Contacts of the strand formed by residues 1130 - 1134 (chain A) in PDB entry 4CLI
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 VAL1130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121A GLY* 3.7 2.9 - - - -
1122A LEU* 2.8 38.0 + - + -
1123A GLY 2.7 18.1 + - - +
1124A HIS* 5.6 1.8 - - - +
1128A GLY 5.0 2.7 - - - +
1129A GLU* 1.3 80.2 - - - +
1131A TYR* 1.3 72.0 + - - +
1148A ALA* 4.4 2.9 - - + -
1149A VAL 3.2 16.2 - - - +
1150A LYS* 4.4 14.1 - - - +
2401A 5P8 3.4 58.6 - - + +
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Residues in contact with TYR1131 (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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1118A LEU* 3.9 35.4 - - + -
1119A ILE 5.8 0.2 - - - -
1120A ARG* 3.2 17.5 - - - +
1121A GLY* 3.7 16.6 - - - -
1122A LEU* 3.7 6.5 - - - +
1129A GLU* 2.5 49.5 + - + -
1130A VAL* 1.3 75.6 - - - +
1132A GLU* 1.3 64.7 + - - +
1148A ALA* 3.3 4.2 - - - -
1149A VAL* 2.6 42.0 + - + -
1151A THR* 3.9 24.2 - - + -
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Residues in contact with GLU1132 (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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1118A LEU* 3.7 2.9 - - - -
1119A ILE* 2.8 36.5 + - + +
1120A ARG* 2.8 59.5 + - + +
1122A LEU* 3.6 17.9 - - + +
1131A TYR* 1.3 75.7 - - - +
1133A GLY* 1.3 64.6 + - - +
1134A GLN* 6.0 0.3 + - - +
1146A GLN* 5.4 3.5 - - + +
1147A VAL 3.4 3.8 - - - -
1198A LEU* 3.9 29.3 - - + +
2401A 5P8 5.5 1.1 + - - -
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Residues in contact with GLY1133 (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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1116A ILE* 5.8 0.2 - - - -
1117A THR 3.2 12.3 - - - -
1118A LEU* 4.4 0.2 - - - -
1119A ILE* 4.2 2.5 - - - -
1131A TYR 3.9 0.4 + - - -
1132A GLU* 1.3 79.9 - - - +
1134A GLN* 1.3 63.4 + - - +
1146A GLN* 3.4 6.4 - - - +
1147A VAL* 2.7 42.0 + - - +
1149A VAL* 4.2 15.0 - - - +
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Residues in contact with GLN1134 (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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1115A ASN 3.4 1.6 - - - +
1116A ILE* 3.3 6.8 - - - +
1117A THR* 2.9 41.7 + - - +
1119A ILE* 4.0 27.7 - - + +
1132A GLU* 6.0 0.9 + - - +
1133A GLY* 1.3 78.6 - - - +
1135A VAL* 1.3 61.3 + - - +
1144A PRO* 4.5 18.0 - - + +
1145A LEU 3.2 10.1 - - - +
1146A GLN* 5.0 5.8 - - + -
1147A VAL* 5.4 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