20.1 + - - +
401A MG 2.1 26.4 - - - -
403A MG 1.9 29.6 - - - -
405A RIS 3.0 24.4 + - + +
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Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU 3.0 19.6 + - - +
101A VAL* 4.0 6.1 - - - +
102A ALA 3.3 0.2 - - - -
103A ASP* 1.4 72.2 - - - +
105A ILE* 1.3 64.3 - - - +
108A SER 3.1 1.7 + - - -
109A SER* 2.9 43.1 + - - -
111A THR 4.9 0.7 - - - +
112A ARG* 2.8 47.7 + - - +
117A CYS* 3.5 34.7 - - + +
119A TYR* 3.3 11.0 - - + -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL 3.4 18.1 + - - +
102A ALA* 3.2 14.0 + - - +
104A ASP* 1.3 76.2 - - - +
106A MET* 1.3 61.7 + - + +
108A SER* 3.1 21.3 + - - -
119A TYR* 3.5 35.5 + - + -
125A GLY 5.1 0.2 - - - +
126A LEU* 3.9 24.9 - - + -
128A ALA* 3.9 24.2 - - + -
129A ILE* 3.9 26.9 - - + +
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA* 3.1 34.1 + - + +
103A ASP* 3.9 10.3 - - - +
105A ILE* 1.3 80.6 - - + +
107A ASP* 1.3 65.3 + - - +
108A SER* 3.3 3.8 + - - -
171A GLN* 4.2 18.4 - - + +
175A LEU* 3.8 37.5 - - + +
266A LYS* 5.4 0.2 + - - -
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 2.8 20.5 + - - +
106A MET* 1.3 76.9 - - - +
108A SER* 1.4 70.8 + - - +
109A SER* 3.2 10.6 + - - +
175A LEU* 4.2 9.4 - - - +
260A THR* 3.8 8.9 + - - +
261A ASP* 5.7 0.2 - - - +
264A ASP* 2.6 32.0 - - - +
266A LYS* 3.0 23.0 + - - +
401A MG 2.0 34.1 - - - -
403A MG 2.1 21.7 - - - -
405A RIS 2.7 1.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
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