Contacts of the strand formed by residues 1092 - 1099 (chain A) in PDB entry 3L8V
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 VAL1092 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A L8V 3.2 46.0 - - + +
1083A VAL* 3.7 6.6 - - - +
1084A ILE* 2.8 54.0 + - + +
1085A GLY 3.6 8.8 + - - +
1090A GLY 5.2 2.5 - - - +
1091A CYS* 1.3 79.5 - - - +
1093A TYR* 1.3 61.8 + - - +
1108A ALA* 4.0 15.5 - - + -
1109A VAL 3.4 6.7 - - - +
1110A LYS* 3.8 13.2 - - + -
1223A PHE* 4.7 10.1 - - + -
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Residues in contact with TYR1093 (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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1078A VAL* 3.9 20.2 - - + -
1079A HIS 3.7 9.4 - - - +
1080A PHE* 3.5 52.4 - + + -
1082A GLU 3.5 4.7 - - - -
1083A VAL* 3.6 22.2 - - + -
1084A ILE* 3.4 7.6 - - - +
1086A ARG* 3.9 13.0 + - - -
1091A CYS* 3.4 34.2 - - + +
1092A VAL* 1.3 72.0 - - - +
1094A HIS* 1.3 65.4 - - - +
1108A ALA* 3.4 5.9 - - - -
1109A VAL* 2.8 43.1 + - + +
1111A SER* 4.1 17.2 - - - -
1112A LEU* 5.4 2.6 - - - +
1154A LEU* 5.9 0.2 - - + -
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Residues in contact with HIS1094 (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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1078A VAL* 3.9 1.6 - - - +
1079A HIS* 2.9 40.5 + - + -
1082A GLU* 3.0 49.7 + - + +
1083A VAL 4.7 3.4 + - - -
1084A ILE* 3.3 28.6 - - + +
1093A TYR* 1.3 76.5 - - - +
1095A GLY* 1.3 58.8 + - - +
1106A HIS* 2.9 26.4 + + - +
1107A CYS 3.8 1.1 - - - -
1109A VAL* 4.9 0.2 - - - -
1159A TYR* 3.5 35.6 + + - -
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Residues in contact with GLY1095 (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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1077A ILE 3.3 10.1 - - - -
1079A HIS* 3.8 3.7 + - - -
1093A TYR 3.7 0.2 + - - -
1094A HIS* 1.3 76.3 - - - +
1096A THR* 1.3 64.1 + - - -
1106A HIS* 3.5 9.7 - - - -
1107A CYS* 2.8 45.7 + - - +
1109A VAL* 4.1 9.9 - - - -
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Residues in contact with THR1096 (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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1076A LEU* 3.4 6.3 - - - +
1077A ILE* 2.8 56.8 + - + +
1079A HIS* 3.0 25.1 + - - -
1095A GLY* 1.3 72.9 + - - -
1097A LEU* 1.3 63.2 + - - +
1098A LEU* 4.8 2.9 - - + -
1104A LYS* 4.3 26.7 - - + +
1105A ILE 3.5 8.7 - - - +
1106A HIS* 5.8 0.9 - - - -
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Residues in contact with LEU1097 (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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1071A ILE* 3.7 42.6 - - + -
1075A SER* 3.4 7.2 - - - +
1076A LEU* 3.9 12.6 - - + -
1096A THR* 1.3 75.7 - - - +
1098A LEU* 1.3 74.2 + - - +
1099A ASP* 5.3 7.2 - - + +
1103A LYS 3.1 3.1 - - - +
1104A LYS* 3.8 1.4 - - - -
1105A ILE* 3.0 60.6 + - + +
1107A CYS* 3.9 11.2 - - - -
1143A LEU* 4.1 26.0 - - + +
1156A VAL* 4.4 4.9 - - + -
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Residues in contact with LEU1098 (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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1074A SER 4.1 5.6 - - - +
1075A SER* 2.7 58.0 + - - +
1077A ILE* 3.7 22.9 - - + -
1096A THR* 4.8 4.9 - - + -
1097A LEU* 1.3 79.4 - - - +
1099A ASP* 1.3 60.4 + - - +
1100A ASN 4.1 1.2 + - - -
1102A GLY* 4.0 18.8 - - - +
1103A LYS 3.2 16.4 - - - +
1104A LYS* 4.1 10.3 - - + -
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Residues in contact with ASP1099 (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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1097A LEU* 3.8 7.3 + - + +
1098A LEU* 1.3 72.5 - - - +
1100A ASN* 1.4 65.9 + - - +
1101A ASP* 2.6 20.8 + - - -
1103A LYS* 3.2 45.4 + - + +
1105A ILE* 4.7 17.6 - - + +
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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