Contacts of the strand formed by residues 1286 - 1289 (chain A) in PDB entry 1WUF
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 LEU1286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211A GLU* 4.5 11.2 - - + +
1212A MET* 3.6 26.9 - - + -
1235A ARG* 3.3 43.1 - - - +
1258A ARG 3.0 6.7 + - - -
1259A ALA* 3.6 10.8 - - + +
1260A ILE* 2.6 33.4 + - - +
1284A GLU 3.7 3.2 + - - -
1285A ILE* 1.3 72.4 - - - +
1287A VAL* 1.3 79.5 + - - +
1288A TRP* 4.4 0.4 - - + -
1312A VAL* 5.7 2.5 - - + +
1313A PHE* 3.8 25.1 - - + +
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Residues in contact with VAL1287 (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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1260A ILE* 3.6 6.7 - - + +
1262A LEU* 3.9 24.0 - - + -
1276A ILE* 5.0 0.2 - - + -
1277A ALA* 4.5 6.7 - - - +
1280A CYS* 3.9 30.5 - - + -
1281A ALA* 5.4 1.1 - - - +
1285A ILE 3.4 1.1 + - - +
1286A LEU* 1.3 83.1 - - - +
1288A TRP* 1.3 67.7 + - - +
1310A GLU* 4.0 28.9 + - + +
1311A PHE* 3.3 40.9 - - + -
1312A VAL 4.2 2.6 + - - -
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Residues in contact with TRP1288 (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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1160A ARG* 4.3 1.1 - - - -
1162A LYS* 3.6 5.6 - - - -
1187A MET* 3.5 28.7 - - + -
1212A MET* 3.2 35.7 - - + -
1214A GLU* 3.7 8.5 - - - -
1237A CYS* 3.6 10.3 - - - -
1260A ILE 3.4 11.1 + - - -
1261A ASN* 3.2 32.8 - - + +
1262A LEU* 2.9 26.4 + - - +
1286A LEU* 4.4 3.1 - - + -
1287A VAL* 1.3 80.6 - - - +
1289A CYS* 1.3 83.7 + - - +
1290A GLY* 3.4 4.0 + - - -
1311A PHE* 3.6 11.2 - - - -
1313A PHE* 3.7 31.2 - + + +
1314A PRO 3.9 12.6 - - - +
1316A ASP* 3.2 30.7 - - - -
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Residues in contact with CYS1289 (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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1262A LEU 3.2 7.2 - - - +
1288A TRP* 1.3 75.7 - - - +
1290A GLY* 1.3 54.6 + - - +
1302A ASN* 3.6 20.2 - - - +
1305A LEU* 3.9 17.0 - - - -
1306A ALA* 3.6 41.3 - - + -
1311A PHE* 3.9 17.4 - - - +
1313A PHE 5.1 0.4 + - - -
1315A GLY* 3.1 12.7 - - - -
1316A ASP 2.7 33.1 + - - -
1317A ILE* 4.7 2.9 - - + -
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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