Contacts of the strand formed by residues 1091 - 1095 (chain B) in PDB entry 6CNB
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 GLU1091 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A HIS* 4.1 11.1 + - - -
1089B ALA* 4.6 3.0 - - - +
1090B PHE* 1.3 99.0 - - - +
1092B VAL* 1.3 59.9 + - - +
1093B ASP* 4.1 9.5 + - - +
1118B LYS* 6.0 4.9 - - + -
1119B MET 3.4 12.3 - - - +
1120B THR* 5.0 7.6 - - - -
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Residues in contact with VAL1092 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 5.6 3.1 - - + +
1090B PHE* 3.4 30.6 + - + -
1091B GLU* 1.3 72.6 - - - +
1093B ASP* 1.3 65.1 + - - +
1094B VAL* 3.7 15.1 + - + -
1101B MET* 3.5 38.6 - - + -
1102B GLY 4.8 1.1 - - - +
1119B MET* 2.9 34.3 + - + +
1121B ILE* 3.4 24.4 - - + +
1126B LYS* 3.8 17.9 - - + -
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Residues in contact with ASP1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 5.7 3.6 + - - -
1091B GLU* 4.1 8.5 + - - +
1092B VAL* 1.3 75.9 + - - +
1094B VAL* 1.3 62.4 + - - +
1101B MET* 3.4 0.9 - - - -
1102B GLY* 2.7 48.1 + - - +
1104B SER* 3.0 40.9 + - - +
1116B ILE* 3.7 11.0 - - + +
1117B ILE 4.1 4.0 - - - -
1118B LYS* 3.1 34.4 - - - +
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Residues in contact with VAL1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092B VAL* 3.7 22.2 - - + +
1093B ASP* 1.3 77.7 - - - +
1095B CYS* 1.3 62.3 + - - +
1099B GLY* 5.9 0.2 - - - -
1100B LEU 3.3 14.4 - - - +
1101B MET* 4.1 8.5 - - + -
1107B CYS* 6.3 0.2 - - - -
1116B ILE* 2.9 28.3 - - - +
1117B ILE 2.9 20.8 + - - +
1119B MET* 4.5 14.6 - - + -
1141B LEU* 4.2 22.0 - - + -
1143B LEU* 3.7 30.5 - - + -
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Residues in contact with CYS1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094B VAL* 1.3 79.2 - - - +
1096B ASP* 1.3 72.0 + - - +
1097B LYS* 2.9 19.6 - - - +
1098B CYS 4.6 0.2 - - - +
1099B GLY* 3.1 15.8 - - - -
1100B LEU 3.1 5.6 + - - +
1107B CYS* 3.1 25.4 - - + -
1110B CYS* 4.0 5.2 - - - -
1112B SER* 4.7 3.8 - - - -
1115B ASN* 3.8 27.8 - - - -
1116B ILE* 4.1 2.9 - - + +
1141B LEU 4.9 0.5 - - - +
2000B ZN 2.5 35.9 - - - -
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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