Contacts of the helix formed by residues 92 - 111 (chain A) in PDB entry 3OTC
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 ARG 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLU* 5.2 11.1 + - - +
14A ALA 4.4 13.4 + - - -
15A ASP* 3.7 21.9 + - - -
16A ASP* 2.6 38.8 + - - +
17A THR* 4.0 7.6 - - - -
89A PHE 2.9 19.0 + - - +
90A LYS* 4.1 11.9 - - + +
91A ARG* 1.3 77.4 - - - +
93A ALA* 1.3 65.4 + - - +
94A SER* 3.2 18.7 + - - +
95A LYS* 3.1 34.1 + - + +
96A PHE* 3.3 13.3 + - - -
130B ARG* 5.5 10.9 - - - +
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Residues in contact with ALA 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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16A ASP* 2.8 29.1 + - + +
18A CYS* 3.9 19.7 - - - -
91A ARG 3.4 2.0 + - - -
92A ARG* 1.3 71.6 - - - +
94A SER* 1.3 64.1 + - - +
96A PHE* 3.0 17.9 + - - +
97A MET* 3.1 24.7 + - + +
131A VAL* 4.0 12.9 - - + +
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Residues in contact with SER 94 (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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16A ASP* 3.1 20.2 + - - -
92A ARG* 3.2 18.4 + - - +
93A ALA* 1.3 76.9 - - - +
95A LYS* 1.3 61.5 + - - +
97A MET* 3.2 13.4 + - - +
98A THR* 2.7 37.7 + - - +
97B MET* 3.7 19.1 - - - -
129B GLY 4.0 10.4 + - - -
130B ARG* 4.5 9.8 - - - +
131B VAL 5.3 0.7 - - - -
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Residues in contact with LYS 95 (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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88A TRP* 4.1 2.8 - - + -
89A PHE* 3.2 61.2 + - + +
92A ARG* 3.1 30.1 + - + +
93A ALA 3.1 1.0 - - - -
94A SER* 1.3 85.3 + - - +
96A PHE* 1.3 62.9 + - + +
98A THR* 3.9 2.0 - - - -
99A HIS* 3.2 31.9 + - + +
128B ASP* 3.1 37.5 - - - +
129B GLY 4.8 2.2 - - - +
130B ARG* 4.9 11.2 - - + +
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Residues in contact with PHE 96 (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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18A CYS* 4.5 1.1 - - - -
24A VAL* 3.8 27.1 - - + -
26A VAL* 3.8 16.0 - - + +
82A PHE* 3.5 44.6 - + - -
86A THR* 4.1 22.4 - - + -
88A TRP* 3.6 31.0 - + + -
89A PHE* 5.1 1.8 - - + -
91A ARG* 3.7 31.0 - - + -
92A ARG 3.3 19.5 + - - -
93A ALA* 3.0 9.4 + - - +
95A LYS* 1.3 78.7 - - - +
97A MET* 1.3 58.0 + - - +
99A HIS* 4.7 0.2 - - - +
100A VAL* 3.0 32.2 + - - +
131A VAL* 4.3 4.3 - - + -
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Residues in contact with MET 97 (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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16A ASP* 5.2 0.7 - - - +
26A VAL* 4.2 9.9 - - - +
28A LEU* 5.3 0.2 - - - +
93A ALA* 3.1 16.1 + - + +
94A SER* 3.2 26.5 - - - +
96A PHE* 1.3 77.1 - - - +
98A THR* 1.3 59.3 + - + +
100A VAL* 3.7 1.6 - - - +
101A ALA* 2.9 30.8 + - - +
130A ARG* 4.1 12.6 - - - +
131A VAL* 3.2 27.1 - - + -
16B ASP* 5.7 0.9 - - - +
94B SER* 3.7 22.2 - - - -
97B MET* 2.9 37.9 - - + -
98B THR* 3.8 19.4 - - + +
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Residues in contact with THR 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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94A SER 2.7 20.2 + - - +
95A LYS 3.7 2.6 + - - -
97A MET* 1.3 76.7 - - + +
99A HIS* 1.3 64.7 + - - +
101A ALA* 4.4 4.7 - - - -
102A SER* 2.8 30.8 + - - -
97B MET* 3.7 37.2 - - + +
98B THR* 4.6 0.9 - - - +
101B ALA* 4.1 7.5 - - + +
127B PHE 3.4 3.2 - - - +
128B ASP* 3.9 4.5 + - - -
129B GLY* 3.1 47.8 + - - +
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Residues in contact with HIS 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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65A LEU* 3.8 20.2 - - + +
88A TRP* 3.8 20.0 - + + -
89A PHE* 3.7 19.7 - + - -
95A LYS* 3.2 25.5 + - + +
96A PHE 4.7 0.2 - - - +
98A THR* 1.3 79.5 + - - +
100A VAL* 1.3 62.7 + - - +
102A SER* 3.5 0.9 + - - -
103A GLN* 3.2 27.0 + - - +
31B ARG* 3.4 46.8 - - + +
126B GLY* 5.2 0.9 - - - -
127B PHE 3.6 9.6 + - - -
128B ASP* 3.6 37.7 + - + -
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Residues in contact with VAL 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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26A VAL* 4.0 15.0 - - + -
28A LEU* 3.9 11.0 - - + -
61A VAL* 3.9 11.7 - - + +
65A LEU* 3.6 22.2 - - + -
80A PHE* 3.7 35.0 - - + -
82A PHE* 3.9 20.4 - - + -
96A PHE 3.0 23.3 + - - +
97A MET 3.5 2.9 + - - +
98A THR 3.2 0.4 - - - -
99A HIS* 1.3 77.5 - - - +
101A ALA* 1.3 63.3 + - - +
104A PHE* 3.0 27.5 + - - +
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Residues in contact with ALA 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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28A LEU* 3.8 25.4 - - + -
97A MET 2.9 18.9 + - - +
98A THR* 4.0 4.7 - - - +
100A VAL* 1.3 78.5 - - - +
102A SER* 1.3 59.8 + - - +
104A PHE* 4.0 1.2 - - - +
105A ALA* 3.2 24.6 + - - +
127A PHE* 5.0 2.2 - - - +
98B THR* 4.0 30.5 - - + +
101B ALA* 4.9 0.4 - - + -
102B SER* 3.7 10.8 - - - +
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Residues in contact with SER 102 (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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98A THR 2.8 25.7 + - - -
99A HIS 3.5 3.3 + - - -
101A ALA* 1.3 72.2 - - - +
103A GLN* 1.3 61.6 + - - +
105A ALA 3.3 0.2 + - - -
106A SER* 2.8 32.4 + - - -
101B ALA* 3.6 21.3 + - - -
105B ALA* 3.3 15.8 - - - +
125B PRO 4.7 1.1 - - - -
126B GLY 3.9 0.2 - - - -
127B PHE* 2.9 39.8 + - - -
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Residues in contact with GLN 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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60A THR* 3.9 14.1 - - + +
61A VAL* 4.0 26.2 - - + -
64A GLU* 3.9 31.5 + - + +
65A LEU* 5.2 4.2 - - + +
99A HIS 3.2 17.0 + - - +
100A VAL 4.0 1.6 - - - +
102A SER* 1.3 81.2 + - - +
104A PHE* 1.3 62.7 + - - +
106A SER* 4.3 1.8 - - - -
107A SER* 3.0 28.4 + - - -
31B ARG* 4.8 8.9 - - - +
124B PRO* 3.0 25.4 + - - +
125B PRO 3.8 4.6 - - - +
126B GLY* 3.8 22.9 - - - +
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Residues in contact with PHE 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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28A LEU* 3.5 24.9 - - + -
54A MET* 3.5 51.6 - - + -
57A CYS* 3.5 31.4 - - + -
58A ALA* 3.5 17.9 - - + -
61A VAL* 3.7 6.4 - - + +
78A TYR* 4.3 9.6 - + + -
80A PHE* 4.0 13.2 - + - -
100A VAL 3.0 17.6 + - - +
101A ALA 4.0 2.7 - - - +
103A GLN* 1.3 77.1 - - - +
105A ALA* 1.3 57.1 + - - +
107A SER* 3.1 7.5 + - - -
108A TYR* 2.8 28.9 + + - +
127A PHE* 3.9 26.5 - + - -
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Residues in contact with ALA 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 ALA 3.2 17.4 + - - +
102A SER 3.7 3.4 - - - +
104A PHE* 1.3 75.9 - - - +
106A SER* 1.3 67.1 + - - +
108A TYR* 3.4 13.4 + - - +
109A VAL* 3.5 6.6 + - - +
127A PHE* 3.9 19.0 - - + -
102B SER* 3.3 35.2 - - - +
105B ALA* 4.2 0.2 - - + -
106B SER* 3.6 19.6 + - - +
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Residues in contact with SER 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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102A SER 2.8 17.8 + - - -
103A GLN 3.6 4.9 - - - -
105A ALA* 1.3 74.4 - - - +
107A SER* 1.3 64.8 + - - +
109A VAL* 3.3 0.9 + - - -
110A PHE* 3.1 21.3 + - - +
105B ALA* 3.6 24.5 + - - +
109B VAL* 3.5 11.2 - - - +
124B PRO* 3.7 13.7 - - - -
125B PRO* 2.7 40.1 + - - +
127B PHE* 4.7 0.2 - - - -
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Residues in contact with SER 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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57A CYS* 3.6 23.9 - - - -
60A THR* 3.0 34.4 + - - +
103A GLN 3.0 9.5 + - - -
104A PHE 3.1 9.2 + - - -
106A SER* 1.3 80.5 - - - +
108A TYR* 1.3 56.3 + - - +
110A PHE* 3.1 2.5 + - - -
111A TYR* 2.9 41.8 + - - +
124B PRO* 3.9 12.0 - - - +
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Residues in contact with TYR 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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33A PHE* 3.6 15.1 - + - -
36A PHE* 3.5 29.1 - + - -
42A PHE* 4.1 8.3 - - - -
50A ALA* 5.2 3.9 + - - +
53A LEU* 3.3 35.2 - - + +
54A MET* 3.9 26.8 - - + +
57A CYS* 3.2 17.5 - - - -
104A PHE* 2.8 13.4 + + - +
105A ALA* 3.5 14.4 - - - +
106A SER 3.2 0.4 - - - -
107A SER* 1.3 76.7 - - - +
109A VAL* 1.3 62.6 + - + +
112A TRP* 3.4 39.0 + + - +
116A PHE* 5.0 0.9 - - - -
121A LEU* 5.1 1.1 - - + -
125A PRO* 3.7 22.2 - - + -
127A PHE* 4.0 17.5 - + + -
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Residues in contact with VAL 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 ALA 3.5 12.3 + - - +
106A SER 3.3 2.3 + - - +
108A TYR* 1.3 74.4 - - - +
110A PHE* 1.3 67.4 + - - +
112A TRP* 3.5 13.2 + - - +
113A ARG* 5.0 0.7 + - - +
121A LEU* 3.6 31.4 - - + +
124A PRO* 4.6 2.5 - - + -
125A PRO* 4.3 10.1 - - + -
106B SER* 3.6 29.4 - - - +
109B VAL* 3.9 14.9 - - + +
110B PHE* 3.9 29.4 - - + +
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Residues in contact with PHE 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 SER 3.1 13.4 + - - +
107A SER* 3.4 8.5 - - - +
109A VAL* 1.3 80.5 - - - +
111A TYR* 1.3 91.8 + + + +
112A TRP 3.3 2.4 + - - -
113A ARG* 4.4 7.4 + - - +
114A ASP* 5.4 1.0 - - - +
109B VAL* 3.9 8.4 - - + +
121B LEU* 3.6 47.1 - - + -
122B LEU 3.6 21.3 - - - -
123B TYR* 3.8 2.7 - - - -
124B PRO* 3.8 27.6 - - + -
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Residues in contact with TYR 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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53A LEU* 3.8 13.5 - - + -
56A LYS* 3.8 41.3 - - + -
57A CYS* 5.3 0.4 - - - -
60A THR* 3.5 25.5 + - - +
107A SER* 2.9 40.4 + - - +
110A PHE* 1.3 100.3 - + - +
112A TRP* 1.3 63.9 + - - +
113A ARG 3.3 3.1 - - - -
114A ASP* 3.1 40.7 + - - +
115A TYR* 3.4 11.3 - - + -
124B PRO* 4.3 11.7 - - + +
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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