Contacts of the helix formed by residues 82 - 88 (chain A) in PDB entry 2O1S
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 ALA 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A TRP* 4.2 14.8 - - + -
79A GLY 3.1 16.7 + - - +
80A HIS 3.4 0.4 - - - -
81A GLN* 1.3 77.6 - - - +
83A TYR* 1.3 65.7 + - - +
84A PRO 3.3 2.0 - - - -
85A HIS* 3.1 19.0 + - + +
86A LYS* 2.9 26.9 + - + +
108A PRO* 3.6 26.9 - - + -
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Residues in contact with TYR 83 (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 LEU* 4.2 11.2 - - + -
43A VAL* 3.8 35.4 - - + -
47A SER* 3.7 4.8 - - - -
49A HIS* 3.5 26.4 - + + +
50A PHE* 3.7 26.7 - - - -
53A GLY* 4.9 3.1 - - - -
79A GLY 5.1 0.7 - - - -
80A HIS 4.4 9.2 - - - -
81A GLN 3.5 0.4 - - - -
82A ALA* 1.3 78.8 - - - +
84A PRO* 1.3 74.2 - - + +
86A LYS* 3.1 9.4 + - + +
87A ILE* 2.9 27.7 + - + +
95A ILE* 4.1 6.4 - - + +
98A ILE* 3.7 30.5 - - + -
99A ARG* 3.4 31.0 - - - +
106A PRO 3.9 13.5 - - - -
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Residues in contact with PRO 84 (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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35A LEU* 3.9 25.4 - - + -
39A LEU* 4.2 8.1 - - + -
53A GLY* 3.7 23.3 - - - +
56A THR* 3.6 20.9 - - - +
57A VAL* 4.5 9.4 - - + +
60A THR* 3.9 15.3 - - - +
81A GLN 3.9 2.2 - - - +
82A ALA 3.6 0.9 - - - -
83A TYR* 1.3 95.0 - - + +
85A HIS* 1.3 55.9 + - - +
87A ILE* 3.2 13.8 + - + +
88A LEU* 2.9 34.0 + - - +
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Residues in contact with HIS 85 (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* 3.6 11.6 - - - +
64A HIS* 2.8 37.6 - + - -
74A LEU* 4.1 5.2 - - + -
76A TRP* 3.3 44.6 + + + +
82A ALA* 3.1 20.8 + - + +
84A PRO* 1.3 82.1 - - - +
86A LYS* 1.3 57.3 + - + +
88A LEU* 3.4 0.9 + - - -
89A THR* 2.7 46.0 + - + +
91A ARG* 4.0 7.0 + - - -
108A PRO* 4.7 3.3 - - + +
115A TYR* 3.5 17.4 + - + -
116A ASP* 3.2 26.1 + - - -
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Residues in contact with LYS 86 (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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82A ALA* 2.9 18.8 + - + +
83A TYR 3.1 7.6 + - - +
85A HIS* 1.3 80.3 - - + +
87A ILE* 1.3 63.1 + - - +
89A THR* 3.2 13.4 + - - -
91A ARG* 3.1 50.9 + - + +
95A ILE* 4.4 9.2 - - + -
98A ILE* 4.1 17.9 - - + +
104A LEU* 4.8 4.0 - - + -
105A HIS 2.7 29.9 + - - +
106A PRO 5.4 0.2 - - - -
107A PHE* 3.0 29.8 + - - +
108A PRO* 3.9 9.6 - - - +
112A GLU* 2.9 30.7 + - - +
116A ASP* 4.0 0.2 - - - -
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Residues in contact with ILE 87 (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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11A LEU* 4.5 6.5 - - + +
14A VAL 5.1 3.8 - - - +
15A ASP* 6.1 0.3 - - - -
35A LEU* 3.5 25.4 - - + -
38A TYR* 4.0 21.3 - - + -
39A LEU* 4.3 20.6 - - + -
83A TYR* 2.9 21.3 + - + +
84A PRO* 3.2 14.3 + - + +
86A LYS* 1.3 76.1 - - - +
88A LEU* 1.3 58.4 + - - +
89A THR 3.2 1.1 + - - -
90A GLY 4.2 1.4 + - - -
91A ARG 4.1 1.7 + - - -
92A ARG* 3.4 48.2 + - + +
95A ILE* 3.8 29.6 - - + -
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Residues in contact with LEU 88 (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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11A LEU* 4.4 17.7 - - + -
14A VAL* 3.9 31.0 - - + +
15A ASP 5.2 1.1 - - - -
16A SER* 4.1 4.2 + - - -
17A THR* 3.8 19.2 + - - +
20A LEU* 4.6 11.9 - - + -
31A LEU* 4.6 15.0 - - + -
35A LEU* 3.9 15.5 - - + -
60A THR* 3.8 23.8 - - + +
61A VAL* 3.8 31.6 - - + -
64A HIS* 4.7 8.1 - - - +
84A PRO 2.9 13.4 + - - +
85A HIS 4.0 3.6 - - - +
86A LYS 3.3 0.2 - - - -
87A ILE* 1.3 75.2 - - - +
89A THR* 1.3 61.4 + - - +
90A GLY 3.6 2.8 + - - -
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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