Contacts of the strand formed by residues 1180 - 1185 (chain A) in PDB entry 2W18
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 ILE1180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860A GLU* 3.3 5.4 - - - +
861A LEU* 2.8 49.5 + - + +
869A SER* 4.8 2.9 - - - +
871A ASP 5.1 0.4 - - - +
872A VAL* 4.0 23.1 - - + -
887A ILE* 5.2 3.8 - - + -
889A THR* 4.2 20.9 - - + -
1161A PHE* 3.6 34.1 - - + -
1172A LEU* 4.4 11.4 - - + -
1173A ALA 3.3 5.6 - - - +
1174A GLY* 3.7 8.7 - - - -
1178A GLY 4.0 9.6 - - - +
1179A ASN* 1.3 75.5 - - - +
1181A PHE* 1.3 72.4 + - - +
1182A VAL* 4.3 12.0 - - + +
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Residues in contact with PHE1181 (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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857A LEU* 3.9 17.0 - - + -
859A SER 3.9 1.1 - - - -
860A GLU* 3.1 43.1 - - + -
1154A VAL* 3.3 20.6 - - + -
1159A TRP* 3.5 22.9 - + + -
1171A LEU 3.7 2.1 - - - +
1172A LEU* 3.7 0.7 - - - -
1173A ALA 2.7 36.2 + - - +
1175A GLN* 3.1 28.0 - - - -
1179A ASN* 4.2 18.6 - - + -
1180A ILE* 1.3 76.1 - - - +
1182A VAL* 1.3 63.0 + - - +
1183A TYR* 3.7 25.1 - - + +
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Residues in contact with VAL1182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 3.5 2.5 - - - +
858A VAL* 2.8 34.3 + - + +
859A SER* 2.9 38.5 + - - +
860A GLU* 4.7 0.4 - - - +
861A LEU* 5.7 0.7 - - + +
887A ILE* 4.1 17.5 - - + -
906A TRP* 4.5 2.5 - - + +
1170A HIS* 3.8 34.5 - - + -
1171A LEU 3.4 2.7 - - - -
1172A LEU* 4.0 21.3 - - + -
1180A ILE* 4.3 9.2 - - + +
1181A PHE* 1.3 77.6 - - - +
1183A TYR* 1.3 55.9 + - - +
2187A GOL 4.1 9.6 - - - -
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Residues in contact with TYR1183 (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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855A LEU* 3.6 34.5 - - + -
856A GLN 3.4 5.4 - - - +
857A LEU* 3.4 39.6 - - + +
1151A LEU* 3.3 39.2 - - + +
1154A VAL* 4.0 11.4 - - - +
1159A TRP* 3.6 20.6 - - - -
1170A HIS* 3.1 8.4 - - - -
1171A LEU* 2.7 50.0 + - + +
1173A ALA* 4.2 7.2 - - + -
1181A PHE* 3.7 32.4 - - + +
1182A VAL* 1.3 73.9 - - - +
1184A HIS* 1.3 62.9 + - - +
1185A TYR 3.5 0.2 + - - -
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Residues in contact with HIS1184 (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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854A ASN 3.2 5.7 - - - +
855A LEU* 3.3 3.5 - - - -
856A GLN* 2.8 43.9 + - + +
858A VAL* 3.9 16.9 - - + +
1169A SER* 3.6 17.8 + - - -
1170A HIS* 3.6 23.5 - + + +
1183A TYR* 1.3 72.0 - - - +
1185A TYR* 1.3 70.7 + - - +
1186A SER* 3.0 29.9 + - - -
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Residues in contact with TYR1185 (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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854A ASN* 3.7 14.4 - - - -
855A LEU* 3.3 25.4 - - + -
1127A CYS* 3.6 25.2 - - - -
1139A ILE* 3.7 24.3 - - + +
1141A ASP* 5.1 1.6 + - - +
1148A THR* 2.4 36.4 + - - +
1149A ALA* 5.0 2.2 - - + -
1164A TRP* 3.9 22.7 - + + -
1169A SER* 2.9 37.6 + - - +
1171A LEU 5.1 0.9 - - - +
1183A TYR 3.5 2.1 + - - +
1184A HIS* 1.3 83.0 - - - +
1186A SER* 1.3 80.0 + - - +
2191A GOL 3.8 15.7 - - - -
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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