Contacts of the helix formed by residues 92 - 113 (chain A) in PDB entry 2OC5
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 ASP 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER* 3.1 22.0 + - - +
36A ARG* 4.0 19.0 + - + +
39A ALA* 3.1 14.0 - - - +
90A GLU 3.5 2.4 + - - +
91A ALA* 1.3 65.5 - - - +
93A MSE 1.3 62.0 + - - +
94A ASP* 3.7 7.4 + - - +
95A PHE* 3.2 34.3 + - + +
96A ALA 3.2 10.0 + - - -
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Residues in contact with MSE 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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39A ALA* 3.9 24.5 - - - +
42A ILE* 3.9 27.6 - - + -
43A GLU* 3.4 36.8 - - + +
46A GLN* 6.3 0.2 - - + -
77A LYS* 5.7 2.7 - - - -
91A ALA* 3.1 24.3 + - + +
92A ASP* 1.3 69.8 + - - +
94A ASP* 1.3 65.2 + - - +
96A ALA* 3.2 1.8 + - - +
97A ARG* 3.0 56.3 + - - +
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Residues in contact with ASP 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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92A ASP* 3.3 6.6 + - - +
93A MSE 1.3 74.3 - - - +
95A PHE* 1.3 67.2 + - - +
97A ARG* 3.2 24.7 + - - +
98A GLU* 3.1 23.7 + - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.9 40.6 - - + -
40A ILE* 3.8 28.9 - - + -
92A ASP* 3.2 29.6 + - - +
94A ASP* 1.3 77.8 - - - +
96A ALA* 1.3 59.2 + - - +
98A GLU* 3.4 6.6 + - + +
99A PHE* 3.0 38.1 + + + +
196A GLN* 5.2 11.0 - - + -
197A VAL* 6.5 0.7 - - - -
200A ASP* 5.0 4.7 - - - -
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Residues in contact with ALA 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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39A ALA* 3.2 42.6 - - + +
40A ILE* 3.6 10.5 - - - +
43A GLU* 3.7 13.9 - - + -
92A ASP 3.2 1.0 + - - -
93A MSE 3.2 10.2 + - + +
94A ASP 3.2 0.6 - - - -
95A PHE* 1.3 80.7 - - - +
97A ARG* 1.3 62.7 + - - +
99A PHE* 3.3 6.7 + - - +
100A PHE* 3.2 30.3 + - - -
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Residues in contact with ARG 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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43A GLU* 3.6 29.0 + - - +
93A MSE 3.0 51.6 + - - +
94A ASP* 3.2 30.0 + - - +
96A ALA* 1.3 76.8 - - - +
98A GLU* 1.3 62.9 + - - +
101A ALA 3.2 6.8 + - - -
104A ARG* 2.9 37.6 + - - +
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Residues in contact with GLU 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 ASP 3.1 13.4 + - - +
95A PHE* 3.6 10.1 - - + +
97A ARG* 1.3 75.6 - - - +
99A PHE* 1.3 64.5 + - - +
101A ALA* 3.1 21.2 + - + +
102A PRO* 3.6 6.4 - - - +
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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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40A ILE* 3.6 47.6 - - + -
95A PHE* 3.0 24.6 + + + +
96A ALA* 3.4 11.7 - - - +
98A GLU* 1.3 78.3 - - - +
100A PHE* 1.3 70.8 + + - +
101A ALA 3.6 0.2 + - - -
102A PRO* 3.9 7.6 - - - +
130A PHE* 4.4 8.7 - + - -
193A MSE 3.4 77.0 - - + +
196A GLN* 3.7 26.9 - - + +
197A VAL* 4.3 10.3 - - + -
304A UNL 5.3 0.2 - - - -
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Residues in contact with PHE 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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40A ILE* 3.2 43.7 - - + -
43A GLU* 3.8 11.2 - - + -
44A GLY* 3.6 22.0 - - - -
47A GLU* 3.5 23.1 - - - +
96A ALA 3.2 21.0 + - - +
98A GLU 3.2 0.2 - - - -
99A PHE* 1.3 83.2 - + - +
101A ALA* 1.3 65.5 + - - +
102A PRO* 3.4 2.5 - - - -
103A LEU* 3.2 10.0 + - + +
104A ARG* 2.8 25.7 + - - +
127A ILE* 5.2 5.6 - - + -
130A PHE* 5.8 0.4 - + - -
193A MSE 3.9 24.2 - - + -
303A ACT 3.7 26.2 - - + -
304A UNL 4.4 15.9 - - - -
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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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97A ARG 3.2 5.3 + - - +
98A GLU* 3.1 14.0 + - + +
100A PHE* 1.3 78.2 - - - +
102A PRO* 1.3 66.0 - - + +
104A ARG* 3.4 27.6 - - - +
105A ASP* 2.8 42.1 + - - +
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Residues in contact with PRO 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 GLU 3.6 9.6 - - - +
99A PHE 3.9 7.9 - - - +
100A PHE 3.6 2.2 - - - -
101A ALA* 1.3 93.9 - - + +
103A LEU* 1.3 60.9 + - - +
105A ASP* 3.5 8.9 + - + +
106A ASN* 3.2 26.2 + - - +
189A LEU* 3.9 13.1 - - + +
192A ARG* 3.2 33.4 - - - +
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Residues in contact with LEU 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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100A PHE* 3.2 7.9 + - + +
102A PRO* 1.3 77.0 - - - +
104A ARG* 1.3 60.7 + - - +
106A ASN* 3.2 3.8 + - - +
107A PHE* 2.9 28.6 + - - +
122A ILE* 3.8 20.6 - - + -
126A LEU* 5.1 3.1 - - + -
127A ILE* 3.7 31.9 - - + -
186A ASN* 3.4 35.9 - - + +
189A LEU* 4.0 16.4 - - + +
190A ILE* 4.0 9.0 - - + -
193A MSE 3.9 32.1 - - + -
303A ACT 4.1 7.4 - - + +
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Residues in contact with ARG 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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43A GLU* 4.4 1.9 + - - -
47A GLU* 2.9 44.1 + - - +
97A ARG* 2.9 33.1 + - - +
100A PHE* 2.8 20.0 + - - +
101A ALA* 3.4 32.9 + - - +
103A LEU* 1.3 76.3 - - - +
105A ASP* 1.3 67.9 + - - +
107A PHE* 3.1 2.4 + - - +
108A GLN* 2.9 44.0 + - + +
303A ACT 3.8 19.1 + - - +
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Residues in contact with ASP 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* 2.8 34.4 + - - +
102A PRO* 3.6 8.5 - - + +
104A ARG* 1.3 79.3 + - - +
106A ASN* 1.3 62.2 + - - +
108A GLN* 3.3 8.3 + - - +
109A THR* 2.9 33.7 + - - +
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Residues in contact with ASN 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 PRO 3.2 9.9 + - - +
103A LEU 3.2 6.0 + - - +
105A ASP* 1.3 84.5 - - - +
107A PHE* 1.3 60.7 + - - +
109A THR* 3.4 7.7 + - - -
110A ALA* 3.1 24.1 + - - +
118A THR* 5.2 0.7 - - - +
122A ILE* 4.1 6.1 - - + +
185A GLU* 4.3 11.5 + - - +
186A ASN* 2.8 34.7 + - - +
189A LEU* 3.4 17.0 - - - +
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Residues in contact with PHE 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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51A ASN* 3.3 58.3 - - + -
54A ALA* 4.3 13.7 - - + -
55A ILE* 4.0 5.8 - - + -
103A LEU 2.9 8.2 + - - +
104A ARG* 3.1 7.6 + - - +
106A ASN* 1.3 74.7 - - - +
108A GLN* 1.3 73.1 + - - +
110A ALA* 3.2 5.6 + - - +
111A LEU* 2.9 30.6 + - + -
119A CYS* 3.5 51.0 - - + -
122A ILE* 3.9 22.8 - - + +
123A GLN* 4.2 4.3 - - + -
303A ACT 3.7 14.6 - - - +
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Residues in contact with GLN 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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51A ASN* 4.2 6.9 + - - -
54A ALA* 5.9 0.8 - - - +
104A ARG* 2.9 35.2 + - + +
105A ASP* 3.7 8.1 - - - +
107A PHE* 1.3 101.3 - - - +
109A THR* 1.3 61.9 + - - +
111A LEU* 3.4 20.2 + - - +
112A GLY* 3.0 21.0 + - - -
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Residues in contact with THR 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 ASP* 2.9 20.3 + - - +
106A ASN* 3.7 9.6 + - - -
107A PHE 3.3 0.2 - - - -
108A GLN* 1.3 76.1 - - - +
110A ALA* 1.3 62.9 + - - +
112A GLY* 3.3 2.1 + - - -
113A GLN* 3.1 45.0 + - - +
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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 ASN 3.1 10.8 + - - +
107A PHE* 3.6 7.6 - - - +
109A THR* 1.3 75.5 - - - +
111A LEU* 1.3 63.3 + - - +
113A GLN* 3.1 9.0 + - - -
114A GLY 3.1 4.7 + - - -
115A LYS* 3.0 32.6 + - + +
118A THR* 3.6 34.5 - - + -
119A CYS* 3.8 14.4 - - - -
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Residues in contact with LEU 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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54A ALA* 3.7 45.1 - - + +
55A ILE* 5.2 0.2 - - - -
57A THR* 4.0 9.0 - - - +
58A LEU* 3.9 23.5 - - + +
107A PHE* 2.9 24.4 + - + +
108A GLN* 3.6 25.4 - - - +
110A ALA* 1.3 76.1 - - - +
112A GLY* 1.3 60.1 + - - +
114A GLY* 3.0 19.5 + - - +
119A CYS* 3.5 11.3 - - - -
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Residues in contact with GLY 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 GLN 3.0 13.9 + - - -
109A THR 3.3 4.7 + - - -
110A ALA 3.2 0.2 - - - -
111A LEU* 1.3 77.5 - - - +
113A GLN* 1.3 58.6 + - - +
114A GLY 3.7 0.2 + - - -
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Residues in contact with GLN 113 (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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109A THR* 3.1 36.0 + - - +
110A ALA* 3.1 6.1 + - - +
112A GLY* 1.3 75.3 - - - +
114A GLY* 1.3 62.1 + - - +
115A LYS* 3.2 43.9 + - + +
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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