Contacts of the strand formed by residues 1090 - 1096 (chain v) in PDB entry 6FF7
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 GLU1090 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1056v VAL* 3.6 5.6 - - - +
1057v ARG* 2.9 36.0 + - - +
1058v LEU* 5.1 0.2 - - - +
1059v PRO* 5.2 3.0 - - + +
1088v LYS 5.5 0.2 - - - +
1089v ALA* 1.3 77.3 - - - +
1091v VAL* 1.3 62.7 + - - +
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Residues in contact with VAL1091 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054v CYS* 6.2 2.2 - - + -
1055v VAL 3.7 10.8 - - - +
1056v VAL* 4.3 5.2 - - + +
1090v GLU* 1.3 77.8 - - - +
1092v ILE* 1.3 61.3 + - - +
1093v MET 3.6 8.3 - - - +
1094v ASN* 6.2 2.0 - - + -
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Residues in contact with ILE1092 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1v MET* 4.5 22.5 - - - +
1055v VAL* 3.1 13.1 + - + +
1057v ARG* 4.8 16.3 - - + +
1090v GLU 4.2 1.4 + - - -
1091v VAL* 1.3 73.3 - - - +
1093v MET* 1.3 62.2 + - + +
1171v LYS* 3.7 15.4 - - - +
1172v ASN* 4.7 2.9 - - - +
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Residues in contact with MET1093 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1v MET 5.0 7.0 - - - +
3v LEU* 6.4 2.0 - - + -
1053v ILE 4.5 0.7 - - - +
1054v CYS* 3.4 4.3 - - - +
1055v VAL* 3.0 38.8 + - + +
1091v VAL* 3.6 6.5 - - - +
1092v ILE* 1.3 82.1 - - - +
1094v ASN* 1.3 63.1 + - - +
1095v TYR* 5.8 1.6 - - + -
1171v LYS* 3.4 21.1 - - - +
1172v ASN 5.6 0.2 - - - +
1173v VAL* 5.4 6.7 - - + -
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Residues in contact with ASN1094 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053v ILE 3.7 4.5 - - - -
1054v CYS* 4.5 6.3 - - + +
1091v VAL* 6.2 2.7 - - + -
1093v MET* 1.3 74.5 - - - +
1095v TYR* 1.3 63.6 + - - +
1168v PHE* 3.7 24.2 - - + -
1169v PRO 3.3 17.9 - - - +
1170v VAL* 3.3 22.9 - - - +
1171v LYS* 3.5 10.4 + - + +
1173v VAL* 5.4 1.2 - - - +
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Residues in contact with TYR1095 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052v ASN* 3.0 11.0 - - - +
1053v ILE* 2.9 44.8 + - + +
1093v MET* 5.7 2.7 - - + -
1094v ASN* 1.3 76.5 - - - +
1096v HIS* 1.3 62.2 + - - +
1164v ARG* 4.5 5.4 - - - -
1168v PHE* 5.5 3.6 - - - +
1170v VAL* 5.2 1.6 - - + +
1173v VAL* 5.0 15.5 - - + -
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Residues in contact with HIS1096 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051v GLY 4.2 2.7 - - - -
1052v ASN* 4.4 4.3 - - + +
1095v TYR* 1.3 76.8 - - - +
1097v VAL* 1.3 61.1 + - - +
1098v GLY 5.0 2.2 - - - +
1163v PHE 3.5 24.8 - - - +
1164v ARG* 3.8 24.8 + - - +
1166v TYR* 4.3 13.7 - - + +
1167v TYR* 5.3 2.0 - - + +
1168v PHE 5.5 1.3 - - - +
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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