Contacts of the helix formed by residues 85 - 107 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D PHE 5.4 2.6 + - - -
23D TYR* 3.0 38.9 + - + +
84D ALA* 1.3 72.8 - - - +
86D PRO* 1.3 74.6 - - + +
87D GLU* 4.4 3.4 - - + +
88D ASP* 3.3 21.8 + - - +
89D THR* 3.1 19.2 + - - -
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Residues in contact with PRO 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ALA 3.4 4.2 - - - +
85D LYS* 1.3 85.8 - - + +
87D GLU* 1.3 59.5 + - + +
89D THR* 3.5 2.3 + - - -
90D LEU* 3.0 27.4 + - - +
118D PRO* 4.2 2.9 - - - +
120D GLN* 4.0 20.4 - - + +
121D ALA* 3.6 30.7 - - + -
124D LEU* 3.9 11.3 - - + +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LYS* 3.3 3.1 + - + +
86D PRO* 1.3 78.5 - - + +
88D ASP* 1.3 63.8 + - - +
90D LEU* 3.6 21.0 + - - +
91D ASN* 3.0 27.7 + - - +
124D LEU* 3.6 28.5 - - + +
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Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PHE* 3.2 51.9 - - + +
23D TYR* 2.5 43.8 + - - +
26D TRP* 4.2 4.9 - - + -
85D LYS* 3.6 16.9 - - - +
86D PRO 3.2 0.2 - - - -
87D GLU* 1.3 82.5 - - - +
89D THR* 1.3 59.7 + - - +
91D ASN* 3.2 1.4 + - - -
92D LEU* 2.9 25.8 + - - +
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TRP* 4.3 4.7 - - - -
80D PHE 3.6 24.9 - - - +
81D SER* 2.8 23.6 + - - +
84D ALA* 3.4 6.4 - - - +
85D LYS 3.1 8.1 + - - -
86D PRO 3.9 2.7 - - - -
88D ASP* 1.3 73.3 - - - +
90D LEU* 1.3 60.7 + - - +
92D LEU* 3.3 7.2 + - + +
93D CYS* 2.8 38.3 + - - -
118D PRO* 3.8 23.6 - - + -
120D GLN* 2.9 22.5 + - - +
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PRO 3.0 18.0 + - - +
87D GLU* 3.7 23.1 - - - +
88D ASP 3.2 0.2 - - - -
89D THR* 1.3 77.4 - - - +
91D ASN* 1.3 62.9 + - - +
93D CYS* 3.1 3.8 + - + +
94D GLN* 3.0 45.7 + - - +
118D PRO* 4.0 21.5 - - + +
124D LEU* 4.4 22.4 - - + +
127D LYS* 6.3 1.8 - - + -
128D GLU* 3.8 33.2 - - + +
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Residues in contact with ASN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ARG* 2.5 34.1 + - - +
21D PHE* 3.3 21.0 - - + -
87D GLU 3.0 18.7 + - - +
88D ASP* 3.4 5.8 - - - +
90D LEU* 1.3 74.7 - - - +
92D LEU* 1.3 62.2 + - - +
94D GLN* 3.3 17.6 + - - +
95D LEU* 3.2 21.5 + - - +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D TRP* 4.9 2.9 - - + -
17D LEU* 4.0 24.9 - - + -
21D PHE* 4.1 7.8 - - + -
26D TRP* 3.5 20.2 - - + -
79D MET* 3.9 23.6 - - + +
81D SER* 3.3 27.8 - - - +
88D ASP 2.9 14.2 + - - +
89D THR 3.6 7.2 - - - +
91D ASN* 1.3 75.8 + - - +
93D CYS* 1.3 66.9 + - - +
94D GLN 3.3 0.2 + - - -
95D LEU* 3.3 16.9 + - + +
96D LEU* 3.0 42.3 + - + +
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Residues in contact with CYS 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D MET 6.1 0.7 - - - -
80D PHE 5.1 2.9 - - - -
89D THR* 2.8 34.0 + - - -
90D LEU* 3.1 8.9 + - - +
92D LEU* 1.3 72.9 - - - +
94D GLN* 1.3 54.2 + - - +
96D LEU* 3.2 1.4 + - - -
97D ASN* 2.6 44.3 + - - +
116D THR* 3.5 34.3 - - - +
117D LEU 3.6 32.3 - - - -
118D PRO* 3.6 7.9 - - + -
128D GLU* 4.6 4.5 - - + -
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU* 3.0 36.3 + - + +
91D ASN* 3.6 19.3 + - - +
93D CYS* 1.3 73.7 - - - +
95D LEU* 1.3 61.4 + - - +
98D ASN* 2.9 43.5 + - - +
128D GLU* 3.6 20.2 + - - +
131D ARG* 3.4 30.8 - - - +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO* 4.8 6.7 - - + -
13D GLU 5.5 0.4 - - - +
14D TRP* 4.0 21.1 - - + -
15D PRO* 3.9 24.0 - - + -
17D LEU* 5.4 3.1 - - + -
20D ARG* 3.9 24.5 - - - +
21D PHE* 6.4 0.2 - - + -
91D ASN* 3.2 9.0 + - - +
92D LEU* 3.4 20.0 - - + +
94D GLN* 1.3 79.5 - - - +
96D LEU* 1.3 69.8 + - + +
98D ASN* 3.9 6.3 - - - +
99D ASP* 3.1 27.8 + - + +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO* 3.7 34.1 - - + -
14D TRP* 5.4 2.2 - - + -
75D THR* 4.1 16.2 - - - +
79D MET* 3.8 41.7 - - + +
92D LEU* 3.0 39.2 + - + +
93D CYS* 3.8 3.1 - - - +
95D LEU* 1.3 80.3 - - + +
97D ASN* 1.3 68.5 + - - +
99D ASP* 3.3 5.3 + - - +
100D LEU* 3.0 28.9 + - + +
116D THR* 4.4 20.0 - - + -
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D CYS 2.6 24.8 + - - +
94D GLN 4.1 1.3 - - - +
96D LEU* 1.3 75.0 - - - +
98D ASN* 1.3 56.2 + - - +
100D LEU* 3.4 4.4 + - - +
101D ALA* 2.9 26.0 + - - +
115D GLY* 3.3 7.0 - - - -
116D THR* 2.8 49.4 + - - +
128D GLU* 2.9 25.4 + - - +
131D ARG* 4.6 0.2 - - - +
132D CYS* 3.3 16.2 - - - -
136D LEU* 3.8 19.5 - - + -
138D PHE* 3.4 14.0 - - + -
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Residues in contact with ASN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLN* 2.9 32.0 + - - +
95D LEU* 3.9 6.5 - - - +
97D ASN* 1.3 75.7 - - - +
99D ASP* 1.3 61.1 + - - +
101D ALA* 3.3 8.3 + - - +
102D SER* 3.1 22.0 + - - -
131D ARG* 2.3 37.9 + - - +
136D LEU* 3.9 4.3 - - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 5.4 3.1 - - - +
10D LEU 4.3 2.1 - - - +
11D PRO* 3.5 44.5 - - + +
12D LYS* 4.7 10.4 + - - +
95D LEU* 3.1 20.0 + - + +
96D LEU 3.8 3.6 - - - +
97D ASN 3.3 0.4 - - - -
98D ASN* 1.3 78.2 - - - +
100D LEU* 1.3 68.4 + - - +
102D SER* 3.2 9.7 + - - -
103D THR* 3.0 28.5 + - - -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.5 31.6 - - + +
73D LEU* 3.6 23.3 - - + +
74D SER* 4.6 8.1 - - - -
75D THR* 4.9 5.4 - - - +
96D LEU* 3.0 16.5 + - + +
97D ASN* 3.4 10.5 - - - +
99D ASP* 1.3 79.3 + - - +
101D ALA* 1.3 63.8 + - - +
103D THR* 3.1 11.2 + - - -
104D VAL* 3.0 26.6 + - + +
113D GLY* 4.3 2.9 - - - -
114D LEU 3.3 35.4 - - - +
115D GLY* 4.2 3.8 - - - -
138D PHE* 3.9 14.6 - - + -
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ASN 2.9 17.0 + - - +
98D ASN 3.5 5.8 - - - +
99D ASP 3.2 0.2 - - - -
100D LEU* 1.3 75.0 - - - +
102D SER* 1.3 57.1 + - - +
104D VAL* 3.2 5.9 + - - +
105D VAL* 3.0 33.2 + - + +
136D LEU* 3.7 40.6 - - + +
138D PHE* 3.8 11.2 - - + -
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASN 3.1 14.0 + - - -
99D ASP* 3.2 13.2 + - - -
101D ALA* 1.3 73.7 - - - +
103D THR* 1.3 66.3 + - - +
105D VAL* 3.5 9.7 + - - +
106D SER* 3.2 25.6 + - - -
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Residues in contact with THR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 4.6 8.9 - - + +
56D PRO* 3.8 31.2 - - + +
73D LEU* 3.9 25.1 - - + -
99D ASP* 3.0 22.1 + - - -
100D LEU* 3.3 10.8 - - - -
102D SER* 1.3 78.0 + - - +
104D VAL* 1.3 61.1 + - - +
106D SER* 3.3 15.2 + - - -
107D TYR* 3.4 10.9 + - - -
111D PHE* 3.9 13.1 - - + -
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LEU* 4.9 5.2 - - + -
100D LEU* 3.0 16.7 + - + +
101D ALA* 3.2 8.7 + - - +
103D THR* 1.3 76.4 - - - +
105D VAL* 1.3 64.0 + - + +
107D TYR 3.3 0.4 + - - +
108D PRO* 3.0 35.6 - - + +
111D PHE* 3.4 32.5 - - + +
112D VAL* 3.9 11.9 - - + +
113D GLY* 3.8 26.7 - - - +
138D PHE* 5.0 3.8 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA* 3.0 23.3 + - + +
102D SER* 3.8 11.2 - - - +
103D THR 3.3 0.2 - - - -
104D VAL* 1.3 78.1 - - + +
106D SER* 1.3 63.8 + - - +
108D PRO* 3.4 14.1 - - - +
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D SER 3.2 13.6 + - - -
103D THR* 3.8 4.7 - - - -
104D VAL 3.3 0.2 - - - -
105D VAL* 1.3 78.8 - - - +
107D TYR* 1.3 93.4 + - - +
108D PRO* 3.7 4.4 - - - +
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D PRO* 3.9 13.7 - - + -
57D GLU* 2.7 46.9 + - + +
60D ILE* 3.5 28.0 - - + -
103D THR 3.4 7.5 + - - -
104D VAL 3.3 5.9 + - - +
106D SER* 1.3 103.0 - - - +
108D PRO* 1.3 61.8 - - - +
109D ARG* 2.9 13.1 + - - -
110D ARG* 3.1 20.0 + - + -
111D PHE* 3.1 33.2 + + + +
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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