Contacts of the helix formed by residues 85 - 106 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE 5.6 1.2 + - - -
23A TYR* 3.1 28.1 + - + +
84A ALA* 1.3 73.4 - - - +
86A PRO* 1.4 76.6 - - + +
87A GLU* 2.9 8.8 + - + +
88A ASP* 3.1 28.4 + - - +
89A THR* 3.4 8.3 + - - -
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Residues in contact with PRO 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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84A ALA 3.9 4.3 - - - +
85A LYS* 1.4 84.3 - - + +
87A GLU* 1.3 62.8 + - + +
89A THR 4.0 1.1 + - - -
90A LEU* 3.4 20.6 + - - +
118A PRO* 4.1 4.5 - - - +
120A GLN* 4.0 23.3 - - + +
121A ALA* 3.5 29.6 - - + -
124A LEU* 3.5 15.0 - - + +
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Residues in contact with GLU 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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85A LYS* 2.9 5.6 + - + -
86A PRO* 1.3 78.8 - - + +
88A ASP* 1.3 68.7 + - - +
90A LEU* 3.3 12.5 - - - +
91A ASN* 3.0 25.3 + - - +
124A LEU* 3.3 28.5 - - - +
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Residues in contact with ASP 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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21A PHE* 3.5 48.4 - - + +
23A TYR* 2.4 43.3 + - - +
26A TRP* 4.1 5.6 - - + -
85A LYS* 3.1 18.5 + - - +
87A GLU* 1.3 82.7 - - - +
89A THR* 1.3 66.7 + - - +
91A ASN* 3.0 5.3 + - - +
92A LEU* 2.8 20.4 + - - +
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Residues in contact with THR 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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26A TRP* 4.4 3.5 - - - -
80A PHE 3.7 23.3 - - - +
81A SER* 2.9 25.4 + - - +
84A ALA* 3.5 9.4 - - - +
85A LYS 3.4 3.3 + - - -
86A PRO 4.3 1.1 - - - -
88A ASP* 1.3 77.0 - - - +
90A LEU* 1.3 52.8 + - - +
92A LEU* 3.1 8.6 + - + +
93A CYS* 2.8 40.1 + - - -
117A LEU 4.4 0.2 - - - +
118A PRO* 3.8 25.4 - - + -
120A GLN* 3.1 22.7 + - - +
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Residues in contact with LEU 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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86A PRO 3.4 13.6 + - - +
87A GLU* 3.3 18.6 + - - +
88A ASP 3.2 0.2 - - - -
89A THR* 1.3 79.4 - - - +
91A ASN* 1.3 60.9 + - - +
93A CYS* 3.3 1.0 + - - +
94A GLN* 3.1 50.5 + - + +
118A PRO* 3.8 30.4 - - + +
124A LEU* 4.0 30.5 - - + +
127A LYS* 6.3 0.4 - - + -
128A GLU* 4.2 17.7 - - + +
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Residues in contact with ASN 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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20A ARG* 2.6 41.9 + - - +
21A PHE* 3.5 17.3 - - + -
87A GLU 3.0 13.4 + - - +
88A ASP* 3.0 9.8 + - - +
90A LEU* 1.3 75.9 - - - +
92A LEU* 1.3 63.1 + - - +
94A GLN* 3.2 17.5 + - - +
95A LEU* 3.1 21.0 + - - +
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Residues in contact with LEU 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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14A TRP* 5.1 2.9 - - + -
17A LEU* 3.9 26.9 - - + -
21A PHE* 4.3 5.6 - - + -
26A TRP* 3.7 21.3 - - + -
79A MET* 3.8 21.8 - - + +
81A SER* 3.2 28.9 - - - +
88A ASP 2.8 12.3 + - - +
89A THR* 3.5 9.4 - - + +
91A ASN* 1.3 76.7 + - - +
93A CYS* 1.3 58.6 + - - +
95A LEU* 3.1 19.8 + - + +
96A LEU* 2.9 47.0 + - + +
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Residues in contact with CYS 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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79A MET 6.0 0.7 - - - -
80A PHE 5.2 2.7 - - - -
89A THR* 2.8 30.6 + - - +
90A LEU 3.6 5.8 - - - +
92A LEU* 1.3 73.9 - - - +
94A GLN* 1.3 58.6 + - - +
96A LEU* 4.3 0.9 - - - +
97A ASN* 2.7 37.8 + - - +
116A THR* 3.5 33.9 - - - +
117A LEU 3.5 33.0 - - - -
118A PRO* 3.7 8.5 - - + -
128A GLU* 3.9 5.4 - - + +
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Residues in contact with GLN 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 LEU* 3.1 34.0 + - + +
91A ASN* 3.2 17.4 + - - +
93A CYS* 1.3 76.3 - - - +
95A LEU* 1.3 66.7 + - - +
98A ASN* 3.1 33.6 + - - +
128A GLU* 3.6 24.4 + - - +
131A ARG* 3.7 22.7 - - - +
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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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11A PRO* 4.6 8.3 - - + -
13A GLU 5.3 0.9 - - - +
14A TRP* 4.1 20.0 - - + -
15A PRO* 3.5 31.9 - - + -
17A LEU* 5.4 2.7 - - + -
20A ARG* 4.3 17.0 - - - +
91A ASN* 3.1 12.7 + - - +
92A LEU* 3.4 18.6 - - + +
94A GLN* 1.3 78.9 - - - +
96A LEU* 1.3 73.3 + - + +
98A ASN* 3.7 4.9 - - - +
99A ASP* 3.0 26.6 + - + +
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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
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11A PRO* 3.9 31.0 - - + -
14A TRP* 5.5 1.6 - - + -
75A THR* 3.7 26.9 - - - +
79A MET* 3.8 34.8 - - + +
92A LEU* 2.9 39.4 + - + +
93A CYS 4.1 2.7 - - - +
95A LEU* 1.3 79.1 - - + +
97A ASN* 1.3 61.1 + - - +
99A ASP* 3.6 5.1 + - - +
100A LEU* 2.9 31.5 + - + +
116A THR* 4.1 22.4 - - + -
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Residues in contact with ASN 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 CYS 2.7 21.0 + - - +
94A GLN 4.2 1.1 - - - +
96A LEU* 1.3 75.8 - - - +
98A ASN* 1.3 51.0 + - - +
100A LEU* 3.2 9.4 - - - +
101A ALA* 2.7 35.2 + - - +
115A GLY* 3.3 8.2 - - - -
116A THR* 2.8 49.8 + - - +
128A GLU* 2.6 28.6 + - - +
131A ARG* 4.4 0.4 - - - +
132A CYS* 3.3 15.7 - - - -
136A LEU* 4.0 9.9 - - + -
138A PHE* 3.4 10.8 - - + -
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Residues in contact with ASN 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 GLN* 3.1 22.6 + - - +
95A LEU* 3.7 5.0 - - - +
97A ASN* 1.3 73.0 - - - +
99A ASP* 1.3 67.2 + - - +
101A ALA* 3.1 6.7 + - - +
102A SER* 2.8 28.4 + - - -
131A ARG* 2.4 36.5 + - - +
136A LEU* 4.0 3.5 - - - +
105B VAL* 4.1 14.5 - - + +
106B SER* 3.8 35.1 + - - +
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Residues in contact with ASP 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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9A ILE* 5.2 4.2 - - - +
10A LEU 4.1 3.1 - - - -
11A PRO* 3.4 51.3 - - + +
12A LYS* 4.8 1.0 + - - +
95A LEU* 3.0 20.5 + - + +
96A LEU 3.8 4.5 - - - +
98A ASN* 1.3 73.0 - - - +
100A LEU* 1.3 70.7 + - - +
102A SER* 3.0 18.8 + - - -
103A THR* 3.1 24.5 + - - -
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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
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9A ILE* 3.6 30.7 - - + -
73A LEU* 3.9 25.4 - - + +
74A SER* 4.5 5.2 - - - +
75A THR* 4.7 7.6 - - - +
96A LEU* 2.9 19.9 + - + +
97A ASN* 3.2 10.3 - - - +
99A ASP* 1.3 79.7 + - - +
101A ALA* 1.3 62.8 + - - +
102A SER 3.2 0.3 + - - -
103A THR* 3.2 7.4 + - - -
104A VAL* 3.1 26.3 + - + +
113A GLY* 4.5 6.5 - - - -
114A LEU 3.4 32.1 - - - +
115A GLY* 4.2 7.9 - - - -
116A THR* 6.3 0.2 - - - -
138A PHE* 3.9 9.2 - - + -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ASN 2.7 20.5 + - - +
98A ASN 3.5 4.9 - - - +
100A LEU* 1.3 73.4 - - - +
102A SER* 1.3 57.6 + - - +
104A VAL* 3.6 4.4 + - - +
105A VAL* 3.1 29.3 + - - +
136A LEU* 4.0 27.8 - - + +
138A PHE* 3.8 21.1 - - + -
105B VAL* 4.1 13.2 - - + +
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Residues in contact with SER 102 (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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98A ASN 2.8 17.1 + - - -
99A ASP* 3.3 12.4 - - - -
101A ALA* 1.3 76.8 - - - +
103A THR* 1.3 64.5 + - - +
105A VAL* 3.3 17.0 + - - +
106A SER* 3.1 18.7 + - - -
98B ASN 5.6 1.8 - - - +
102B SER* 2.9 42.5 + - - +
105B VAL* 4.2 6.5 - - - +
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Residues in contact with THR 103 (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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9A ILE* 4.4 12.4 - - + +
56A PRO* 4.0 33.1 - - + +
73A LEU* 3.7 25.6 - - + -
99A ASP* 3.1 22.0 + - - -
100A LEU* 3.5 10.1 - - - +
102A SER* 1.3 77.7 - - - +
104A VAL* 1.3 60.3 + - - +
106A SER* 3.3 16.3 + - - -
107A TYR* 3.5 13.0 + - - -
111A PHE* 3.9 6.8 - - + -
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Residues in contact with VAL 104 (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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73A LEU* 4.6 5.4 - - + -
100A LEU 3.1 20.5 + - - +
101A ALA* 3.9 8.3 - - - +
102A SER 3.3 0.2 - - - -
103A THR* 1.3 74.1 - - - +
105A VAL* 1.3 63.0 + - - +
107A TYR 3.0 2.1 + - - +
108A PRO* 3.0 33.1 - - + +
111A PHE* 3.9 27.8 - - + +
112A VAL* 3.7 12.1 - - - +
113A GLY* 3.6 30.1 - - - +
136A LEU 6.2 0.2 - - - +
138A PHE* 4.8 4.5 - - + -
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Residues in contact with VAL 105 (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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101A ALA 3.1 16.4 + - - +
102A SER* 3.3 15.4 + - - +
104A VAL* 1.3 78.9 - - + +
106A SER* 1.3 66.6 + - - +
107A TYR 3.4 0.5 + - - -
108A PRO* 3.4 18.1 - - + +
98B ASN 5.6 0.9 - - - +
101B ALA* 4.0 17.7 - - + -
105B VAL* 5.4 8.7 - - + -
131B ARG* 4.4 0.7 + - - -
135B GLU* 3.4 28.2 - - - +
136B LEU* 3.5 31.4 - - + +
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Residues in contact with SER 106 (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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56A PRO* 6.2 0.7 - - - -
102A SER 3.1 13.9 + - - -
103A THR* 3.6 10.7 - - - -
104A VAL 3.2 0.6 - - - -
105A VAL* 1.3 82.3 - - - +
107A TYR* 1.3 84.6 + - - +
108A PRO* 3.7 2.6 - - - +
98B ASN* 3.4 36.2 + - - +
131B ARG* 3.5 23.0 + - - +
135B GLU* 4.9 0.7 - - - +
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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