Contacts of the strand formed by residues 1133 - 1137 (chain A) in PDB entry 3AVR
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 GLN1133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1087A ASN* 2.9 42.2 + - - +
1088A ILE 3.2 8.1 - - - +
1089A ASP* 3.0 30.8 + - - +
1127A LEU 3.7 2.8 + - - -
1128A GLY* 3.3 21.6 - - - -
1131A THR 3.6 0.6 + - - -
1132A VAL* 1.3 76.6 - - - +
1134A LEU* 1.3 60.5 + - - +
1135A TYR* 4.3 5.1 - - + -
1236A ASN 4.0 0.2 - - - +
1237A ILE* 3.3 4.5 - - - -
1238A ALA 2.9 38.5 + - - +
26B ARG* 3.9 3.4 - - - +
27B M3L 2.9 43.8 + - - +
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Residues in contact with LEU1134 (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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984A PHE* 4.8 2.2 - - + +
989A LEU* 3.5 34.8 - - + -
1032A ILE* 4.3 5.4 - - + -
1087A ASN 3.5 5.7 + - - -
1088A ILE* 2.8 63.8 + - + +
1090A LEU* 4.0 24.0 - - + +
1133A GLN* 1.3 75.6 - - - +
1135A TYR* 1.3 72.6 + - - +
1136A MET* 4.0 13.2 - - + -
1235A ASN* 4.1 11.0 - - + -
1236A ASN 3.4 15.9 - - - +
1237A ILE* 4.0 13.2 - - + -
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Residues in contact with TYR1135 (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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1084A PHE* 3.7 16.2 - + + -
1085A GLY 3.4 6.1 - - - +
1086A THR* 3.2 27.4 - - - -
1087A ASN* 3.3 30.1 + - - -
1133A GLN 4.3 8.5 - - - -
1134A LEU* 1.3 76.7 - - - +
1136A MET* 1.3 62.5 + - - +
1137A LYS* 3.7 20.0 - - - -
1143A THR* 4.6 3.0 - - + +
1235A ASN* 3.0 9.4 - - - +
1236A ASN* 2.8 44.0 + - + +
1238A ALA* 4.1 22.0 - - + -
1501A OGA 4.1 32.9 + - - -
27B M3L 3.3 27.8 - - - -
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Residues in contact with MET1136 (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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986A THR* 3.6 39.5 - - + +
989A LEU* 5.1 0.7 - - + -
998A VAL* 4.9 2.2 - - - -
1032A ILE* 3.8 34.5 - - + -
1035A TYR* 3.1 34.6 + - + -
1036A ALA* 4.4 5.6 - - - +
1039A GLN* 4.0 2.9 - - - +
1084A PHE* 3.6 1.4 - - - -
1085A GLY 2.8 36.1 + - - +
1088A ILE* 3.7 23.1 - - + -
1134A LEU* 4.0 11.4 - - + -
1135A TYR* 1.3 75.9 - - - +
1137A LYS* 1.3 60.8 + - - +
1235A ASN* 3.5 14.1 - - - +
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Residues in contact with LYS1137 (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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1035A TYR* 3.9 1.3 - - - -
1039A GLN* 3.0 20.8 + - - +
1084A PHE* 3.6 18.8 - - + -
1135A TYR* 3.7 14.1 - - + -
1136A MET* 1.3 81.0 - - - +
1138A VAL* 1.3 63.4 + - - +
1141A SER* 3.9 8.7 + - - +
1164A CYS* 3.4 14.6 - - - -
1228A VAL* 4.2 6.3 - - - +
1229A GLN 5.3 0.2 - - - -
1230A ALA* 3.8 29.9 - - + +
1233A TRP* 3.7 3.1 - - - -
1234A CYS* 2.8 32.8 + - - +
1236A ASN* 3.1 27.5 + - - +
1501A OGA 2.8 41.2 + - - -
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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