Contacts of the strand formed by residues 1081 - 1089 (chain A) in PDB entry 3AVS
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 THR1081 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002A THR* 3.6 28.1 - - + +
1003A GLN 3.5 5.1 + - - +
1004A LEU* 3.8 16.7 - - - +
1024A GLU* 5.6 0.2 + - - -
1038A TYR* 4.4 3.1 + - - -
1079A PHE 3.8 1.9 + - - -
1080A LYS* 1.3 82.4 + - - +
1082A ILE* 1.3 69.2 + - - +
1083A LYS* 5.0 4.5 - - + -
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Residues in contact with ILE1082 (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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1002A THR* 3.4 6.1 - - - +
1003A GLN* 2.9 50.3 + - + +
1004A LEU 4.8 0.9 - - - -
1005A LEU* 4.2 21.1 - - + +
1038A TYR* 3.4 12.6 - - - +
1080A LYS* 3.8 22.9 + - + +
1081A THR* 1.3 78.6 - - - +
1083A LYS* 1.3 67.4 + - - +
1084A PHE* 5.9 0.4 - - + -
1138A VAL* 4.1 7.2 - - + -
1139A PRO 3.6 15.9 - - - +
1140A GLY* 3.4 37.2 - - - +
1141A SER* 3.7 11.4 - - - +
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Residues in contact with LYS1083 (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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1000A VAL* 3.8 12.6 - - + -
1001A ARG 3.5 3.4 - - - -
1002A THR* 3.7 22.4 - - + +
1035A TYR* 2.8 25.6 + - + -
1038A TYR* 3.1 48.1 + - + +
1081A THR* 5.0 3.6 - - + -
1082A ILE* 1.3 83.2 - - - +
1084A PHE* 1.3 55.9 + - - +
1138A VAL* 3.5 9.2 - - - +
1141A SER* 4.4 1.1 - - - -
1510A EDO 3.0 44.0 + - - +
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Residues in contact with PHE1084 (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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1000A VAL* 3.4 4.0 - - - -
1001A ARG* 2.9 49.4 + - + +
1003A GLN* 4.1 9.9 - - - +
1035A TYR* 3.6 3.8 - - - -
1082A ILE* 5.9 0.9 - - + -
1083A LYS* 1.3 73.9 - - - +
1085A GLY* 1.3 80.2 + - - +
1086A THR* 3.5 11.1 + - - -
1135A TYR* 3.6 25.6 - + - -
1136A MET 3.6 5.2 - - - -
1137A LYS* 3.6 22.4 - - + -
1141A SER* 3.5 21.8 - - - +
1142A ARG 3.4 38.1 - - - -
1143A THR* 3.6 16.4 - - - -
1501A OGA 3.9 6.1 - - - -
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Residues in contact with GLY1085 (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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998A VAL* 3.7 17.9 - - - -
999A GLU 3.5 6.3 - - - -
1000A VAL* 4.8 0.4 - - - -
1035A TYR* 3.3 16.2 + - - -
1084A PHE* 1.3 78.3 - - - +
1086A THR* 1.3 58.8 + - - -
1088A ILE* 4.3 2.0 - - - -
1135A TYR* 3.4 1.0 - - - -
1136A MET* 2.8 44.7 + - - +
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Residues in contact with THR1086 (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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998A VAL* 4.2 0.6 - - - +
999A GLU* 2.8 57.5 + - + +
1001A ARG* 4.0 18.2 - - + +
1084A PHE* 4.0 16.2 - - - +
1085A GLY* 1.3 75.0 - - - -
1087A ASN* 1.3 85.0 + - - +
1088A ILE* 3.1 5.7 + - - +
1134A LEU 4.0 0.9 - - - -
1135A TYR* 3.2 25.0 - - - -
1143A THR* 5.3 0.2 + - - -
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Residues in contact with ASN1087 (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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999A GLU* 3.5 32.8 + - - +
1086A THR* 1.3 89.4 + - - +
1088A ILE* 1.3 62.8 + - - +
1089A ASP* 3.5 5.5 + - - +
1133A GLN* 2.4 48.1 + - - +
1134A LEU 3.7 3.2 + - - -
1135A TYR* 4.2 1.3 + - - -
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Residues in contact with ILE1088 (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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996A HIS* 3.9 14.1 - - + -
997A MET 3.8 15.5 - - - +
998A VAL* 3.7 39.0 - - + +
1032A ILE* 4.5 11.0 - - + -
1085A GLY 4.3 2.9 - - - -
1086A THR 3.8 4.3 - - - +
1087A ASN* 1.3 75.4 - - - +
1089A ASP* 1.3 64.2 + - - +
1090A LEU* 3.3 16.5 + - + +
1133A GLN* 3.4 4.8 - - - -
1134A LEU* 2.9 64.5 + - + +
1136A MET* 3.7 25.1 - - + +
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Residues in contact with ASP1089 (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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996A HIS* 2.8 37.6 + - + +
997A MET 4.8 1.2 + - - -
1087A ASN 3.5 6.2 + - - +
1088A ILE* 1.3 71.6 - - - +
1090A LEU* 1.3 60.2 + - - +
1091A SER* 2.7 38.3 + - - -
1092A ASP* 5.0 0.7 + - - +
1096A TRP* 3.6 2.1 + - - -
1127A LEU* 3.6 24.5 - - + +
1131A THR* 4.5 0.9 + - - -
1132A VAL 4.3 3.4 - - - +
1133A GLN* 5.2 0.4 - - - +
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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