Contacts of the helix formed by residues 85 - 107 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E PHE 5.5 2.4 + - - -
23E TYR* 3.0 36.5 + - + +
84E ALA* 1.3 70.1 - - - +
86E PRO* 1.3 75.1 - - + +
87E GLU* 3.2 7.6 - - + +
88E ASP* 3.1 24.1 + - - +
89E THR* 3.0 21.1 + - - -
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Residues in contact with PRO 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E ALA 3.3 6.3 - - - +
85E LYS* 1.3 86.4 - - + +
87E GLU* 1.3 73.4 + - - +
89E THR* 3.7 2.3 + - - -
90E LEU* 3.3 21.0 + - - +
118E PRO* 4.1 3.3 - - - +
120E GLN* 3.9 26.9 - - + +
121E ALA* 3.9 22.9 - - + -
124E LEU* 3.6 10.4 - - + +
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Residues in contact with GLU 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E LYS* 5.1 8.3 - - + -
86E PRO* 1.3 89.4 - - - +
88E ASP* 1.3 68.1 + - - +
90E LEU* 3.3 12.2 - - + +
91E ASN* 2.9 27.7 + - - +
124E LEU* 4.0 14.9 - - - +
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Residues in contact with ASP 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E PHE* 3.5 45.0 - - + +
23E TYR* 2.7 44.0 + - - +
26E TRP* 4.2 6.1 - - + -
85E LYS* 3.1 18.2 + - - +
87E GLU* 1.3 82.4 - - - +
89E THR* 1.3 60.3 + - - +
91E ASN* 3.1 4.2 + - - +
92E LEU* 2.8 26.9 + - - +
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Residues in contact with THR 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E TRP* 4.4 4.0 - - - -
80E PHE 3.5 23.1 - - - +
81E SER* 2.6 24.6 + - - +
84E ALA* 3.6 6.1 - - - +
85E LYS 3.0 8.8 + - - -
86E PRO 4.0 2.7 - - - -
88E ASP* 1.3 74.8 - - - +
90E LEU* 1.3 52.1 + - - +
92E LEU* 3.2 7.0 + - + +
93E CYS* 2.8 39.2 + - - -
117E LEU 4.6 0.7 - - - +
118E PRO* 3.7 24.9 - - + -
120E GLN* 3.0 22.0 + - - +
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Residues in contact with LEU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E PRO 3.3 12.6 + - - +
87E GLU* 3.3 14.4 - - + +
89E THR* 1.3 75.0 - - - +
91E ASN* 1.3 65.9 + - - +
93E CYS* 3.0 5.5 + - - +
94E GLN* 2.7 53.9 + - - +
118E PRO* 4.0 24.4 - - + +
124E LEU* 4.1 30.5 - - + +
127E LYS* 6.3 0.9 - - + -
128E GLU* 4.1 21.5 - - + -
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Residues in contact with ASN 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 2.7 41.7 + - - +
21E PHE* 3.7 13.5 - - + -
87E GLU 2.9 15.7 + - - +
88E ASP* 3.1 8.3 + - - +
90E LEU* 1.3 78.4 - - - +
92E LEU* 1.3 63.9 + - - +
94E GLN* 3.1 21.9 + - - +
95E LEU* 3.1 13.5 + - - +
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E TRP* 5.2 3.1 - - + -
17E LEU* 4.1 21.3 - - + -
21E PHE* 4.2 8.0 - - + -
26E TRP* 3.7 18.2 - - + -
79E MET* 3.7 29.8 - - + +
81E SER* 3.7 22.9 - - - +
88E ASP 2.8 16.1 + - - +
89E THR* 3.7 6.5 - - + +
91E ASN* 1.3 77.4 + - - +
93E CYS* 1.3 62.9 + - - +
95E LEU* 3.3 22.6 + - + +
96E LEU* 3.0 39.7 + - + +
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Residues in contact with CYS 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E MET 6.2 0.2 - - - -
80E PHE 5.5 2.2 - - - -
89E THR* 2.8 26.9 + - - +
90E LEU* 3.4 9.4 - - - +
92E LEU* 1.3 72.2 - - - +
94E GLN* 1.3 58.9 + - - +
96E LEU* 4.4 0.9 - - - +
97E ASN* 2.7 38.2 + - - +
116E THR* 3.4 45.5 - - - +
117E LEU 3.6 23.3 - - - -
118E PRO* 3.7 4.9 - - - -
128E GLU* 4.0 9.4 - - + +
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Residues in contact with GLN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LEU* 2.7 46.2 + - - +
91E ASN* 3.1 18.9 + - - +
93E CYS* 1.3 72.5 - - - +
95E LEU* 1.3 57.9 + - - +
97E ASN* 3.8 1.0 - - - +
98E ASN* 2.9 42.4 + - - +
128E GLU* 3.3 24.3 + - - +
131E ARG* 3.5 18.1 - - - +
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Residues in contact with LEU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PRO* 4.6 8.5 - - + -
13E GLU 5.4 0.7 - - - +
14E TRP* 4.2 19.1 - - + -
15E PRO* 3.8 26.2 - - + -
17E LEU* 5.4 2.7 - - + -
20E ARG* 4.4 21.8 - - - +
91E ASN* 3.1 11.1 + - - +
92E LEU* 3.4 23.1 - - + +
94E GLN* 1.3 75.4 - - - +
96E LEU* 1.3 70.4 + - + +
98E ASN* 3.2 8.5 + - - +
99E ASP* 3.0 27.0 + - + +
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PRO* 3.6 33.7 - - + -
14E TRP* 5.6 1.6 - - + -
75E THR* 3.7 26.5 - - - +
79E MET* 3.9 37.9 - - + +
92E LEU* 3.0 34.7 + - + +
93E CYS* 4.0 2.2 - - - +
95E LEU* 1.3 76.8 - - + +
97E ASN* 1.3 61.4 + - - +
99E ASP* 3.7 4.8 + - - +
100E LEU* 3.1 34.3 + - + +
116E THR* 4.3 20.4 - - + -
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Residues in contact with ASN 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E CYS 2.7 20.2 + - - +
94E GLN 3.9 2.2 - - - +
96E LEU* 1.3 72.6 - - - +
98E ASN* 1.3 57.3 + - - +
100E LEU* 3.4 6.2 + - - +
101E ALA* 3.0 24.9 + - - +
115E GLY* 3.2 9.3 - - - -
116E THR* 2.9 48.2 + - - +
128E GLU* 3.2 23.8 + - - +
131E ARG* 4.4 0.4 - - - +
132E CYS* 3.3 19.2 - - - -
136E LEU* 3.6 18.5 - - + +
138E PHE* 3.5 10.0 - - + -
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Residues in contact with ASN 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLN* 2.9 32.5 + - - +
95E LEU* 3.2 7.3 + - - +
97E ASN* 1.3 74.9 - - - +
99E ASP* 1.3 60.0 + - - +
101E ALA* 3.3 6.3 + - - +
102E SER* 2.9 31.8 + - - +
131E ARG* 2.4 34.5 + - - +
136E LEU* 4.1 6.5 - - - +
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Residues in contact with ASP 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 5.5 4.2 - - - +
10E LEU 4.3 3.1 - - - +
11E PRO* 3.7 39.1 - - + +
12E LYS* 3.2 21.6 + - - +
95E LEU* 3.0 16.9 + - + +
96E LEU 4.1 3.7 - - - +
97E ASN 3.4 0.2 - - - -
98E ASN* 1.3 72.7 - - - +
100E LEU* 1.3 73.9 + - - +
102E SER* 3.3 10.2 + - - -
103E THR* 3.1 27.6 + - - -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 3.7 30.7 - - + +
73E LEU* 3.4 23.8 - - + +
74E SER* 4.4 10.1 - - - -
75E THR* 4.6 7.2 - - - +
96E LEU* 3.1 24.5 + - + +
97E ASN* 3.6 8.1 - - - +
98E ASN 3.3 0.2 - - - -
99E ASP* 1.3 83.2 + - - +
101E ALA* 1.3 63.1 + - - +
103E THR* 3.3 6.2 + - - -
104E VAL* 3.0 24.7 + - + +
113E GLY* 4.2 2.5 - - - -
114E LEU 3.4 33.7 - - - +
115E GLY* 4.3 3.6 - - - -
138E PHE* 3.7 16.2 - - + -
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASN 3.0 17.4 + - - +
98E ASN* 3.3 4.9 + - - +
100E LEU* 1.3 76.7 - - - +
102E SER* 1.3 52.1 + - - +
104E VAL* 3.1 5.0 + - - +
105E VAL* 2.7 39.1 + - - +
136E LEU* 3.8 31.2 - - + +
138E PHE* 3.6 18.6 - - + -
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Residues in contact with SER 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ASN* 2.9 19.2 + - - +
99E ASP* 3.4 16.8 - - - -
101E ALA* 1.3 75.4 - - - +
103E THR* 1.3 62.3 + - - +
105E VAL* 3.2 13.2 - - - +
106E SER* 3.1 23.6 + - - -
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Residues in contact with THR 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 4.4 13.8 - - + +
56E PRO* 3.7 36.4 - - + +
73E LEU* 4.2 14.1 - - + -
99E ASP* 3.1 18.6 + - - -
100E LEU* 3.8 7.4 - - - -
102E SER* 1.3 73.7 - - - +
104E VAL* 1.3 69.0 + - - +
106E SER* 3.2 18.5 + - - -
107E TYR* 3.4 4.5 + - + -
111E PHE* 3.8 21.3 - - + -
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Residues in contact with VAL 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E LEU* 4.7 5.2 - - + -
100E LEU* 3.0 18.1 + - + +
101E ALA* 3.1 10.0 + - - +
103E THR* 1.3 74.6 - - - +
105E VAL* 1.3 60.1 + - - +
107E TYR 2.9 6.4 + - - -
108E PRO* 2.9 37.4 - - + +
111E PHE* 3.9 22.0 - - + +
112E VAL* 3.6 38.4 - - - +
113E GLY* 3.9 6.7 - - - +
136E LEU 5.8 3.6 - - - +
138E PHE* 4.8 6.3 - - + -
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Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ALA 2.7 18.6 + - - +
102E SER* 3.2 23.1 - - - +
104E VAL* 1.3 75.3 - - - +
106E SER* 1.3 61.7 + - - +
108E PRO* 3.3 14.5 - - + +
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E PRO* 5.9 1.3 - - - +
102E SER 3.1 14.5 + - - -
103E THR* 3.3 14.7 - - - -
105E VAL* 1.3 79.7 - - - +
107E TYR* 1.3 87.0 + - - +
108E PRO* 3.5 3.4 - - - +
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Residues in contact with TYR 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E PRO* 3.6 24.9 - - + +
57E GLU* 3.5 30.2 + - + +
60E ILE* 3.6 29.8 - - + -
103E THR 3.4 3.5 + - - -
104E VAL 2.9 7.3 + - - +
106E SER* 1.3 101.2 - - - +
108E PRO* 1.3 54.2 - - - +
109E ARG 2.8 17.0 + - - -
110E ARG* 2.9 18.0 + - + -
111E PHE* 3.3 35.1 + + + +
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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
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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