Contacts of the strand formed by residues 583 - 594 (chain B) in PDB entry 2W77
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 TYR 583 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ARG* 3.1 10.3 + - - -
578B ASP* 3.8 0.2 - - - -
579B LEU* 3.3 30.5 + - + -
580B ASN* 2.9 34.5 + - - +
581B ASP 3.7 0.2 - - - -
582B THR* 1.3 90.5 - - + +
584B SER* 1.3 67.2 + - - +
620B ILE* 4.3 20.9 - - + -
621B LYS 3.4 7.0 - - - -
622B GLY* 3.6 20.6 - - - -
624B TYR* 3.0 27.7 + - - -
631B THR* 4.7 0.9 - - - -
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Residues in contact with SER 584 (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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163B ARG* 3.3 24.3 + - - +
576B VAL* 3.8 17.8 - - - +
577B TYR 3.2 13.5 - - - -
578B ASP* 2.8 24.5 + - - +
579B LEU* 4.3 2.2 - - - +
583B TYR* 1.3 79.4 + - - +
585B VAL* 1.3 61.7 + - - +
586B TYR* 4.1 2.2 + - - -
620B ILE* 3.4 4.1 - - - -
621B LYS* 2.8 36.9 + - - +
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Residues in contact with VAL 585 (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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576B VAL* 3.6 1.7 - - - +
577B TYR* 2.9 57.2 + - + +
579B LEU* 4.1 25.1 - - + +
584B SER* 1.3 74.6 - - - +
586B TYR* 1.3 63.9 + - - +
618B ILE* 5.9 6.7 - - + -
619B GLY 3.2 10.3 - - - +
620B ILE* 4.1 15.7 - - + -
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Residues in contact with TYR 586 (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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163B ARG 5.6 1.6 - - - +
165B THR 4.9 0.7 - - - +
166B PRO* 3.0 42.8 - - + -
167B GLN 4.0 0.7 - - - -
168B SER* 4.2 4.3 + - - -
575B ALA 3.2 15.7 - - - +
576B VAL* 3.9 11.7 - - + -
584B SER* 4.7 1.8 - - - -
585B VAL* 1.3 78.1 - - - +
587B ALA* 1.3 65.9 + - - +
588B SER* 4.8 0.7 - - - -
617B GLU* 2.7 34.7 + - + -
618B ILE* 3.4 4.4 - - - +
619B GLY* 2.8 69.5 + - - +
620B ILE* 3.8 4.5 - - - -
621B LYS* 3.9 37.6 - - + -
632B SER* 5.5 2.1 - - - -
633B LEU 4.8 0.6 + - - -
634B ALA* 3.6 14.4 - - - +
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Residues in contact with ALA 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 4.3 0.9 - - - +
574B GLY* 3.0 2.3 - - - -
575B ALA* 2.9 34.8 + - + +
586B TYR* 1.3 80.9 - - - +
588B SER* 1.3 65.0 + - - +
617B GLU 3.0 11.2 - - - +
618B ILE* 3.6 18.6 - - + -
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Residues in contact with SER 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 2.9 28.6 + - - -
167B GLN* 4.5 8.2 - - - +
572B TYR* 5.6 1.6 - - - -
573B VAL 3.3 14.1 - - - -
574B GLY* 3.8 5.8 - - - -
587B ALA* 1.3 77.5 - - - +
589B TYR* 1.3 61.4 + - - +
590B THR* 4.2 7.9 - - - +
615B ASN* 3.5 6.1 + - - +
616B TYR* 3.6 2.1 - - - -
617B GLU* 2.7 45.6 + - - +
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Residues in contact with TYR 589 (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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571B PRO* 3.6 33.8 - - + +
572B TYR* 3.9 2.6 - - - -
573B VAL* 2.8 48.0 + - + +
588B SER* 1.3 72.0 - - - +
590B THR* 1.3 66.0 + - - +
591B ASP* 5.0 3.1 + - + -
614B GLN* 3.5 29.8 - - + +
615B ASN 3.5 2.5 - - - -
616B TYR* 3.5 46.1 + + + +
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Residues in contact with THR 590 (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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167B GLN* 3.9 13.7 + - + +
252B ALA* 3.3 26.2 + - - +
571B PRO 4.3 2.9 - - - +
572B TYR* 3.5 36.1 - - + -
588B SER* 4.9 4.9 - - - +
589B TYR* 1.3 82.1 - - - +
591B ASP* 1.3 61.3 + - - +
614B GLN* 2.9 7.9 - - - +
615B ASN* 2.6 60.3 + - - +
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Residues in contact with ASP 591 (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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252B ALA* 3.6 5.3 - - - +
254B GLY 3.2 19.6 + - - -
255B LEU 4.5 0.3 + - - -
569B PHE 4.1 3.7 - - - +
570B ILE* 3.2 35.1 - - + +
571B PRO* 3.7 32.6 + - + +
589B TYR* 5.0 1.7 + - + -
590B THR* 1.3 75.5 - - - +
592B ILE* 1.3 68.5 + - - +
593B PHE* 4.9 2.3 - - - -
612B GLU* 4.3 8.5 - - - +
613B GLY 3.4 4.2 - - - +
614B GLN* 2.6 37.4 + - + +
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Residues in contact with ILE 592 (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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216B ASN* 4.3 0.7 - - - +
252B ALA* 4.4 4.9 - - + -
253B THR* 4.0 12.8 - - - +
254B GLY* 3.7 17.7 - - - +
257B THR* 4.0 9.2 - - + -
258B GLY 3.6 24.2 - - - +
260B GLY* 3.5 24.5 - - - +
261B SER 3.5 23.8 - - - +
262B LEU* 3.2 34.3 - - + -
570B ILE* 4.9 2.2 - - - -
591B ASP* 1.3 81.9 - - - +
593B PHE* 1.3 68.6 + - - +
612B GLU* 3.3 3.3 - - - +
613B GLY 3.0 30.1 + - - +
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Residues in contact with PHE 593 (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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259B ALA* 3.3 15.9 - - + -
260B GLY 2.7 31.0 + - - -
552B VAL* 3.5 37.2 - - + -
554B TYR* 5.3 1.1 - - + -
565B GLU* 4.5 11.7 - - + -
568B ARG* 3.8 39.3 - - + +
569B PHE 5.5 1.1 - - - -
570B ILE* 4.0 24.6 - - + +
591B ASP* 4.9 2.9 - - - +
592B ILE* 1.3 77.0 - - - +
594B MET* 1.3 60.0 + - - +
595B PRO* 3.9 24.0 - - + -
610B PRO* 4.0 14.1 - - + -
611B ASP 3.4 6.1 - - - +
612B GLU* 3.6 22.4 - - + +
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Residues in contact with MET 594 (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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215B ASN* 5.6 1.3 - - - +
227B ARG* 3.2 36.8 - - + +
259B ALA* 4.4 6.5 - - - -
260B GLY* 3.2 36.8 - - - +
261B SER* 5.0 2.0 - - - +
554B TYR* 4.2 14.8 - - + +
593B PHE* 1.3 72.6 - - - +
595B PRO* 1.4 90.5 - - - +
596B GLN* 3.5 0.3 + - - -
597B ASP* 5.7 4.5 - - - +
610B PRO* 4.0 2.0 - - - -
611B ASP* 2.7 46.9 + - + +
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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