Contacts of the helix formed by residues 78 - 100 (chain A) in PDB entry 3P4P
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 GLU 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A CYS* 1.3 68.1 - - - +
79A GLN* 1.3 55.7 + - - +
80A ASP* 3.2 11.9 - - - +
81A VAL* 2.7 35.6 + - + +
82A VAL* 3.0 12.1 + - - +
224A ARG* 4.6 8.3 - - - +
365A GLN* 5.8 1.6 + - - -
383A VAL 4.3 3.8 - - - +
384A GLY* 2.6 32.7 + - - +
550A HIS* 2.7 31.0 + - - +
567A ASP 3.6 4.7 - - - +
568A VAL* 3.3 8.0 - - - +
569A LYS* 3.1 39.0 + - - +
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Residues in contact with GLN 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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66A PHE* 3.4 14.1 - - + -
70A VAL* 3.8 30.5 - - + +
75A TRP* 4.0 2.8 + - - +
77A CYS 4.1 6.5 + - - +
78A GLU* 1.3 72.9 - - - +
80A ASP* 1.3 61.6 + - - +
82A VAL* 4.2 6.5 - - - -
83A ASP* 3.2 19.6 + - - +
569A LYS 3.1 17.2 + - - +
570A ILE* 3.7 16.3 - - - +
571A THR* 2.9 38.4 + - - +
573A LEU* 2.7 51.6 + - - +
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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
----------------------------------------------------------
78A GLU* 3.7 9.2 - - - +
79A GLN* 1.3 74.4 - - - +
81A VAL* 1.3 70.1 + - - +
83A ASP* 3.8 8.5 - - - +
84A TYR* 3.4 20.4 + - - +
365A GLN* 2.9 35.6 + - - +
569A LYS* 3.8 27.7 + - + +
571A THR* 4.2 17.6 - - + +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.7 22.0 + - + +
80A ASP* 1.3 78.0 + - - +
82A VAL* 1.3 65.8 + - - +
83A ASP 3.1 1.8 - - - -
84A TYR* 3.4 7.5 + - - +
85A PHE* 3.1 20.6 + - - +
365A GLN* 3.8 35.0 - - + +
383A VAL* 3.6 25.8 - - + +
384A GLY 4.0 0.4 - - - -
385A LEU* 3.9 27.4 - - + +
402A PHE* 3.8 23.2 - - + -
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.5 35.0 - - + +
69A THR* 3.7 24.9 - - + -
70A VAL* 4.4 4.0 - - + -
77A CYS* 3.8 25.1 - - + -
78A GLU 3.0 14.3 + - - +
79A GLN* 3.8 8.1 - - - +
80A ASP 3.4 0.2 - - - -
81A VAL* 1.3 77.4 - - - +
83A ASP* 1.3 56.7 + - - +
85A PHE* 3.3 1.2 + - - +
86A VAL* 3.1 31.3 + - + +
384A GLY 4.4 1.3 - - - +
385A LEU* 3.9 22.9 - - + +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.9 15.6 - - + -
79A GLN 3.2 15.1 + - - +
80A ASP* 3.8 8.9 - - - +
82A VAL* 1.3 76.8 - - - +
84A TYR* 1.3 66.5 + - - +
86A VAL* 3.2 9.0 - - - +
87A HIS* 3.1 50.5 + - - -
571A THR* 5.8 1.1 - - + +
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Residues in contact with TYR 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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80A ASP 3.4 11.6 + - - +
81A VAL* 3.4 9.3 + - - +
83A ASP* 1.3 83.8 + - - +
85A PHE* 1.3 56.6 + - - +
87A HIS* 4.1 2.4 - - - +
88A HIS* 3.0 75.0 + + - +
365A GLN 5.7 0.4 - - - -
401A VAL* 4.0 20.2 + - + +
402A PHE* 3.8 20.6 - + - -
404A ARG* 5.5 4.2 - - - -
405A LEU* 3.5 46.6 - - + +
408A GLU* 5.5 0.7 + - - -
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Residues in contact with PHE 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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65A HIS* 3.9 7.6 - + - -
69A THR* 5.2 0.9 - - - -
81A VAL 3.1 18.0 + - - +
82A VAL* 3.5 4.3 - - + +
83A ASP 3.1 0.2 - - - -
84A TYR* 1.3 78.5 - - - +
86A VAL* 1.3 79.8 + - + +
88A HIS* 3.4 1.0 + - - +
89A CYS* 3.0 52.3 + - - -
385A LEU* 3.5 23.6 - - + -
394A ASN* 3.6 46.0 - - - -
397A ALA* 3.7 6.7 - - + -
398A GLU* 3.4 28.0 - - - -
401A VAL* 4.2 7.5 - - + +
402A PHE* 3.4 26.0 - + + -
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Residues in contact with VAL 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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55A VAL* 5.3 0.2 - - - +
62A PHE* 3.0 41.5 - - + +
65A HIS* 3.4 40.8 + - + +
66A PHE* 3.6 20.4 - - + +
69A THR* 4.9 0.2 - - - +
82A VAL* 3.1 16.5 + - + +
83A ASP* 3.2 17.3 - - - +
85A PHE* 1.3 87.0 - - + +
87A HIS* 1.3 70.2 - - + +
89A CYS* 3.3 4.5 + - - +
90A PRO* 3.0 15.1 - - - +
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Residues in contact with HIS 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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62A PHE* 3.7 43.8 - + + +
83A ASP* 3.1 41.4 + - - +
84A TYR* 4.1 4.0 - - - +
86A VAL* 1.3 85.1 - - + +
88A HIS* 1.3 66.5 + - + +
90A PRO* 3.6 9.0 - - - +
91A THR* 4.8 4.5 + - - -
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Residues in contact with HIS 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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84A TYR* 3.0 68.2 + + - +
85A PHE 3.4 0.4 + - - -
87A HIS* 1.3 81.7 - - + +
89A CYS* 1.3 65.8 + - - +
90A PRO 3.4 0.7 - - - -
91A THR* 3.3 20.6 + - + -
92A GLU* 3.2 24.9 + - + +
401A VAL* 3.5 21.1 - - + -
404A ARG* 5.7 8.5 - - - -
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Residues in contact with CYS 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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53A ALA 3.5 25.8 - - - +
54A ALA* 3.7 7.4 - - - +
65A HIS* 4.1 6.1 - - + -
85A PHE* 3.0 57.6 + - - +
86A VAL* 3.5 4.0 - - - +
88A HIS* 1.3 76.9 - - - +
90A PRO* 1.3 74.1 - - + +
92A GLU 3.1 10.9 + - - -
93A MET* 3.1 18.9 + - + +
397A ALA* 3.7 7.0 - - - -
401A VAL* 3.8 9.2 - - - -
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Residues in contact with PRO 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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54A ALA* 3.9 9.6 - - + -
55A VAL 3.5 24.2 - - - +
62A PHE* 3.3 30.1 - - + -
86A VAL 3.0 15.3 - - - +
87A HIS 3.6 7.9 - - - +
89A CYS* 1.3 92.8 - - + +
91A THR* 1.3 60.7 + - - +
93A MET* 4.1 1.5 - - + +
94A THR* 3.1 30.1 + - - +
125A TRP* 4.7 4.3 - - + -
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Residues in contact with THR 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 HIS 4.8 3.6 + - - -
88A HIS* 3.3 26.2 + - + +
89A CYS 3.2 0.6 - - - -
90A PRO* 1.3 79.7 - - - +
92A GLU* 1.3 74.6 + - - +
94A THR* 3.8 5.3 - - - -
95A GLN* 3.0 26.0 + - + +
404A ARG* 4.2 11.0 - - - +
127B ALA* 4.1 16.0 - - + +
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Residues in contact with GLU 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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18A ARG* 2.2 33.9 + - - -
88A HIS* 3.2 15.5 + - + +
89A CYS 3.1 4.9 + - - +
91A THR* 1.3 84.0 - - + +
93A MET* 1.3 62.4 + - - +
94A THR 3.2 0.2 - - - -
95A GLN* 3.4 8.7 + - - +
96A LEU* 3.1 30.8 + - - +
99A TRP* 5.2 0.3 - - - -
400A VAL* 3.5 37.5 - - + +
401A VAL* 3.9 10.1 - - + -
404A ARG* 2.7 37.5 + - - -
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Residues in contact with MET 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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52A SER* 3.2 27.4 - - - +
53A ALA 3.8 18.2 - - - +
54A ALA* 3.9 6.5 - - + -
89A CYS* 3.1 38.3 + - - +
90A PRO 4.2 0.2 - - - +
92A GLU* 1.3 74.3 - - - +
94A THR* 1.3 64.5 + - - +
96A LEU* 3.6 12.2 + - - +
97A GLU* 3.1 16.1 + - - +
103A TRP* 3.3 23.6 + - + -
125A TRP* 3.5 46.0 - - + -
135A MET* 4.9 0.2 - - - -
397A ALA* 3.9 13.7 - - + +
400A VAL* 4.0 19.7 - - + -
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Residues in contact with THR 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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90A PRO* 3.1 19.6 + - - +
91A THR* 3.8 3.4 - - - -
93A MET* 1.3 76.2 - - - +
95A GLN* 1.3 53.8 + - - +
97A GLU* 2.9 9.5 + - - +
98A LEU* 2.7 35.4 + - + +
125A TRP* 3.8 8.4 - - - -
127B ALA* 3.5 37.7 - - - +
130B GLY* 3.8 22.2 - - - +
131B THR* 3.8 16.2 - - + +
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Residues in contact with GLN 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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18A ARG* 4.8 2.9 - - - +
91A THR* 3.0 19.1 + - + +
92A GLU* 3.4 18.8 + - - +
94A THR* 1.3 77.0 - - - +
96A LEU* 1.3 57.1 + - - +
98A LEU* 3.2 19.2 + - - +
99A TRP* 2.8 76.6 + - + -
404A ARG* 5.3 6.0 - - - +
126B THR* 5.6 0.8 - - - +
127B ALA* 3.9 20.0 - - + +
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Residues in contact with LEU 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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18A ARG* 6.1 0.4 - - - -
92A GLU* 3.1 20.3 + - - +
93A MET* 3.8 10.1 - - - +
95A GLN* 1.3 75.8 - - - +
97A GLU* 1.3 58.4 + - - +
99A TRP* 2.9 25.1 + - + +
100A GLY 3.0 10.0 + - - -
101A CYS* 3.0 18.6 + - + +
103A TRP* 4.0 16.2 - - + -
135A MET* 3.6 40.6 - - + +
138A THR* 4.0 21.6 - - + +
139A LEU* 3.9 34.1 - - + -
400A VAL* 4.0 10.8 - - + -
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Residues in contact with GLU 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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93A MET 3.1 7.7 + - - +
94A THR 2.9 7.7 + - - +
96A LEU* 1.3 74.6 - - - +
98A LEU* 1.3 71.3 + - - +
100A GLY* 2.9 15.2 + - - -
101A CYS 4.1 4.3 - - - -
103A TRP* 3.6 28.4 - - + +
105A ARG* 2.4 35.3 + - - +
111A VAL* 4.5 0.9 - - + -
131B THR* 3.1 25.5 - - + -
132B ASN* 3.0 30.6 + - - +
184B ARG* 3.0 29.5 + - - +
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Residues in contact with LEU 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 THR* 2.7 23.7 + - + +
95A GLN* 3.4 25.1 - - - +
97A GLU* 1.3 83.5 + - - +
99A TRP* 1.3 63.6 + - + +
100A GLY 3.3 1.0 + - - -
120B ILE* 3.8 19.8 - - - +
123B ASN* 5.6 2.6 - - - +
125B ARG* 3.1 42.6 - - + +
126B THR* 3.6 2.7 - - - -
127B ALA* 3.5 27.4 - - - +
130B GLY 4.1 7.6 - - - +
131B THR* 4.3 0.9 - - - -
132B ASN* 3.2 28.5 + - - +
184B ARG* 5.9 1.7 - - - +
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Residues in contact with TRP 99 (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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18A ARG* 3.5 42.4 - - - -
21A ILE* 3.7 25.6 - - + -
25A GLN* 4.0 15.5 - - - +
92A GLU* 5.2 0.2 - - - -
95A GLN* 2.8 48.9 + - + -
96A LEU* 2.9 19.0 + - + +
98A LEU* 1.3 75.5 - - + +
100A GLY* 1.3 57.6 + - - +
138A THR* 3.9 10.2 - - + +
139A LEU* 3.9 24.0 - - + -
142A THR* 3.5 42.1 + - + +
145A GLN* 4.8 6.3 - - - +
146A PHE* 5.3 2.1 - + - -
120B ILE* 3.2 22.1 + - + +
179B TYR* 4.4 5.7 + - - -
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Residues in contact with GLY 100 (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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97A GLU 2.9 9.9 + - - -
98A LEU 3.2 0.8 - - - -
99A TRP* 1.3 79.6 - - - +
101A CYS* 1.3 63.3 + - - +
102A PRO* 3.2 0.7 - - - +
138A THR* 4.3 4.6 + - - -
120B ILE* 3.7 15.9 - - - -
178B ARG* 3.0 21.2 + - - -
179B TYR* 5.1 2.5 - - - -
184B ARG* 2.9 26.1 + - - -
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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
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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) + - + + + + + -
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il