Contacts of the strand formed by residues 1532 - 1536 (chain B) in PDB entry 5YWB
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 THR1532 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343B GLY* 3.7 15.8 + - - +
1345B ILE* 5.2 1.8 - - + -
1369B ILE* 3.8 22.4 - - + -
1370B SER 4.0 1.2 + - - -
1372B GLY* 3.1 23.4 + - - -
1373B GLN 3.2 22.7 + - - +
1375B ILE* 4.1 6.1 - - + -
1501B SER 3.3 4.7 + - - +
1502B ILE* 3.5 23.2 - - + +
1503B PHE* 2.9 24.7 + - - +
1531B ARG* 1.3 74.4 - - - +
1533B VAL* 1.3 63.2 + - - +
1534B VAL* 4.4 9.4 - - + -
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Residues in contact with VAL1533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373B GLN 3.9 3.4 + - - -
1374B LYS* 3.6 14.2 - - + +
1375B ILE* 2.7 34.1 + - - +
1503B PHE* 3.6 32.5 - - + +
1505B MET* 4.4 15.3 - - + -
1524B VAL 6.0 0.2 - - - +
1525B MET* 5.3 9.4 - - + -
1528B PHE* 4.5 20.0 - - + +
1531B ARG 3.7 10.0 + - - +
1532B THR* 1.3 80.0 - - - +
1534B VAL* 1.3 61.3 + - - +
1535B THR* 3.8 22.8 + - + +
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Residues in contact with VAL1534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345B ILE* 5.1 5.2 - - + -
1369B ILE* 4.0 16.6 - - + -
1375B ILE* 3.2 24.0 - - + +
1377B ILE* 3.6 33.4 - - + -
1388B PHE* 4.8 10.3 - - + -
1392B PHE* 6.1 2.0 - - + -
1502B ILE* 5.3 2.5 - - + -
1503B PHE 2.9 15.7 + - - +
1504B ILE* 3.4 19.9 - - + +
1505B MET* 2.9 24.8 + - - +
1532B THR* 4.4 7.9 - - + -
1533B VAL* 1.3 75.4 - - - +
1535B THR* 1.3 64.5 + - - +
1536B ILE* 5.0 2.7 - - + +
1550B MET* 5.1 1.1 - - + -
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Residues in contact with THR1535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374B LYS* 6.6 0.4 - - + -
1375B ILE 2.9 15.3 + - - +
1376B GLY* 3.8 7.8 - - - -
1377B ILE* 3.0 28.8 + - - +
1505B MET* 3.6 27.4 - - + -
1521B GLN* 5.3 1.1 - - - +
1525B MET* 4.7 14.8 - - + -
1533B VAL* 3.8 22.0 - - + +
1534B VAL* 1.3 77.0 - - - +
1536B ILE* 1.3 68.0 + - - +
1537B ALA* 5.1 5.1 - - - +
1542B THR* 5.4 7.0 + - - -
1543B ILE* 4.9 6.6 - - - +
1546B ALA* 5.7 1.4 - - - +
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Residues in contact with ILE1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377B ILE* 3.5 42.8 - - + +
1378B CYS* 5.3 0.9 - - - -
1385B LYS* 3.5 53.8 - - + +
1388B PHE* 6.1 1.6 - - + -
1389B SER* 4.6 8.7 - - - -
1504B ILE* 5.2 4.5 - - + -
1505B MET 2.9 18.3 + - - +
1506B ASP* 3.6 28.7 - - + +
1507B GLU* 2.8 37.0 + - - +
1534B VAL* 5.0 3.4 - - + +
1535B THR* 1.3 72.9 - - - +
1537B ALA* 1.3 56.4 + - - +
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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