Contacts of the strand formed by residues 76 - 85 (chain A) in PDB entry 5OAB
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 VAL 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.4 10.3 - - + -
45A HIS 4.9 2.2 - - - +
46A ASP* 3.5 33.2 - - + +
74A LYS* 4.1 6.1 - - + +
75A PRO* 1.3 79.3 - - - +
77A ASN* 1.3 73.9 + - - +
78A MET* 3.6 20.6 + - + +
99A TYR* 3.3 8.9 - - - -
100A LYS 2.9 26.7 + - - +
102A PHE* 3.8 29.8 - - + -
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Residues in contact with ASN 77 (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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45A HIS* 2.8 47.0 + - + +
76A VAL* 1.3 79.3 - - - +
78A MET* 1.3 60.1 + - - +
98A GLN 3.4 10.4 + - - -
99A TYR* 3.6 19.6 - - - +
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Residues in contact with MET 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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42A THR* 3.9 17.5 - - + -
43A PHE 3.1 21.5 - - - +
44A LEU* 3.8 13.5 - - + -
45A HIS* 3.5 5.1 - - - -
76A VAL* 3.7 17.9 - - + +
77A ASN* 1.3 76.3 - - - +
79A THR* 1.3 59.9 + - - +
97A ALA* 3.7 2.8 - - - +
98A GLN* 2.8 64.3 + - + +
100A LYS* 3.3 41.5 - - + +
101A PHE 4.2 5.8 - - - +
102A PHE* 4.5 2.2 - - + -
126A ILE* 3.9 17.7 - - + -
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Residues in contact with THR 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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17A GLN* 5.3 0.7 - - - -
20A PRO* 5.1 1.4 - - - +
21A LEU 5.0 9.4 + - - +
23A CYS* 3.8 28.9 - - - -
41A ASN 3.7 1.2 - - - +
42A THR* 3.5 4.9 - - - -
43A PHE* 2.9 37.5 + - + +
45A HIS* 2.6 29.0 + - - -
78A MET* 1.3 72.6 + - - +
80A ASP* 1.3 61.6 + - - +
81A CYS* 3.8 2.0 + - - -
95A ALA* 4.0 14.1 - - + -
96A ALA 3.6 7.0 - - - +
97A ALA* 5.2 3.0 - - - +
98A GLN* 4.6 2.2 - - - -
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Residues in contact with ASP 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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40A GLN* 2.9 25.5 + - - +
41A ASN 3.8 2.7 - - - -
42A THR* 4.6 2.5 - - - +
79A THR* 1.3 70.3 - - - +
81A CYS* 1.3 61.9 + - - +
82A ARG* 2.9 44.1 + - - +
94A SER 3.5 1.4 - - - +
95A ALA* 3.3 5.0 - - - -
96A ALA* 2.9 50.3 + - + +
98A GLN* 3.6 30.1 + - - +
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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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21A LEU 5.8 0.2 - - - -
23A CYS* 2.0 52.3 - - + -
27A MET* 4.2 9.2 - - - -
39A HIS 4.1 0.2 - - - +
40A GLN* 3.3 5.2 - - - -
41A ASN 2.9 37.9 + - - +
43A PHE* 3.6 29.8 - - - -
79A THR* 4.0 4.5 - - - -
80A ASP* 1.3 72.0 - - - +
82A ARG* 1.3 61.9 + - - +
93A TYR* 3.9 12.6 - - + -
94A SER 3.3 4.7 - - - -
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Residues in contact with ARG 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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39A HIS 3.5 5.8 - - - +
40A GLN* 3.7 28.5 - - + +
80A ASP* 2.9 37.3 + - - +
81A CYS* 1.3 71.7 - - - +
83A LEU* 1.3 67.4 + - - +
84A THR* 3.3 1.6 + - + +
93A TYR* 3.2 4.7 - - - -
94A SER* 2.8 49.1 + - - +
96A ALA* 6.5 0.7 - - - -
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Residues in contact with LEU 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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37A CYS* 3.7 35.0 - - + +
38A LYS 3.8 6.3 - - - +
39A HIS* 2.9 43.1 + - + +
82A ARG* 1.3 73.8 - - - +
84A THR* 1.3 61.1 + - - +
85A SER* 3.5 18.8 - - - +
86A GLY 4.3 9.4 - - - +
91A CYS* 4.1 0.7 - - + -
92A ARG 3.4 22.2 - - - +
93A TYR* 3.4 17.6 - - + -
203A PO4 5.7 0.2 - - - +
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Residues in contact with THR 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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82A ARG* 3.3 11.4 + - + +
83A LEU* 1.3 78.6 - - - +
85A SER* 1.3 60.6 + - - +
92A ARG 2.8 23.7 + - - -
93A TYR 3.8 6.1 + - - -
94A SER* 3.8 21.8 - - - +
204A PO4 4.1 14.7 + - - -
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Residues in contact with SER 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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83A LEU* 3.5 12.0 - - - +
84A THR* 1.3 81.0 - - - +
86A GLY* 1.3 63.5 + - - +
92A ARG* 3.0 51.8 + - - +
204A PO4 4.5 4.0 + - - -
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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