Contacts of the strand formed by residues 1091 - 1095 (chain A) in PDB entry 3OV6
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 LYS1091 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A THR* 4.9 6.4 + - - +
1005A PRO 3.1 26.5 + - - -
1006A LYS* 5.1 0.8 - - - +
1007A ILE* 3.6 27.3 - - + +
1080A CYS 3.5 1.7 - - - +
1081A ARG* 3.2 3.8 - - - -
1082A VAL* 2.9 34.0 + - - +
1087A LEU* 3.6 29.7 - - + +
1089A GLN 3.0 8.1 + - - +
1090A PRO* 1.3 70.9 - - - +
1092A ILE* 1.3 59.2 + - - +
1093A VAL* 4.0 8.9 - - + +
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Residues in contact with ILE1092 (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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1040A LEU* 4.1 15.7 - - + -
1079A ALA* 3.6 27.1 - - + -
1080A CYS 3.5 3.4 - - - +
1081A ARG* 4.0 19.1 - - + +
1090A PRO* 3.6 9.4 + - + +
1091A LYS* 1.3 76.4 - - - +
1093A VAL* 1.3 63.6 + - - +
1094A LYS* 4.0 8.4 + - + +
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Residues in contact with VAL1093 (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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1007A ILE* 4.0 34.8 - - + -
1009A VAL* 3.2 30.5 - - + +
1079A ALA* 3.4 3.3 - - - -
1080A CYS* 3.0 29.6 + - + +
1091A LYS* 4.6 7.9 - - + -
1092A ILE* 1.3 79.1 - - - +
1094A LYS* 1.3 65.8 + - - +
1095A TRP 3.6 0.2 + - - -
1103A GLY* 3.9 31.9 - - - +
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Residues in contact with LYS1094 (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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1009A VAL* 5.0 0.4 - - - -
1077A GLU* 4.2 25.8 + - + +
1078A TYR 3.3 13.5 - - - +
1079A ALA* 4.1 6.3 - - + -
1092A ILE* 4.0 7.4 + - + +
1093A VAL* 1.3 78.0 - - - +
1095A TRP* 1.3 68.4 + - - +
1096A ASP* 3.9 10.4 + - + +
1099A MET* 4.8 10.2 - - + +
1101A GLY 3.8 16.2 - - - +
1102A GLY* 4.3 1.9 + - - -
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Residues in contact with TRP1095 (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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1009A VAL* 3.7 20.1 - - + +
1010A TYR* 4.4 1.6 - - - -
1011A SER* 3.8 29.0 + - - +
1015A ALA* 3.5 21.1 - - + -
1023A LEU* 3.6 21.1 - - + -
1070A PHE* 3.7 38.1 - + - -
1072A PRO* 4.1 6.3 - - + -
1077A GLU* 6.1 0.2 - - - +
1078A TYR* 3.0 30.4 + + + +
1079A ALA* 4.4 0.2 - - - +
1093A VAL 3.6 1.8 + - - -
1094A LYS* 1.3 80.3 - - - +
1096A ASP* 1.3 58.9 + - - +
1097A ARG* 3.2 50.9 - - + -
1100A GLY 4.5 3.0 + - - -
1101A GLY* 3.5 21.8 - - - +
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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