Contacts of the helix formed by residues 91 - 113 (chain B) in PDB entry 2JC2
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 GLY 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 1.3 79.4 - - - +
92B PHE* 1.3 64.6 - - - -
93B ASN 3.4 2.5 - - - -
94B GLU* 2.7 18.6 + - - -
95B PHE* 3.2 19.1 + - - +
39D PHE* 3.7 5.3 - - - -
47D GLY 4.6 2.0 - - - -
48D GLN* 3.4 17.0 + - - -
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Residues in contact with PHE 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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91B GLY* 1.3 69.9 - - - -
93B ASN* 1.3 78.2 + - - +
95B PHE* 3.1 5.4 + + - +
96B LYS* 3.0 53.0 + - + +
33D ASP* 3.7 21.8 - - + -
35D LEU* 4.1 7.0 - - + -
36D TYR* 3.6 52.3 - + + -
39D PHE* 3.5 42.1 - + + -
47D GLY 4.9 1.4 + - - +
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLY 3.4 1.0 - - - -
92B PHE* 1.3 89.8 - - - +
94B GLU* 1.3 61.5 + - + +
96B LYS* 3.3 11.3 + - - +
97B GLU* 3.1 27.4 + - - +
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 2.9 48.2 - - + +
83B ASP* 5.0 0.7 - - - +
84B ARG* 4.0 15.9 + - - +
85B ASP* 4.7 6.2 - - - +
89B THR 4.5 1.7 - - - +
90B MET* 3.5 20.8 - - + -
91B GLY* 2.7 31.4 + - - +
92B PHE 3.3 0.2 - - - -
93B ASN* 1.3 76.3 - - + +
95B PHE* 1.3 60.4 + - - +
97B GLU* 3.3 12.8 + - - +
98B LEU 2.8 23.6 + - - -
48D GLN* 4.7 1.0 - - - +
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 3.8 11.8 - - - -
91B GLY 3.2 13.5 + - - +
92B PHE* 3.1 16.5 + + - +
94B GLU* 1.3 73.2 - - - +
96B LYS* 1.3 59.9 + - - +
98B LEU* 3.2 6.0 + - + +
99B TRP* 2.9 38.5 + + - +
35D LEU* 4.1 33.2 - - + -
39D PHE* 3.9 23.8 - + + -
49D ILE* 4.1 4.9 - - + -
54D LEU* 3.7 29.4 - - + -
57D CYS* 3.5 31.0 - - + -
58D LEU* 3.9 14.4 - - + -
61D SER* 3.9 16.4 - - - -
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Residues in contact with LYS 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 PHE* 3.0 41.9 + - + +
93B ASN* 3.3 13.0 + - - +
95B PHE* 1.3 74.8 - - - +
97B GLU* 1.3 62.5 + - - +
99B TRP* 3.4 2.8 + - - +
100B ALA* 3.2 23.9 + - - +
33D ASP* 2.8 30.6 + - - +
34D PRO* 5.9 0.2 - - - +
35D LEU* 4.1 23.4 - - + +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 4.0 20.9 - - + +
93B ASN 3.1 14.1 + - - +
94B GLU* 3.4 14.3 - - - +
95B PHE 3.2 0.2 - - - -
96B LYS* 1.3 76.7 - - - +
98B LEU* 1.3 61.4 + - - +
100B ALA* 3.7 5.7 + - - +
101B VAL* 3.3 33.0 + - + +
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Residues in contact with LEU 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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78B MET* 3.9 24.2 - - + -
81B MET* 3.8 26.5 - - + -
82B LEU* 3.4 17.0 - - + +
90B MET* 3.8 16.6 - - + -
94B GLU 2.8 8.0 + - - +
95B PHE* 3.2 8.9 + - + +
97B GLU* 1.3 75.0 - - - +
99B TRP* 1.3 59.1 + - - +
101B VAL* 3.2 5.7 + - + +
102B LEU* 2.9 54.1 + - + +
105B TRP* 6.3 0.2 - - + -
164B VAL* 5.5 0.2 - - + -
54D LEU* 3.7 35.9 - - + -
58D LEU* 4.7 2.7 - - + -
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Residues in contact with TRP 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 PHE* 2.9 27.0 + + + +
96B LYS 3.4 4.9 + - - +
98B LEU* 1.3 76.6 - - - +
100B ALA* 1.3 63.8 + - + +
102B LEU* 3.4 6.2 + - - +
103B ASN* 2.9 61.6 + - + +
106B ARG* 4.8 4.0 - - - -
35D LEU* 3.8 38.5 - - + +
58D LEU* 4.4 6.1 - - + -
61D SER* 3.4 45.6 - - - -
62D GLY* 5.8 0.4 - - - -
63D ILE* 3.4 26.9 - - + +
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Residues in contact with ALA 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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96B LYS 3.2 14.0 + - - +
97B GLU* 3.9 6.3 - - - +
98B LEU 3.3 0.2 - - - -
99B TRP* 1.3 87.4 - - + +
101B VAL* 1.3 58.8 + - + +
103B ASN* 3.7 3.3 + - - +
104B GLY* 3.1 23.4 + - - -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B MET* 5.2 10.1 - - + -
97B GLU* 3.3 22.8 + - + +
98B LEU* 3.2 7.5 + - + +
100B ALA* 1.3 77.6 - - + +
102B LEU* 1.3 61.1 + - + +
104B GLY* 3.3 2.2 + - - -
105B TRP* 3.0 69.3 + - + +
167B ARG* 4.2 15.7 - - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 4.7 7.9 - - + -
78B MET* 3.9 19.5 - - + -
98B LEU* 2.9 42.1 + - + +
99B TRP 3.9 3.4 - - - +
101B VAL* 1.3 76.5 - - + +
103B ASN* 1.3 58.2 + - - +
105B TRP* 3.3 15.8 + - + +
106B ARG* 2.8 30.9 + - - +
156B PHE* 5.1 3.0 - - + -
160B ILE* 3.8 37.4 - - + +
164B VAL* 4.9 1.1 - - + -
58D LEU* 3.8 25.8 - - + -
63D ILE* 4.0 16.2 - - + -
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Residues in contact with ASN 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 TRP* 2.9 47.2 + - + +
100B ALA* 3.9 4.9 - - - +
102B LEU* 1.3 73.3 - - - +
104B GLY* 1.3 60.3 + - - +
106B ARG* 3.0 37.8 - - - +
107B GLN* 3.0 40.9 + - - +
63D ILE* 4.3 3.7 - - + +
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Residues in contact with GLY 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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100B ALA 3.1 15.6 + - - -
101B VAL* 3.6 4.0 - - - -
102B LEU 3.3 0.2 - - - -
103B ASN* 1.3 78.9 + - - +
105B TRP* 1.3 64.0 + - - +
107B GLN* 3.4 7.6 + - - +
108B HIS* 3.2 21.3 + - - +
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Residues in contact with TRP 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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81B MET* 4.9 3.1 - - + -
101B VAL* 3.0 37.5 + - + +
102B LEU* 3.8 11.2 - - + +
104B GLY* 1.3 74.6 - - - +
106B ARG* 1.3 59.4 + - - +
108B HIS* 3.4 8.7 + - + +
109B PHE* 2.9 27.5 + - - +
132B MET* 3.6 24.3 - - + +
156B PHE* 4.9 1.1 - - - -
159B TYR* 4.0 25.9 - + + -
160B ILE* 4.2 23.1 - - + -
163B CYS* 3.9 28.0 - - + -
164B VAL* 3.7 28.3 - - + -
167B ARG* 3.6 29.6 - - - +
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Residues in contact with ARG 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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99B TRP* 4.8 5.3 - - - -
102B LEU 2.8 18.5 + - - +
103B ASN* 3.0 33.1 + - - +
105B TRP* 1.3 75.9 - - - +
107B GLN* 1.3 55.3 + - - +
109B PHE* 3.1 1.4 + - - +
110B ILE* 2.8 60.7 + - + +
156B PHE* 3.8 29.8 - - + -
62D GLY* 2.7 30.9 + - - -
63D ILE* 3.4 29.1 - - + +
64D ALA 4.5 0.8 - - - +
116D ARG* 4.0 13.8 - - - +
1199D SO4 4.2 16.1 + - - +
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Residues in contact with GLN 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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103B ASN* 3.0 34.2 + - - +
104B GLY* 3.7 6.7 - - - +
106B ARG* 1.3 78.2 - - + +
108B HIS* 1.3 57.1 + - - +
110B ILE* 4.1 8.9 - - + +
111B SER* 3.2 27.0 + - - -
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Residues in contact with HIS 108 (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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104B GLY 3.2 13.0 + - - +
105B TRP* 3.6 12.8 - + + +
107B GLN* 1.3 73.4 - - - +
109B PHE* 1.3 64.1 + - - +
111B SER* 3.4 8.1 - - - -
112B LEU* 3.3 58.6 + - + +
124B GLU 5.6 1.4 + - - -
128B ALA* 5.1 9.7 - - + +
159B TYR* 3.3 23.8 - - - +
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Residues in contact with PHE 109 (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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105B TRP 2.9 17.5 + - - +
106B ARG 3.1 4.7 + - - +
108B HIS* 1.3 75.6 - - - +
110B ILE* 1.3 62.6 + - + +
112B LEU* 3.0 10.7 + - + +
113B ASP* 2.9 34.5 + - + -
118B GLY* 3.5 34.5 - - - -
119B THR* 4.0 0.7 - - - -
120B VAL* 3.6 43.0 - - + +
154B ILE 4.0 0.4 - - - -
155B THR 4.1 1.6 - - - -
156B PHE* 3.6 35.9 - + + -
159B TYR* 3.6 43.1 - + + -
1199D SO4 4.8 6.1 - - - -
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Residues in contact with ILE 110 (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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106B ARG* 2.8 49.2 + - + +
107B GLN* 4.2 8.3 - - + +
109B PHE* 1.3 73.7 - - + +
111B SER* 1.3 62.2 + - - +
112B LEU 3.4 0.5 + - - -
113B ASP* 3.5 23.9 + - + +
116D ARG* 6.0 3.1 - - - +
1199D SO4 5.0 14.8 - - - +
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Residues in contact with SER 111 (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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107B GLN 3.2 20.2 + - - -
108B HIS* 3.4 13.0 - - - -
109B PHE 3.1 0.2 - - - -
110B ILE* 1.3 78.9 - - - +
112B LEU* 1.3 62.4 + - - +
113B ASP 5.0 1.2 - - - +
114B THR* 5.8 0.5 - - - -
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Residues in contact with LEU 112 (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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108B HIS* 3.3 48.0 + - + +
109B PHE* 3.0 9.1 + - - +
111B SER* 1.3 78.7 - - - +
113B ASP* 1.3 60.9 + - - +
114B THR* 3.0 18.3 + - - -
120B VAL* 4.1 18.7 - - + +
121B ASP* 5.6 1.4 - - - +
124B GLU* 3.5 45.3 - - + +
159B TYR* 5.3 4.9 - - + +
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 2.9 25.4 + - + +
110B ILE* 3.5 18.6 + - + +
111B SER 5.0 1.2 - - - +
112B LEU* 1.3 72.7 - - - +
114B THR* 1.3 67.0 + - - +
115B ASP 3.5 0.5 + - - -
116B ARG* 3.4 13.8 + - - +
117B SER* 2.7 36.2 + - - -
118B GLY* 2.8 29.1 + - - -
119B THR 3.4 8.4 - - - +
120B VAL* 4.2 5.3 - - - +
67D TYR* 5.7 0.3 - - - -
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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
------------------------------------------------------------
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