Contacts of the helix formed by residues 86 - 108 (chain B) in PDB entry 4DKE
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 SER 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B VAL* 1.3 77.1 - - - +
87B GLU* 1.3 64.2 + - - +
88B ARG* 3.4 16.5 + - - +
89B GLU* 3.0 27.6 + - - +
90B LEU* 3.0 21.8 + - - +
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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
----------------------------------------------------------
81B GLN* 4.4 19.9 + - - +
85B VAL 3.3 4.2 + - - +
86B SER* 1.3 72.8 + - - +
88B ARG* 1.3 61.8 + - + +
90B LEU* 3.6 13.7 + - - +
91B ARG* 3.5 44.9 + - + +
174B LEU 4.9 2.3 - - - +
175B LEU* 4.7 22.1 - - - +
178B SER* 6.2 0.5 - - - -
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 5.3 7.5 + - - -
86B SER* 3.4 10.7 + - - +
87B GLU* 1.3 79.4 - - + +
89B GLU* 1.3 64.1 + - - +
91B ARG* 3.4 22.4 + - - +
92B TYR* 3.3 20.6 + - - +
132B GLY 3.3 26.1 + - - -
133B LEU* 3.8 29.4 + - - +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.7 23.6 - - + +
86B SER* 3.0 26.6 + - - +
88B ARG* 1.3 79.7 - - - +
90B LEU* 1.3 58.8 + - - +
92B TYR* 3.3 13.8 + - + +
93B LEU* 3.0 31.7 + - + +
142B VAL* 3.7 32.3 - - - +
143B GLU* 4.6 8.2 - - - +
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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
----------------------------------------------------------
72B PHE* 4.3 8.7 - - + -
77B VAL* 4.0 25.1 - - + -
80B LEU* 3.4 39.7 - - + -
81B GLN* 4.1 20.9 - - + +
85B VAL* 3.8 30.3 - - + +
86B SER 3.0 12.9 + - - +
87B GLU* 3.9 14.6 - - - +
88B ARG 3.2 0.2 - - - -
89B GLU* 1.3 76.1 - - - +
91B ARG* 1.3 59.8 + - - +
93B LEU* 3.8 6.6 - - + +
94B TRP* 3.0 26.3 + - - +
175B LEU* 3.6 18.3 - - + +
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 4.0 19.1 + - - -
87B GLU* 3.5 32.5 + - - +
88B ARG* 3.4 30.9 + - - +
89B GLU 3.3 0.6 - - - -
90B LEU* 1.3 75.6 - - - +
92B TYR* 1.3 60.8 + - - +
94B TRP* 3.7 7.4 - - + -
95B VAL* 3.0 30.3 + - - +
129B VAL* 5.6 1.1 - - + +
133B LEU* 4.6 12.2 - - + +
175B LEU* 3.2 39.0 + - + +
176B TYR* 3.1 41.7 - - + +
179B CYS* 4.1 25.7 - - - +
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Residues in contact with TYR 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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88B ARG 3.3 11.5 + - - +
89B GLU* 3.4 17.7 - - + +
91B ARG* 1.3 77.7 - - - +
93B LEU* 1.3 64.7 + - + +
95B VAL* 2.9 29.1 - - + +
96B LEU* 3.2 36.1 - - + +
130B GLN* 4.5 18.6 + - + -
133B LEU* 3.9 39.2 - - + +
143B GLU* 5.7 6.3 - - - -
146B LEU* 5.2 12.0 - - + +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.8 25.6 - - + -
80B LEU* 4.3 21.8 - - + -
85B VAL* 6.2 2.7 - - + -
89B GLU* 3.0 20.4 + - + +
90B LEU* 3.8 9.4 - - + +
92B TYR* 1.3 81.3 - - + +
94B TRP* 1.3 60.2 + - - +
96B LEU* 3.4 7.7 + - - +
97B VAL* 3.3 35.4 + - + +
143B GLU* 5.7 6.7 - - + -
145B VAL* 4.7 22.0 - - + -
1D NAG 4.3 8.7 - - + -
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Residues in contact with TRP 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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38B THR* 5.1 1.6 - - + -
41B LEU* 3.9 15.7 - - + -
72B PHE* 3.7 19.9 - + + -
90B LEU 3.0 18.9 + - - +
91B ARG* 3.7 11.4 - - - +
92B TYR 3.3 0.2 - - - -
93B LEU* 1.3 78.6 - - - +
95B VAL* 1.3 84.4 + - + +
97B VAL* 3.7 1.6 + - - +
98B SER* 2.8 36.8 + - - -
126B LEU* 4.5 4.5 - - + -
129B VAL* 4.6 15.0 - - + -
168B CYS* 2.8 42.2 + - - -
171B VAL* 3.5 26.2 - - + -
172B MET* 3.3 44.6 - - + +
175B LEU* 4.1 8.5 - - + -
176B TYR* 4.4 20.0 - + - -
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Residues in contact with VAL 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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91B ARG 3.0 16.2 + - - +
92B TYR* 2.9 33.2 - - + +
94B TRP* 1.3 87.7 - - + +
96B LEU* 1.3 63.7 + - + +
98B SER* 3.5 4.3 - - - -
99B LEU* 3.0 29.8 + - + +
126B LEU* 3.4 34.8 - - + +
129B VAL* 4.1 15.7 - - + -
130B GLN* 4.2 22.0 - - + -
133B LEU* 5.0 6.1 - - + -
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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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92B TYR* 3.2 46.4 + - + +
93B LEU* 3.8 6.3 - - - +
94B TRP 3.2 0.4 - - - -
95B VAL* 1.3 79.3 - - + +
97B VAL* 1.3 61.2 + - + +
99B LEU* 3.1 10.6 + - + +
100B SER* 2.8 30.6 + - - -
130B GLN* 3.2 33.4 - - - +
146B LEU* 4.0 27.4 - - + -
149B LEU* 4.7 6.5 - - + +
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Residues in contact with VAL 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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69B GLU 3.8 16.6 - - - +
70B GLY* 3.3 30.3 - - - +
72B PHE* 3.7 24.9 - - + +
93B LEU* 3.3 33.0 + - + +
94B TRP 4.1 2.9 - - - +
96B LEU* 1.3 76.1 - - + +
98B SER* 1.3 59.1 + - - +
100B SER* 3.4 2.3 + - - -
101B ALA* 2.9 30.0 + - + +
149B LEU* 4.2 16.1 - - + +
167B ASN* 6.5 0.2 - - + -
1D NAG 4.6 1.3 - - + -
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 2.8 28.8 + - - -
95B VAL 3.5 0.9 - - - -
97B VAL* 1.3 79.3 - - - +
99B LEU* 1.3 62.4 + - - +
101B ALA* 3.1 9.4 + - - +
102B THR* 3.1 24.8 + - - +
126B LEU* 3.3 29.4 - - - -
165B LEU* 5.7 0.7 - - - +
168B CYS* 2.9 34.0 - - - +
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Residues in contact with LEU 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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95B VAL* 3.0 25.4 + - + +
96B LEU* 3.5 11.2 - - + +
98B SER* 1.3 74.1 - - - +
100B SER* 1.3 64.6 + - - +
102B THR* 2.5 23.3 + - - -
103B GLU* 3.1 14.9 + - + +
123B GLU* 3.8 24.2 - - + +
126B LEU* 3.5 29.4 - - + +
127B LEU* 4.1 20.2 - - + +
130B GLN* 4.1 34.1 - - + +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO* 5.4 6.4 - - - +
70B GLY* 5.4 4.2 - - - -
96B LEU 2.8 16.0 + - - -
97B VAL* 3.5 8.5 + - - -
99B LEU* 1.3 71.2 - - - +
101B ALA* 1.3 54.1 + - - +
103B GLU* 3.1 14.7 + - - +
104B SER* 2.8 44.0 + - - -
149B LEU* 3.8 26.8 + - - +
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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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66B VAL* 6.1 0.4 - - - -
70B GLY 5.5 0.4 - - - +
97B VAL* 2.9 16.3 + - + +
98B SER* 3.2 13.5 - - - +
100B SER* 1.3 77.3 + - - +
102B THR* 1.3 56.5 + - - +
104B SER* 3.2 6.8 + - - -
105B VAL* 2.9 35.2 + - - +
119B LEU* 5.3 0.2 - - - -
164B LEU* 4.1 36.6 - - + +
165B LEU* 5.0 8.7 - - + -
168B CYS* 6.3 0.9 - - + -
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Residues in contact with THR 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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98B SER 3.1 13.1 + - - +
99B LEU* 2.5 26.7 + - - -
101B ALA* 1.3 74.7 - - - +
103B GLU* 1.3 55.8 + - - +
106B GLN* 2.9 33.9 + - - +
119B LEU* 3.7 36.7 - - + +
122B VAL* 3.8 18.4 - - + -
123B GLU* 4.0 16.7 + - - +
126B LEU* 3.8 19.2 - - + +
165B LEU* 4.6 8.1 - - + -
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Residues in contact with GLU 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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99B LEU* 3.9 8.3 - - - +
100B SER* 3.1 15.9 + - - +
102B THR* 1.3 78.9 + - - +
104B SER* 1.3 57.6 + - - +
106B GLN* 3.6 6.0 - - - +
107B ASP* 2.8 38.4 + - - +
123B GLU* 3.3 21.0 - - - +
98I LYS* 4.1 36.0 + - + +
99I GLY 4.5 0.2 + - - -
100I LYS* 2.1 39.0 - - - -
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Residues in contact with SER 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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64B ILE* 3.6 22.8 - - - +
65B SER 5.1 2.8 + - - -
66B VAL* 4.3 15.5 - - - +
67B PRO* 5.6 3.6 - - - +
100B SER* 2.8 25.5 + - - -
101B ALA* 3.5 7.2 - - - -
103B GLU* 1.3 78.5 - - - +
105B VAL* 1.3 60.5 + - - +
107B ASP* 3.7 4.7 + - - +
108B VAL* 3.7 17.0 + - - +
54I TYR* 4.9 0.5 + - - -
98I LYS* 3.6 23.3 + - - +
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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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54B MET* 4.4 5.4 - - - -
58B PHE* 3.8 26.2 - - + -
64B ILE* 3.7 20.0 - - + -
101B ALA 2.9 17.8 + - - +
102B THR 4.2 0.7 - - - +
104B SER* 1.3 75.4 - - - +
106B GLN* 1.3 61.9 + - - +
108B VAL* 3.0 26.3 - - + +
109B LEU* 3.3 6.2 - - - +
119B LEU* 3.6 26.9 - - + -
161B PRO* 4.1 22.7 - - + +
164B LEU* 3.8 14.6 - - + -
165B LEU* 6.0 1.8 - - + -
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Residues in contact with GLN 106 (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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102B THR 2.9 21.1 + - - +
103B GLU* 3.8 3.8 - - - +
105B VAL* 1.3 76.7 - - - +
107B ASP* 1.3 64.7 + - - +
109B LEU* 3.2 13.5 + - - +
116B TRP* 3.3 60.7 + - + +
119B LEU* 4.1 17.9 - - + +
120B GLN* 3.1 32.1 + - - +
123B GLU* 4.1 14.4 - - - +
98I LYS 4.4 2.1 - - - +
99I GLY* 3.7 5.4 - - - -
100I SER* 3.6 23.5 + - - +
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Residues in contact with ASP 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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60A ILE* 3.5 7.3 - - - +
103B GLU 2.8 20.2 + - - +
104B SER 4.0 4.5 - - - +
105B VAL 3.3 0.4 - - - -
106B GLN* 1.3 69.5 - - - +
108B VAL* 1.3 57.8 + - - +
109B LEU 2.9 8.3 + - - +
33I TRP* 3.3 22.0 + - - -
54I TYR* 2.5 34.8 + - - +
98I LYS* 3.5 27.5 - - + +
99I GLY* 3.0 19.7 + - - +
100I ARG* 2.6 28.2 + - - -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 3.5 3.5 - - - +
60A ILE* 2.7 38.6 + - + +
58B PHE* 5.0 2.0 - - + -
62B TYR* 4.2 19.7 - - + +
64B ILE* 4.0 30.3 - - + -
104B SER 3.7 11.9 - - - +
105B VAL* 3.0 23.8 - - - +
107B ASP* 1.3 73.8 - - - +
109B LEU* 1.3 66.5 + - + +
54I TYR* 3.8 24.5 - - + +
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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