Contacts of the helix formed by residues 74 - 101 (chain A) in PDB entry 4LOU
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 ASN 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR 3.8 3.9 + - - +
73A ASP* 1.3 79.1 + - + +
75A TYR* 1.3 50.0 + - - +
76A PRO* 3.1 19.4 - - - +
77A LEU* 2.8 39.3 + - + +
78A LEU* 2.8 31.1 + - - +
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 5.9 0.9 - - - -
73A ASP 3.3 7.3 + - - +
74A ASN* 1.3 70.6 - - - +
76A PRO* 1.3 71.3 - - + +
78A LEU* 3.2 10.6 + - + +
79A LEU* 2.9 71.9 + - + +
307A PHE* 4.1 18.4 - + - -
308A VAL* 3.9 11.5 - - + +
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.1 14.4 - - - +
75A TYR* 1.3 102.0 - - + +
77A LEU* 1.3 53.2 + - - +
79A LEU* 3.6 8.2 + - + +
80A THR* 2.6 33.4 + - - -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 3.9 26.9 - - + -
73A ASP* 5.9 0.4 - - - +
74A ASN* 2.8 37.1 + - + +
76A PRO* 1.3 75.5 - - - +
78A LEU* 1.3 63.3 + - - +
80A THR* 3.3 8.9 + - + -
81A VAL* 3.0 44.3 + - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.1 38.4 - - + +
71A THR* 3.1 36.5 + - - +
72A ALA* 3.9 8.1 - - - -
74A ASN 2.8 8.1 + - - +
75A TYR* 3.2 17.3 - - + +
77A LEU* 1.3 72.8 - - - +
79A LEU* 1.3 59.1 + - + +
80A THR 2.9 10.2 + - - -
81A VAL* 3.3 4.3 + - - +
82A ALA* 3.0 22.7 + - + +
307A PHE* 3.3 53.6 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 2.9 68.2 + - + +
76A PRO* 4.0 7.9 - - + +
77A LEU 3.5 0.2 - - - -
78A LEU* 1.3 72.1 - - + +
80A THR* 1.3 59.2 - - - +
82A ALA* 3.9 5.6 - - + +
83A PHE* 3.4 11.1 + - - +
304A LEU* 3.3 34.4 - - + +
307A PHE* 3.8 14.6 - - + -
308A VAL* 3.8 20.9 - - + -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO 2.6 23.1 + - - -
77A LEU* 3.3 11.8 + - + -
78A LEU 2.9 1.0 + - - -
79A LEU* 1.3 78.0 - - - +
81A VAL* 1.3 61.0 + - + +
82A ALA 3.1 4.5 - - - -
83A PHE* 3.4 4.6 + - + +
84A LEU* 2.9 44.7 + - + +
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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
----------------------------------------------------------
67A ALA* 4.5 16.6 - - + +
68A LEU* 3.7 20.8 - - + +
71A THR* 3.9 21.1 - - + +
77A LEU* 3.0 32.8 + - + +
78A LEU 3.3 4.0 + - - +
80A THR* 1.3 75.3 - - + +
82A ALA* 1.3 65.2 + - - +
84A LEU* 4.1 7.6 - - - +
85A CYS* 3.3 31.8 - - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 4.8 2.4 + - - +
68A LEU* 3.8 17.5 - - + -
78A LEU 3.0 17.3 + - - +
79A LEU* 3.9 9.9 - - - +
81A VAL* 1.3 77.6 - - - +
83A PHE* 1.3 65.6 + - - +
85A CYS* 4.2 1.8 - - - +
86A SER* 3.5 23.0 + - - -
303A GLY 3.8 21.7 - - - +
304A LEU* 4.5 5.4 - - + -
307A PHE* 4.7 11.7 - - + -
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 3.4 16.1 + - - +
80A THR* 3.4 5.8 + - + +
82A ALA* 1.3 79.7 - - - +
84A LEU* 1.3 76.7 + - + +
86A SER 3.2 2.1 + - - -
87A ALA* 2.8 38.2 + - + -
296A GLY 4.1 5.2 - - - -
297A ALA* 3.8 17.0 - - + -
300A GLY* 3.3 48.3 - - - +
301A LEU* 3.8 6.5 - - + -
304A LEU* 4.3 12.0 - - + +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A THR* 2.9 33.9 + - + +
81A VAL* 4.6 4.5 - - + -
83A PHE* 1.3 95.9 - - + +
85A CYS* 1.3 59.1 + - - +
87A ALA* 3.5 6.0 - - + +
88A VAL* 3.0 40.0 + - + +
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Residues in contact with CYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 4.0 25.1 - - + +
67A ALA* 4.7 17.0 - - - -
81A VAL* 3.3 28.3 + - - +
82A ALA* 4.2 1.8 - - - +
83A PHE 3.3 0.6 - - - -
84A LEU* 1.3 79.4 - - - +
86A SER* 1.3 60.3 + - - +
88A VAL* 4.1 4.6 + - - +
89A LEU* 3.5 30.3 + - - +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 2.8 18.9 + - - -
82A ALA 3.5 5.7 + - - -
83A PHE 3.2 3.6 + - - -
85A CYS* 1.3 76.6 - - - +
87A ALA* 1.3 59.5 + - - +
89A LEU* 4.1 1.2 - - - +
90A ALA* 3.1 29.5 + - - +
141A GLY* 2.6 33.9 + - - -
143A MET* 5.8 0.3 - - - +
299A GLY* 3.1 27.7 - - - -
303A GLY* 3.1 11.3 - - - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 2.8 28.1 + - + +
84A LEU* 3.5 15.3 - - + +
86A SER* 1.3 75.6 - - - +
88A VAL* 1.3 66.3 + - + +
90A ALA 3.4 0.3 + - - -
91A MET* 3.0 37.0 + - + +
296A GLY* 3.1 29.2 - - - +
300A GLY 3.9 0.2 - - - +
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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
----------------------------------------------------------
84A LEU* 3.0 25.6 + - + +
85A CYS* 4.4 4.9 - - - +
87A ALA* 1.3 76.4 - - + +
89A LEU* 1.3 65.8 + - + +
91A MET* 3.5 18.9 + - + +
92A PHE* 2.9 31.9 + - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.0 30.7 - - + -
64A ARG* 4.7 8.7 - - + -
85A CYS 3.5 19.9 + - - +
86A SER 4.3 2.2 - - - +
87A ALA 3.3 0.2 - - - -
88A VAL* 1.3 80.5 - - + +
90A ALA* 1.3 69.0 + - - +
92A PHE* 3.5 14.0 + - + +
93A GLY 3.2 13.3 + - - -
136A LEU 4.9 2.2 - - - +
137A GLY* 3.3 33.8 - - - +
140A GLY 4.0 23.8 - - - +
141A GLY* 4.2 3.8 - - - -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER 3.1 20.6 + - - +
87A ALA 3.5 3.8 - - - +
89A LEU* 1.3 74.5 - - - +
91A MET* 1.3 53.3 + - - +
93A GLY* 2.9 5.0 + - - -
94A TYR* 2.8 45.4 + - + -
137A GLY 4.0 3.2 + - - -
138A THR* 4.1 10.9 - - - +
141A GLY* 5.5 0.2 - - - -
143A MET* 4.2 5.8 - - + -
295A GLY 3.4 24.0 - - - +
296A GLY* 3.8 0.4 - - - -
299A GLY* 3.8 11.9 - - - -
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Residues in contact with MET 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 3.0 24.5 + - + +
88A VAL* 3.6 23.8 - - + +
90A ALA* 1.3 75.8 - - - +
92A PHE* 1.3 56.0 + - - +
93A GLY 2.9 0.3 + - - -
94A TYR* 3.1 3.2 + - - -
95A PHE* 2.6 38.6 + - - +
292A VAL* 3.1 39.8 - - + +
293A LEU* 4.3 21.3 - - - +
296A GLY* 3.3 13.0 - - - -
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 2.9 23.4 + - + +
89A LEU* 3.7 16.8 - - + +
91A MET* 1.3 75.3 - - - +
93A GLY* 1.3 58.2 + - - +
95A PHE* 4.0 9.6 - + - +
96A LEU* 3.3 46.9 + - + +
133A PHE* 3.8 37.0 - + + -
136A LEU* 6.3 0.2 - - + -
137A GLY* 5.0 4.5 - - - -
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Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU 3.2 6.6 + - - -
90A ALA 2.9 6.8 + - - -
92A PHE* 1.3 77.6 - - - +
94A TYR* 1.3 68.6 + - - +
95A PHE 3.3 0.7 - - - -
96A LEU* 3.6 3.2 + - - +
97A VAL* 3.5 23.9 + - - +
133A PHE 4.9 0.2 - - - -
134A GLY* 3.5 34.7 - - - -
137A GLY* 5.0 0.2 - - - -
138A THR* 4.8 0.4 - - - -
353A PRO* 4.1 5.5 - - - +
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Residues in contact with TYR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 2.8 33.4 + - + -
91A MET* 3.5 8.5 - - - +
93A GLY* 1.3 75.3 - - - +
95A PHE* 1.3 57.9 + - - +
97A VAL* 2.8 23.0 + - - +
98A ARG* 3.2 19.5 + - + +
138A THR* 4.4 2.9 - - + -
143A MET* 3.6 14.4 - - + +
291A TRP* 4.0 30.1 - + - -
292A VAL* 4.2 13.7 - - + -
294A MET* 5.0 0.9 - - + -
295A GLY* 3.2 37.5 - - - -
298A ILE* 3.8 6.6 - - - +
350A SER* 2.4 35.7 + - - -
351A GLY 5.0 1.3 - - - -
352A ALA* 3.3 31.4 - - + +
353A PRO* 4.6 3.3 - - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET 2.6 23.1 + - - +
92A PHE* 4.3 8.7 - + - +
94A TYR* 1.3 74.8 - - - +
96A LEU* 1.3 80.8 + - + +
97A VAL 3.0 1.2 + - - -
98A ARG* 3.5 1.8 + - - +
99A LYS* 3.2 59.1 + - + +
100A TYR* 4.5 10.8 - + - -
288A ILE* 4.1 16.2 - - + -
292A VAL* 3.5 22.6 - - + +
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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
----------------------------------------------------------
92A PHE* 3.3 43.3 + - + +
93A GLY 3.9 6.3 - - - +
94A TYR 3.3 0.4 - - - -
95A PHE* 1.3 98.8 - - + +
97A VAL* 1.3 60.3 + - - +
99A LYS 4.3 0.7 - - - -
100A TYR* 3.6 24.4 + - + -
129A PRO* 4.7 1.8 - - + +
130A VAL* 3.1 45.0 - - + +
133A PHE* 4.3 23.6 - - + -
134A GLY* 4.5 5.4 - - - +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY 3.5 12.9 + - - +
94A TYR* 2.8 13.4 + - - +
96A LEU* 1.3 77.5 - - - +
98A ARG* 1.3 73.3 + - + +
99A LYS 3.2 1.6 - - - -
101A ALA 2.6 42.5 + - - +
102A PRO* 3.1 10.8 - - + +
104A ALA 3.8 20.0 - - - +
105A GLY* 3.8 21.1 - - - +
130A VAL* 3.7 17.9 - - + +
131A LYS* 5.9 0.2 - - - -
351A GLY 4.9 4.0 - - - +
353A PRO* 4.4 13.2 - - + -
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.2 20.5 + - + +
95A PHE 4.5 0.2 - - - +
97A VAL* 1.3 82.4 - - + +
99A LYS* 1.3 59.7 + - - +
100A TYR 3.6 0.2 - - - -
102A PRO* 3.3 44.4 + - - +
286A GLY* 4.2 10.7 + - - -
288A ILE* 3.8 29.8 - - + +
291A TRP* 3.2 64.5 - - + +
292A VAL* 4.9 3.4 - - + -
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.2 39.0 + - + +
97A VAL 3.2 0.4 - - - -
98A ARG* 1.3 80.3 - - - +
100A TYR* 1.3 94.3 + - + +
126A ARG* 4.7 1.7 + - - -
288A ILE* 3.9 14.1 - - + -
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 4.5 17.5 - + - -
96A LEU* 3.6 25.3 + - + -
99A LYS* 1.3 114.2 - - + +
101A ALA* 1.3 62.1 + - - +
102A PRO* 4.3 2.9 - - - -
123A ARG* 3.8 2.0 + - - -
126A ARG* 2.6 47.7 + - + +
130A VAL* 3.7 18.2 - - + -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU 4.0 1.0 + - - -
97A VAL* 2.6 25.4 + - - +
100A TYR* 1.3 82.9 - - - +
102A PRO* 1.3 68.9 - - - +
103A GLU* 3.3 11.0 - - - +
104A ALA* 3.4 18.0 + - + +
123A ARG* 4.4 1.8 - - - +
126A ARG* 4.1 14.6 - - + +
127A VAL* 4.4 3.1 - - + -
130A VAL* 3.7 25.1 - - + -
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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
------------------------------------------------------------
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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il