Contacts of the strand formed by residues 597 - 603 (chain B) in PDB entry 2W3S
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 SER 597 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B LEU* 4.4 3.1 - - - +
471B VAL 3.5 5.6 + - - -
472B GLN* 2.9 22.5 + - - -
547B LEU* 3.9 0.7 - - - -
550B ARG* 2.6 28.7 + - - -
595B SER* 3.2 11.4 + - - -
596B LEU* 1.3 80.5 - - - +
598B ALA* 1.3 58.9 + - - +
520D LYS 4.5 3.5 + - - -
522D PRO* 3.5 19.9 - - - +
599D THR* 3.7 24.1 + - - +
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Residues in contact with ALA 598 (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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470B LEU* 3.6 2.0 - - - +
471B VAL 2.9 33.7 + - - -
543B ALA* 3.7 17.5 - - + +
546B THR* 3.9 18.8 - - + -
547B LEU* 3.6 23.5 - - + +
550B ARG* 4.3 2.5 - - - +
597B SER* 1.3 78.6 + - - +
599B THR* 1.3 68.0 + - - +
599D THR* 4.3 5.6 - - - -
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Residues in contact with THR 599 (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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469B ALA 3.3 7.6 - - - +
470B LEU* 3.8 14.4 - - + +
542B ASP* 4.1 2.9 - - - +
543B ALA* 3.6 11.2 - - - +
546B THR* 4.7 4.0 + - - +
598B ALA* 1.3 78.9 - - - +
600B GLY* 1.3 60.1 + - - +
470D LEU* 4.0 2.9 - - + -
550D ARG* 4.3 7.3 + - - -
595D SER* 5.4 2.5 + - - -
597D SER* 3.5 43.2 + - - +
598D ALA* 4.4 2.4 - - - -
599D THR* 3.6 29.6 + - + +
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Residues in contact with GLY 600 (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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468B GLY* 3.1 3.6 - - - -
469B ALA 2.6 42.3 + - - +
539B ALA* 3.4 17.5 - - - -
542B ASP* 3.1 12.6 - - - -
543B ALA* 3.7 5.1 - - - +
599B THR* 1.3 76.8 - - - +
601B PHE* 1.3 61.0 + - - +
595D SER* 5.3 0.6 + - - -
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Residues in contact with PHE 601 (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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466B GLN* 3.6 38.1 - - + -
467B ALA 3.3 17.3 - - - -
468B GLY* 4.5 4.0 - - - -
539B ALA* 4.0 4.3 + - - -
542B ASP* 3.0 23.5 + - - +
600B GLY* 1.3 74.8 - - - +
602B TYR* 1.3 71.3 + - - +
603B ALA* 4.2 5.8 - - + -
593D ARG* 3.2 35.9 - - + -
594D ILE* 4.5 0.2 - - - -
595D SER* 3.5 45.5 - - - +
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Residues in contact with TYR 602 (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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466B GLN* 2.9 5.5 - - - +
467B ALA 2.7 39.0 + - - +
534B ASP* 4.8 1.6 - - + -
535B MET* 3.7 37.7 - - + +
538B MET* 3.2 50.5 - - + +
539B ALA 3.8 3.4 - - - +
601B PHE* 1.3 82.4 - - - +
603B ALA* 1.3 74.2 + - - +
604B THR* 3.5 27.0 - - + +
605B PRO* 3.0 25.4 - - + +
620B LEU* 4.9 3.3 - - - +
720B GLU 4.6 8.4 + - - -
721B THR* 5.7 1.4 - - - -
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Residues in contact with ALA 603 (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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465B ASN 3.2 6.7 - - - +
601B PHE* 4.2 11.3 - - + -
602B TYR* 1.3 89.0 - - - +
604B THR* 1.3 63.9 + - - +
605B PRO* 3.5 4.5 - - - +
593D ARG* 3.7 37.9 - - + +
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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