Contacts of the strand formed by residues 77 - 85 (chain A) in PDB entry 2OM5
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A MET* 5.6 1.1 - - - -
46A ASN* 3.4 13.0 - - - -
75A ASP 3.4 2.9 + - - -
76A ALA* 1.3 74.7 - - - +
78A VAL* 1.3 65.3 + - - -
79A TYR* 3.7 9.3 - - - -
96A ILE* 3.6 5.4 - - - +
97A LEU 2.9 33.7 + - - -
98A ARG* 4.8 10.3 - - - +
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Residues in contact with VAL 78 (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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44A LYS 3.6 0.7 - - - +
45A MET* 3.2 5.2 - - - +
46A ASN* 2.6 52.8 + - - +
77A GLY* 1.3 75.6 - - - +
79A TYR* 1.3 65.5 + - - +
80A GLN* 5.9 0.4 - - + -
94A GLU* 3.3 43.7 - - + +
95A ALA 3.7 5.8 - - - +
96A ILE* 4.4 17.7 - - + -
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Residues in contact with TYR 79 (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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13A PRO* 4.8 0.2 - - - +
29A LEU* 3.7 22.9 - - + -
43A TRP* 3.8 9.5 - - + -
44A LYS 3.2 4.7 - - - -
45A MET* 3.9 31.2 - - + -
50A MET* 4.1 14.1 - - + -
58A HIS* 5.2 2.8 + + - -
65A LEU* 3.7 18.6 - - + -
67A ILE* 3.8 17.7 - - + +
75A ASP* 2.4 40.3 + - - +
77A GLY 3.7 14.1 - - - -
78A VAL* 1.3 76.8 - - - +
80A GLN* 1.3 61.0 + - - +
93A ARG 4.1 0.5 - - - +
94A GLU* 3.4 5.9 - - - -
95A ALA* 3.0 37.8 + - + +
97A LEU* 3.6 27.6 - - + +
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Residues in contact with GLN 80 (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 TRP* 3.1 10.2 - - - -
44A LYS* 2.8 52.5 + - + +
78A VAL* 5.9 0.7 - - + -
79A TYR* 1.3 78.0 - - - +
81A CYS* 1.3 68.3 + - - +
82A LEU* 4.2 3.4 - - + +
91A VAL* 3.5 25.5 - - - +
92A SER* 3.1 31.8 + - - +
93A ARG 4.3 3.8 - - - +
94A GLU* 4.4 13.1 - - + +
375A TYR* 3.5 20.6 + - - -
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Residues in contact with CYS 81 (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 PHE* 4.4 2.5 - - - -
13A PRO* 4.3 0.4 - - + -
31A CYS* 2.0 53.8 - - + -
41A TYR* 4.0 14.6 - - - -
42A ARG 3.7 4.9 - - - -
43A TRP* 3.6 23.6 - - + -
80A GLN* 1.3 74.1 - - - +
82A LEU* 1.3 67.2 + - - +
83A ALA 4.2 0.2 - - - -
90A VAL 4.1 0.2 - - - +
91A VAL* 3.5 4.9 - - - +
92A SER* 2.9 41.8 + - - +
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Residues in contact with LEU 82 (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 THR 3.8 0.9 - - - +
41A TYR* 3.4 6.1 - - - -
42A ARG* 2.7 86.3 + - + +
44A LYS* 3.7 42.2 - - + +
49A GLU* 6.3 0.2 - - + -
80A GLN* 4.2 8.3 - - + +
81A CYS* 1.3 81.7 - - - +
83A ALA* 1.3 60.7 + - - +
84A SER* 3.9 1.7 + - - -
89A THR* 3.9 16.8 - - + -
90A VAL 3.6 1.8 - - - -
91A VAL* 3.7 23.3 - - + -
333A ASN 5.5 0.7 - - - +
334A GLY 5.1 6.1 - - - +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.3 15.0 - - + +
9A PHE* 3.7 29.3 - - + -
33A ALA* 3.9 20.9 - - + -
39A ALA* 5.1 1.3 - - + -
40A THR 3.7 5.2 - - - +
41A TYR* 4.3 11.4 - - + -
82A LEU* 1.3 71.8 - - - +
84A SER* 1.3 60.4 + - - +
89A THR* 4.2 0.6 - - - +
90A VAL* 2.9 35.7 + - + +
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Residues in contact with SER 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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7A PRO* 3.9 3.4 - - - -
39A ALA* 3.5 2.0 - - - +
40A THR* 2.9 46.7 + - - +
42A ARG* 4.6 15.9 + - - -
82A LEU 4.7 1.6 + - - -
83A ALA* 1.3 73.1 - - - +
85A ASN* 1.3 63.4 + - - +
88A GLY 3.1 9.6 - - - -
89A THR* 2.8 30.8 + - - +
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Residues in contact with ASN 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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5A PHE 3.3 20.0 + - - -
7A PRO* 3.3 20.5 - - - +
35A ALA* 4.1 7.9 - - + -
36A SER 3.4 10.7 + - - +
37A PRO* 3.2 32.2 + - - +
38A PRO 4.3 1.8 - - - +
39A ALA* 4.2 7.9 - - - -
40A THR* 5.1 3.1 - - - +
84A SER* 1.3 77.9 - - - +
86A PRO* 1.3 64.0 - - + +
87A VAL* 2.6 29.1 + - - +
88A GLY* 2.7 15.5 + - - -
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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