Contacts of the strand formed by residues 597 - 603 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520B LYS 4.2 2.9 + - - -
521B VAL* 6.1 0.2 - - - -
522B PRO* 3.7 17.7 - - - +
599B THR* 3.5 28.6 + - - +
470D LEU* 4.0 4.2 - - - +
471D VAL 3.5 3.9 + - - -
472D GLN* 2.8 25.2 + - - -
550D ARG* 2.9 19.2 + - - +
595D SER* 3.5 10.3 + - - -
596D LEU* 1.3 79.0 - - - +
598D ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B THR* 4.3 2.2 - - - -
470D LEU* 3.5 4.1 - - - +
471D VAL 2.9 32.2 + - - -
543D ALA* 3.7 18.6 - - - +
546D THR* 3.8 18.6 - - + -
547D LEU* 3.7 26.4 - - + +
550D ARG* 3.9 3.6 - - - +
597D SER* 1.3 75.1 + - - +
599D THR* 1.3 67.0 + - - +
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Residues in contact with THR 599 (chain D).
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* 4.2 1.6 - - + -
550B ARG* 4.6 6.8 + - - -
597B SER* 3.7 36.1 + - - +
598B ALA* 4.3 2.9 - - - -
599B THR* 3.6 33.6 + - + +
469D ALA 3.1 11.0 - - - +
470D LEU* 3.8 13.5 - - + +
542D ASP* 4.7 1.0 - - - +
543D ALA* 3.4 13.3 + - - -
546D THR* 4.8 4.3 + - - +
598D ALA* 1.3 78.9 - - - +
600D GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D GLY* 3.0 4.5 - - - -
469D ALA 2.7 32.5 + - - +
539D ALA* 3.3 22.4 - - - -
542D ASP* 3.3 10.8 - - - -
543D ALA 3.8 3.8 - - - -
599D THR* 1.3 77.1 + - - +
601D PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B ARG 3.3 32.5 - - - -
594B ILE* 4.0 0.7 - - - -
595B SER* 3.4 47.3 - - - +
466D GLN* 3.8 31.9 - - + -
467D ALA 3.2 25.1 - - - -
468D GLY* 4.5 3.8 - - - -
539D ALA* 3.7 6.7 - - - +
542D ASP* 2.9 21.7 + - - +
600D GLY* 1.3 75.6 - - - +
602D TYR* 1.3 75.1 + - - +
603D ALA* 4.2 5.2 - - + -
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Residues in contact with TYR 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D GLN* 3.2 4.2 - - - +
467D ALA 2.8 32.4 + - - +
534D ASP* 4.6 2.0 - - + -
535D MET* 3.7 38.6 - - + +
538D MET* 3.4 53.3 - - + +
539D ALA 3.8 2.0 - - - +
601D PHE* 1.3 82.2 - - - +
603D ALA* 1.3 70.6 + - - +
604D THR* 3.4 33.5 - - + +
605D PRO* 3.3 22.4 - - + +
620D LEU* 4.7 6.6 - - - +
720D GLU 5.0 4.2 + - - -
721D THR* 5.5 2.8 - - - -
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Residues in contact with ALA 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B ARG* 3.6 37.9 - - + +
465D ASN 3.2 8.3 - - - +
466D GLN* 4.7 0.4 - - + -
601D PHE* 4.2 10.0 - - + -
602D TYR* 1.3 87.1 - - - +
604D THR* 1.3 65.1 + - - +
605D PRO* 3.4 8.0 - - - +
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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