Contacts of the helix formed by residues 85 - 107 (chain B) in PDB entry 4IGM
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 LYS 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE 5.2 2.2 + - - -
23B TYR* 3.1 33.3 + - + +
84B ALA* 1.3 72.7 - - - +
86B PRO* 1.3 75.1 - - + +
87B GLU* 4.5 2.2 - - + +
88B ASP* 3.1 22.0 + - - +
89B THR* 3.0 21.7 + - - -
120B GLN* 3.9 0.2 - - - -
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Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA 3.5 6.0 - - - +
85B LYS* 1.3 85.3 - - + +
87B GLU* 1.3 59.1 + - + +
89B THR* 3.3 2.4 + - - -
90B LEU* 3.0 26.9 + - - +
118B PRO* 4.2 2.9 - - - +
120B GLN* 3.9 22.2 - - + +
121B ALA* 3.7 28.7 - - + -
124B LEU* 4.0 11.5 - - + +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS* 3.2 3.3 + - + +
86B PRO* 1.3 80.2 - - + +
88B ASP* 1.3 63.0 + - - +
90B LEU* 3.6 17.4 + - - +
91B ASN* 3.0 26.2 + - - +
124B LEU* 3.3 31.2 - - + +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.4 43.6 - - + +
23B TYR* 2.6 43.0 + - - +
26B TRP* 4.2 6.5 - - + -
85B LYS* 3.1 17.4 + - - +
87B GLU* 1.3 79.1 - - - +
89B THR* 1.3 61.3 + - - +
91B ASN* 3.2 4.0 + - - +
92B LEU* 2.9 25.1 + - - +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TRP* 4.9 3.6 - - - -
80B PHE 3.5 17.5 - - - +
81B SER* 2.8 31.6 + - - +
82B TYR* 4.9 0.4 - - + -
84B ALA* 3.5 6.8 - - - +
85B LYS 3.0 8.2 + - - -
86B PRO 3.3 2.9 + - - -
88B ASP* 1.3 76.0 - - - +
90B LEU* 1.4 58.5 + - - +
92B LEU* 3.2 6.8 + - + +
93B CYS* 2.9 38.4 + - - -
118B PRO* 3.9 15.0 - - + -
120B GLN* 2.8 31.7 + - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO 3.0 16.1 + - - +
87B GLU* 3.7 23.8 - - - +
89B THR* 1.4 74.3 - - - +
91B ASN* 1.3 63.3 + - - +
93B CYS* 3.3 2.1 + - + +
94B GLN* 3.0 50.6 + - + +
118B PRO* 3.9 18.5 - - + +
124B LEU* 4.3 25.4 - - + +
127B LYS* 6.2 2.2 - - + -
128B GLU* 3.8 32.8 - - + +
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Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 5.4 3.6 + - - -
17B LEU* 5.8 0.2 - - - +
20B ARG* 3.1 31.5 + - - +
21B PHE* 3.2 27.7 - - + -
87B GLU 3.0 15.6 + - - +
88B ASP 3.2 9.2 + - - +
90B LEU* 1.3 80.2 - - - +
92B LEU* 1.3 63.4 + - - +
94B GLN* 3.3 14.8 + - - +
95B LEU* 3.3 19.4 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TRP* 4.9 5.4 - - + -
17B LEU* 3.7 31.4 - - + -
21B PHE* 4.5 5.4 - - + -
26B TRP* 3.7 19.3 - - + -
79B MET* 3.9 23.6 - - + +
81B SER* 3.4 26.2 - - - +
88B ASP 2.9 13.9 + - - +
89B THR* 3.2 6.9 + - + +
91B ASN* 1.3 79.5 + - - +
93B CYS* 1.3 57.1 + - - +
95B LEU* 3.3 14.7 + - + +
96B LEU* 2.8 48.5 + - + +
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Residues in contact with CYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B MET 6.0 1.1 - - - -
80B PHE 5.1 2.9 - - - -
89B THR* 2.9 32.6 + - - +
90B LEU* 3.8 6.5 - - - +
92B LEU* 1.3 76.6 - - - +
94B GLN* 1.3 56.9 + - - +
96B LEU 4.5 0.2 - - - +
97B ASN* 2.9 36.6 + - - +
116B THR* 3.6 34.5 - - - +
117B LEU 3.5 32.8 - - - -
118B PRO* 3.6 8.7 - - + -
128B GLU* 3.9 5.8 - - + +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.0 44.8 + - + +
91B ASN* 3.8 17.1 + - - +
92B LEU 3.2 0.2 - - - -
93B CYS* 1.3 76.0 - - - +
95B LEU* 1.3 56.5 + - - +
97B ASN* 3.9 0.2 - - - +
98B ASN* 2.9 44.6 + - - +
128B GLU* 3.5 25.3 + - - +
131B ARG* 4.0 14.3 - - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 5.1 5.8 - - - +
11B PRO* 4.6 8.1 - - + -
13B GLU 5.4 0.4 - - - +
14B TRP* 4.2 18.4 - - + -
15B PRO* 3.6 31.4 - - + -
17B LEU* 5.7 1.6 - - + -
20B ARG* 4.3 16.4 - - - +
91B ASN* 3.3 10.1 + - - +
92B LEU* 3.3 18.3 + - + +
94B GLN* 1.3 78.8 - - - +
96B LEU* 1.3 75.3 + - + +
98B ASN* 3.5 6.2 + - - +
99B ASP* 3.1 22.2 + - + +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PRO* 3.7 33.8 - - + +
14B TRP* 5.5 2.2 - - + -
75B THR* 3.9 20.0 - - + +
79B MET* 3.8 42.4 - - + +
92B LEU* 2.8 42.7 + - + +
93B CYS 4.0 2.5 - - - +
95B LEU* 1.3 78.4 - - + +
97B ASN* 1.3 63.1 + - - +
99B ASP* 3.3 5.4 + - - +
100B LEU* 3.0 26.6 + - + +
116B THR* 4.5 14.1 - - + -
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B CYS 2.9 19.6 + - - +
94B GLN 3.9 1.6 - - - +
96B LEU* 1.3 73.2 - - - +
98B ASN* 1.3 58.0 + - - +
100B LEU* 3.1 12.0 + - - +
101B ALA* 2.8 26.3 + - - +
115B GLY* 3.1 9.5 - - - -
116B THR* 2.9 46.0 + - - +
128B GLU* 2.8 26.5 + - - +
131B ARG* 4.4 0.4 - - - +
132B CYS* 3.3 17.2 - - - -
136B LEU* 4.0 16.6 - - + -
138B PHE* 3.6 6.4 - - + -
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 5.6 1.4 - - - +
105A VAL* 5.6 0.5 - - - +
106A SER* 3.4 30.6 + - - +
107A TYR* 4.9 8.9 + - - -
94B GLN* 2.9 32.9 + - - +
95B LEU* 3.8 5.8 - - - +
97B ASN* 1.3 69.2 - - - +
99B ASP* 1.3 61.3 + - - +
101B ALA* 3.2 15.8 + - - +
102B SER* 3.2 14.3 + - - -
131B ARG* 2.4 38.1 + - - +
136B LEU* 3.9 4.7 - - - +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 5.8 0.2 + - - -
9B ILE* 5.7 2.8 - - - +
10B LEU 4.4 2.6 - - - -
11B PRO* 3.6 43.1 - - + +
12B LYS* 3.9 18.8 + - - -
95B LEU* 3.1 19.6 + - + +
96B LEU 3.8 4.1 - - - +
98B ASN* 1.3 73.2 - - - +
100B LEU* 1.3 68.0 + - - +
102B SER* 3.2 18.6 + - - -
103B THR* 3.3 19.0 + - - -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.6 31.4 - - + +
73B LEU* 3.5 26.2 - - + +
74B SER* 4.3 6.7 - - - -
75B THR* 4.8 5.4 - - - +
96B LEU 3.0 14.9 + - - +
97B ASN* 3.1 12.5 + - - +
99B ASP* 1.3 80.9 + - - +
101B ALA* 1.3 63.0 + - - +
103B THR* 3.2 7.3 + - - +
104B VAL* 3.1 26.4 + - + +
113B GLY* 4.4 6.5 - - - -
114B LEU 3.3 32.8 - - - +
115B GLY* 4.4 2.9 - - - -
138B PHE* 3.7 15.5 - - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 4.0 24.9 - - + -
97B ASN 2.8 16.2 + - - +
98B ASN 3.2 7.8 + - - +
100B LEU* 1.3 72.8 - - - +
102B SER* 1.4 57.0 + - - +
104B VAL* 3.3 7.1 + - - +
105B VAL* 2.9 32.7 + - + +
136B LEU* 4.0 26.9 - - + +
138B PHE* 4.0 9.5 - - + -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 2.9 38.2 + - - +
98B ASN 3.2 12.3 + - - -
99B ASP* 3.2 19.1 + - - -
101B ALA* 1.4 70.1 - - - +
103B THR* 1.3 64.4 + - - +
105B VAL* 3.2 3.7 + - - +
106B SER* 3.0 26.3 + - - -
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.5 10.2 - - + +
56B PRO* 4.0 30.3 - - + +
73B LEU* 3.7 28.3 - - + -
99B ASP* 3.3 17.4 + - - -
100B LEU* 3.2 11.4 + - - +
102B SER* 1.3 76.5 - - - +
104B VAL* 1.3 65.1 + - - +
106B SER* 3.1 14.9 + - - -
107B TYR* 3.2 11.8 + - - +
111B PHE* 3.9 15.7 - - + -
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 5.2 3.1 - - + -
100B LEU* 3.1 15.2 + - + +
101B ALA* 3.6 9.2 - - - +
103B THR* 1.3 75.9 - - - +
105B VAL* 1.3 67.6 + - + +
107B TYR 2.9 1.8 + - - -
108B PRO* 2.8 37.1 - - + +
111B PHE* 4.2 25.8 - - + +
112B VAL* 4.0 9.9 - - + -
113B GLY* 3.8 27.6 - - - +
136B LEU 6.0 1.6 - - - +
138B PHE* 5.0 5.2 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASN* 4.1 41.1 + - + +
101A ALA* 4.1 20.9 - - + +
102A SER* 4.2 6.3 - - - +
105A VAL* 5.4 10.1 - - + -
131A ARG* 4.6 4.9 + - - -
135A GLU* 5.1 1.9 - - - +
136A LEU* 4.3 10.5 - - + +
101B ALA* 2.9 22.9 + - + +
102B SER* 3.2 7.8 + - - +
104B VAL* 1.3 78.9 - - + +
106B SER* 1.3 63.8 + - - +
107B TYR 3.4 0.2 + - - -
108B PRO* 3.4 13.5 - - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN* 3.8 29.8 + - - +
56B PRO* 6.5 0.4 - - - -
102B SER* 3.0 13.6 + - - -
103B THR* 3.7 7.2 - - - -
104B VAL 3.1 0.2 - - - -
105B VAL* 1.3 78.3 - - - +
107B TYR* 1.3 88.3 + - - +
108B PRO* 3.7 3.4 - - - +
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PRO* 4.0 21.1 - - + -
57B GLU* 3.3 30.7 + - + +
60B ILE* 3.8 29.5 - - + +
103B THR 3.2 5.5 + - - -
104B VAL 2.9 6.5 + - - +
106B SER* 1.3 101.2 - - - +
108B PRO* 1.3 58.5 - - - +
109B ARG* 3.0 5.4 - - - -
110B ARG* 2.8 29.9 + - + -
111B PHE* 3.2 39.5 + + + +
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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
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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