Contacts of the helix formed by residues 91 - 112 (chain A) in PDB entry 2J3W
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 GLN 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.7 19.8 - - + -
87A HIS* 4.4 1.0 + - - -
89A VAL* 3.2 11.7 + - + +
90A ARG* 1.3 74.8 - - - +
92A GLU* 1.3 57.7 + - - +
93A ASP 3.4 1.6 - - - +
94A GLY* 3.8 14.0 - - - +
95A ILE* 2.7 51.2 + - + +
137A HIS 3.1 22.4 - - - +
138A LEU* 3.2 23.7 + - - +
140A SER* 4.0 16.2 + - - -
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 2.9 33.5 + - + +
62A LYS* 3.1 41.8 + - + +
90A ARG* 3.9 1.6 - - - +
91A GLN* 1.3 74.0 - - - +
93A ASP* 1.3 68.4 + - - +
95A ILE* 4.8 0.7 - - - -
96A LYS* 2.9 28.7 + - - +
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Residues in contact with ASP 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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91A GLN 3.4 0.4 - - - -
92A GLU* 1.3 90.8 - - - +
94A GLY* 1.3 63.7 + - - +
96A LYS* 3.2 10.2 + - - +
97A ASN* 2.9 35.8 + - - +
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 3.2 18.8 + - - +
93A ASP* 1.3 79.7 - - - +
95A ILE* 1.3 62.4 + - - +
97A ASN* 3.2 6.4 + - - +
98A PHE* 3.1 18.9 + - - +
137A HIS* 3.6 31.2 - - - +
138A LEU* 4.7 1.6 - - - -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.6 4.5 - - + -
60A TYR* 4.0 9.4 - - - +
73A SER* 4.2 8.1 - - - +
85A MET* 4.3 11.2 - - + -
87A HIS* 3.4 50.7 - - + +
91A GLN* 2.7 34.8 + - + +
92A GLU 3.9 2.5 - - - +
94A GLY* 1.3 71.0 - - - -
96A LYS* 1.3 62.7 + - - +
98A PHE* 3.4 1.9 + - - +
99A PHE* 3.0 51.4 + - + -
138A LEU* 4.3 20.6 - - + +
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.6 44.4 + - + -
75A PHE* 5.3 1.7 - - + -
92A GLU 2.9 18.0 + - - +
93A ASP* 3.5 11.0 - - - +
94A GLY 3.2 0.2 - - - -
95A ILE* 1.3 77.3 - - - +
97A ASN* 1.3 64.9 + - - +
99A PHE* 3.1 7.0 + - - +
100A THR* 2.9 39.0 + - - +
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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
----------------------------------------------------------
93A ASP* 2.9 26.1 + - - +
94A GLY* 3.2 5.4 + - - +
96A LYS* 1.3 83.4 - - - +
98A PHE* 1.3 62.2 + - - +
100A THR* 3.9 6.2 - - - -
101A ASP* 3.0 30.8 + - - +
137A HIS* 3.2 31.5 + - + +
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Residues in contact with PHE 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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7A PHE* 3.8 22.2 - + - -
22A PHE* 4.4 5.2 - + - -
85A MET* 3.3 31.2 - - + -
94A GLY 3.1 12.8 + - - +
95A ILE 3.6 7.9 - - - +
96A LYS 3.2 0.2 - - - -
97A ASN* 1.3 78.0 - - - +
99A PHE* 1.3 64.9 + + - +
101A ASP* 3.9 1.4 - - - +
102A VAL* 3.0 49.3 + - + +
130A VAL* 3.8 21.1 - - + -
133A LEU* 3.6 26.9 - - + -
134A GLY* 3.5 23.6 - - - -
137A HIS* 3.8 11.1 - - + -
138A LEU* 3.7 23.8 - - + -
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Residues in contact with PHE 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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7A PHE* 3.5 37.5 - + - -
60A TYR* 3.9 15.0 - + - -
73A SER 4.3 1.6 - - - -
74A ALA 3.8 22.4 - - - -
75A PHE* 3.5 29.2 - - + -
83A PHE* 3.7 26.3 - + + -
85A MET* 3.4 35.9 - - + -
95A ILE* 3.0 29.8 + - + -
96A LYS* 3.1 7.4 + - - +
98A PHE* 1.3 81.9 - + - +
100A THR* 1.3 57.0 + - - +
102A VAL* 3.3 1.8 + - - -
103A TYR* 2.8 32.7 + - - +
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Residues in contact with THR 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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59A MET* 6.0 0.2 - - - +
75A PHE* 4.2 16.6 - - - -
96A LYS* 2.9 28.4 + - - +
97A ASN* 3.9 7.9 - - - -
99A PHE* 1.3 76.6 - - - +
101A ASP* 1.3 66.3 + - - +
103A TYR* 3.6 9.5 - - + +
104A ASP* 3.2 24.7 + - + +
49F GLU* 4.5 16.4 - - - +
53F ARG* 6.0 4.0 - - - +
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Residues in contact with ASP 101 (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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97A ASN 3.0 18.6 + - - +
98A PHE 3.9 2.0 - - - +
100A THR* 1.3 81.7 - - - +
102A VAL* 1.3 61.4 + - - +
103A TYR 3.2 0.2 - - - -
104A ASP* 3.3 10.5 + - - +
105A LEU* 3.0 24.4 + - - +
133A LEU* 3.7 29.0 - - + +
136A LYS* 4.0 9.7 + - - -
137A HIS* 2.7 27.4 + - - +
53F ARG* 4.2 16.7 + - - -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.9 25.6 - - + -
9A ILE* 4.3 14.6 - - + -
83A PHE* 4.3 4.7 - - + -
98A PHE* 3.0 49.9 + - + +
99A PHE* 3.8 4.3 - - - +
101A ASP* 1.3 73.2 - - - +
103A TYR* 1.3 54.5 + - - +
105A LEU* 3.0 4.4 + - - +
106A TYR* 2.6 33.1 + - - +
126A PHE* 4.6 4.5 - - + -
130A VAL* 4.3 17.0 - - + -
133A LEU* 3.6 21.1 - - + -
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Residues in contact with TYR 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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59A MET* 3.5 26.9 - - + -
75A PHE* 3.9 16.8 - + + -
77A THR* 3.3 29.4 - - + -
78A ALA* 3.2 18.7 + - - +
83A PHE* 3.9 10.9 - + + -
99A PHE 2.8 18.1 + - - +
100A THR* 3.6 8.3 - - + +
102A VAL* 1.3 77.1 - - - +
104A ASP* 1.3 53.2 + - - +
106A TYR* 2.8 15.1 + + - +
107A ILE* 2.7 61.0 + - + +
67B ASP* 2.6 31.2 + - - +
71B MET* 3.9 16.0 - - + +
45F TYR* 6.2 1.8 - + - -
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Residues in contact with ASP 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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100A THR 3.2 12.1 + - - +
101A ASP* 3.3 14.1 - - - +
103A TYR* 1.3 78.9 - - - +
105A LEU* 1.3 63.1 + - - +
107A ILE* 3.5 10.0 + - - +
108A LYS* 2.8 51.4 + - - +
43F ARG 5.6 2.9 - - - +
45F TYR* 2.9 35.3 + - + +
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Residues in contact with LEU 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 ASP 3.0 12.9 + - - +
102A VAL* 3.0 9.6 + - - +
104A ASP* 1.3 78.0 + - - +
106A TYR* 1.3 63.7 + - - +
108A LYS* 3.7 13.4 + - + +
109A PHE* 3.1 23.2 + - - +
126A PHE* 3.6 22.2 - - + +
129A LYS* 3.3 55.4 - - + +
130A VAL* 3.7 28.3 - - + +
133A LEU* 4.3 9.9 - - + -
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Residues in contact with TYR 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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9A ILE* 5.0 9.0 - - + -
17A VAL* 5.4 0.2 - - + -
77A THR* 5.1 0.2 - - + -
81A MET* 3.4 49.7 - - + +
83A PHE* 4.5 11.4 - + + -
102A VAL* 2.6 17.9 + - + +
103A TYR* 3.3 30.1 - + - +
105A LEU* 1.3 73.3 - - - +
107A ILE* 1.3 62.8 + - + +
109A PHE* 3.3 1.1 + + - -
110A ALA* 2.8 52.1 + - + +
115A TYR* 4.3 16.2 - + - -
118A ASN 5.3 1.4 + - - -
121A ILE* 3.9 27.4 - - + -
126A PHE* 4.2 10.5 - - + -
67B ASP* 5.0 8.1 - - - -
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Residues in contact with ILE 107 (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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103A TYR* 2.7 56.1 + - + +
104A ASP* 3.7 5.8 - - - +
106A TYR* 1.3 75.9 - - + +
108A LYS* 1.3 58.8 + - + +
110A ALA* 3.7 3.0 - - - +
111A MET* 2.9 50.9 + - + +
67B ASP* 3.2 35.4 - - + +
68B VAL* 4.3 15.0 - - + -
71B MET* 5.3 2.5 - - + -
45F TYR* 3.8 23.8 - - + +
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Residues in contact with LYS 108 (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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104A ASP* 2.8 46.4 + - - +
105A LEU* 3.8 15.9 - - + +
107A ILE* 1.3 79.4 - - + +
109A PHE* 1.3 66.8 + - - +
111A MET* 3.4 15.1 + - - +
112A ASN* 3.9 3.3 + - - +
129A LYS* 6.2 1.6 - - - +
115E PHE* 3.7 44.0 - - + +
45F TYR* 4.1 6.2 + - - +
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Residues in contact with PHE 109 (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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105A LEU 3.1 15.7 + - - +
106A TYR* 3.3 4.5 + - - +
108A LYS* 1.3 78.3 - - - +
110A ALA* 1.3 63.9 + - + +
111A MET 3.3 0.9 + - - -
112A ASN* 3.3 24.7 + - + +
115A TYR* 3.4 39.3 - + + +
121A ILE* 3.6 38.4 - - + -
122A ARG 4.6 4.5 - - - -
123A SER* 3.8 26.2 - - - -
126A PHE* 4.1 21.1 - + + -
117E GLU* 4.8 13.0 - - - -
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Residues in contact with ALA 110 (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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106A TYR* 2.8 42.6 + - + +
107A ILE* 3.9 3.6 - - - +
109A PHE* 1.3 73.3 - - - +
111A MET* 1.3 63.5 + - + +
112A ASN 3.2 9.4 + - - +
115A TYR* 3.7 31.5 - - + +
64B SER* 4.1 7.9 + - - -
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Residues in contact with MET 111 (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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107A ILE* 2.9 36.6 + - + +
108A LYS* 3.6 9.4 - - - +
109A PHE 3.2 0.8 - - - -
110A ALA* 1.3 76.6 - - + +
112A ASN* 1.3 64.7 + - - +
113A PRO* 3.1 9.4 - - - +
64B SER* 3.0 48.7 + - - +
67B ASP* 5.7 1.6 - - + +
68B VAL* 4.4 14.1 - - + -
17E GLU* 5.4 4.9 - - - +
21E LEU* 4.2 24.9 - - + +
114E ASP 5.4 0.2 - - - +
115E PHE* 3.9 36.9 - - + +
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Residues in contact with ASN 112 (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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108A LYS 3.9 1.5 + - - +
109A PHE* 3.3 19.0 + - + +
110A ALA 3.2 3.0 - - - +
111A MET* 1.3 77.5 - - - +
113A PRO* 1.3 76.5 - - - +
114A PHE* 3.0 19.6 + - - +
115A TYR* 2.8 27.1 + - + +
115E PHE 3.0 16.4 + - - +
116E VAL* 3.4 0.2 - - - -
117E GLU* 3.0 59.1 + - + +
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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
------------------------------------------------------------
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