Contacts of the strand formed by residues 597 - 603 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470F LEU* 4.4 1.2 - - - +
471F VAL 3.6 4.0 - - - -
472F GLN* 2.6 26.3 + - - -
550F ARG* 3.0 22.0 + - - +
595F SER* 3.4 12.7 + - - -
596F LEU* 1.3 78.9 - - - +
598F ALA* 1.3 59.6 + - - +
520H LYS 4.1 3.6 + - - -
521H VAL* 5.6 1.3 - - - +
522H PRO* 3.6 16.5 - - - +
599H THR* 3.4 26.3 + - - +
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Residues in contact with ALA 598 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470F LEU* 3.4 2.4 - - - -
471F VAL 2.8 37.6 + - - -
543F ALA* 3.7 26.8 - - + +
546F THR* 4.1 11.7 - - + -
547F LEU* 3.8 17.4 - - + +
550F ARG* 4.1 11.0 - - - +
597F SER* 1.3 76.0 + - - +
599F THR* 1.3 64.9 + - - +
599H THR* 4.3 4.0 - - - -
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Residues in contact with THR 599 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469F ALA 3.1 9.4 - - - +
470F LEU* 3.9 13.7 - - + +
542F ASP* 4.7 1.0 - - - +
543F ALA* 3.7 7.3 - - - +
546F THR* 5.0 3.5 + - - +
598F ALA* 1.3 78.1 - - - +
600F GLY* 1.3 59.9 + - - +
470H LEU* 4.0 3.1 - - + -
550H ARG* 4.6 6.4 + - - -
597H SER* 3.4 35.9 + - - +
598H ALA* 4.1 4.7 - - - +
599H THR* 3.5 33.1 + - + +
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Residues in contact with GLY 600 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468F GLY* 3.0 4.5 - - - -
469F ALA 2.6 39.2 + - - +
539F ALA* 3.5 21.1 - - - -
542F ASP* 3.4 10.1 - - - -
543F ALA* 3.5 9.1 - - - +
599F THR* 1.3 75.8 - - - +
601F PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 601 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466F GLN* 3.8 36.3 - - + -
467F ALA 3.0 26.5 - - - -
468F GLY* 4.5 2.9 - - - -
539F ALA* 3.9 3.4 - - - -
542F ASP* 2.8 26.5 + - - +
600F GLY* 1.3 75.9 - - - +
602F TYR* 1.3 81.6 + - - +
603F ALA* 4.2 5.2 - - + -
593H ARG* 3.4 30.3 - - + -
595H SER* 3.4 46.0 - - - +
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Residues in contact with TYR 602 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466F GLN* 3.2 5.9 - - - +
467F ALA 2.8 37.9 + - - +
534F ASP 4.9 1.1 - - - -
535F MET* 3.8 37.5 - - + +
538F MET* 3.4 53.5 - - + +
539F ALA* 3.9 2.7 - - - +
601F PHE* 1.3 82.9 - - - +
603F ALA* 1.3 74.1 + - - +
604F THR* 3.3 31.2 - - - +
605F PRO* 3.4 21.6 - - + +
620F LEU* 4.5 7.1 - - - +
720F GLU 5.1 4.3 + - - -
721F THR* 5.9 1.6 - - - -
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Residues in contact with ALA 603 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465F ASN 3.6 5.6 - - - +
601F PHE* 4.2 9.3 - - + -
602F TYR* 1.3 87.3 - - - +
604F THR* 1.3 64.1 + - - +
605F PRO* 3.4 8.7 - - - +
593H ARG* 3.8 38.1 - - + +
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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