Contacts of the strand formed by residues 1374 - 1378 (chain B) in PDB entry 5TWV
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 LYS1374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372B GLY 3.8 1.8 + - - +
1373B GLN* 1.3 72.9 - - - +
1375B ILE* 1.3 55.1 + - - +
1528B PHE* 4.7 10.8 - - + +
1533B VAL* 4.2 13.7 - - + -
1545B SER 5.8 0.2 - - - +
1546B ALA* 4.9 5.2 - - + -
1547B ASP* 3.2 25.6 + - + +
1548B LEU* 2.8 33.6 + - - +
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Residues in contact with ILE1375 (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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1369B ILE* 5.0 16.6 - - + -
1373B GLN* 3.9 4.9 + - + +
1374B LYS* 1.3 74.3 - - - +
1376B GLY* 1.3 62.1 - - - +
1533B VAL* 3.1 16.9 + - - +
1534B VAL* 3.9 2.3 - - - -
1535B THR* 3.0 29.2 + - - -
1546B ALA* 5.4 1.1 - - - -
1548B LEU* 3.5 10.8 - - + -
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Residues in contact with GLY1376 (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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1375B ILE* 1.3 75.0 - - - +
1377B ILE* 1.3 58.4 + - - -
1378B CYS* 5.4 0.4 - - - -
1535B THR* 3.8 11.2 - - - -
1537B ALA* 4.9 7.4 - - - -
1543B ILE* 5.9 2.7 - - - -
1546B ALA* 4.8 6.2 - - - +
1548B LEU 2.6 18.1 + - - -
1549B VAL* 4.2 4.7 - - - -
1550B MET* 2.5 38.1 + - - +
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Residues in contact with ILE1377 (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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1375B ILE 4.2 0.4 + - - -
1376B GLY* 1.3 71.2 - - - -
1378B CYS* 1.3 60.0 + - - +
1384B GLY 4.6 15.9 - - - +
1388B PHE* 4.9 8.7 - - + -
1535B THR 3.0 15.8 + - - +
1536B ILE* 4.4 3.3 - - - -
1537B ALA* 3.0 29.1 + - - +
1550B MET* 3.6 8.1 - - + -
1552B LEU* 4.7 11.2 - - + -
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Residues in contact with CYS1378 (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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1376B GLY 4.0 0.6 + - - +
1377B ILE* 1.3 75.7 - - - +
1379B GLY* 1.3 53.0 + - - +
1380B ARG 4.9 1.1 - - - -
1537B ALA* 4.2 14.6 - - + +
1538B HIS 6.0 2.2 - - - +
1540B VAL* 6.4 1.8 - - + -
1549B VAL* 5.7 6.1 - - + -
1550B MET 2.6 21.1 + - - +
1551B VAL* 4.2 5.8 - - + -
1552B LEU* 2.6 39.3 + - - +
1573B VAL* 6.1 3.1 - - + -
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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