Contacts of the strand formed by residues 611 - 624 (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 ASP 611 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B GLY 5.0 0.3 - - - +
262B LEU* 4.3 5.4 - - - +
593B PHE* 3.4 0.2 - - - -
594B MET* 2.7 49.6 + - + +
596B GLN* 3.3 18.2 - - - +
609B GLU 3.3 2.8 + - - -
610B PRO* 1.3 69.3 - - - +
612B GLU* 1.3 68.2 + - - +
640B GLU* 2.5 34.3 - - - +
641B GLU 3.8 0.2 - - - -
642B ASN 3.4 21.7 - - - +
643B ARG* 3.8 6.2 - - - +
644B ALA 4.3 1.6 + - - -
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Residues in contact with GLU 612 (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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262B LEU* 3.8 8.7 - - - -
568B ARG* 3.3 29.6 + - - -
591B ASP* 4.3 12.6 - - - +
592B ILE* 3.3 13.5 - - - +
593B PHE* 3.6 12.4 - - + +
609B GLU* 5.9 0.2 - - - +
610B PRO 3.8 5.1 - - - +
611B ASP* 1.3 79.3 + - - +
613B GLY* 1.3 61.1 + - - +
614B GLN* 4.3 2.3 + - - -
640B GLU* 3.2 9.0 - - - +
641B GLU* 2.8 61.2 + - + +
642B ASN* 4.0 11.2 + - - +
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Residues in contact with GLY 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA* 4.1 0.5 - - - +
262B LEU* 3.8 22.2 - - - +
590B THR 4.0 0.2 - - - +
591B ASP* 3.4 3.1 - - - +
592B ILE 3.0 31.5 + - - +
612B GLU* 1.3 80.5 - - - +
614B GLN* 1.3 69.4 + - - +
639B HIS 3.0 13.0 - - - -
641B GLU* 3.7 0.2 - - - -
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Residues in contact with GLN 614 (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* 4.7 0.4 - - - -
589B TYR* 3.5 32.5 - - + +
590B THR 2.9 9.2 - - - +
591B ASP* 2.6 27.0 + - - +
612B GLU* 4.3 7.3 + - - -
613B GLY* 1.3 85.0 - - - +
615B ASN* 1.3 60.2 + - - +
616B TYR* 3.7 23.5 + - + +
637B GLU 3.7 1.4 - - - +
638B ILE* 3.3 5.7 - - - +
639B HIS* 3.0 34.4 + - - +
641B GLU* 2.1 39.6 + - - +
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Residues in contact with ASN 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLN* 6.2 1.6 - - - +
210B ARG* 3.4 22.2 + - - -
250B LYS 5.4 0.2 + - - -
251B GLY* 3.5 13.6 - - - -
252B ALA* 3.7 14.6 - - + +
588B SER* 3.5 3.9 + - - +
589B TYR* 3.5 5.2 - - - -
590B THR* 2.6 48.5 + - - +
614B GLN* 1.3 73.9 - - - +
616B TYR* 1.3 62.3 + - - +
617B GLU* 3.7 26.7 + - - +
636B PHE* 4.2 6.2 - - - +
637B GLU 3.6 3.1 - - - -
638B ILE* 4.0 16.7 - - + +
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Residues in contact with TYR 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B SER 3.6 5.6 - - - -
589B TYR* 3.5 34.3 + + + -
614B GLN* 3.7 26.3 + - + +
615B ASN* 1.3 74.8 - - - +
617B GLU* 1.3 60.4 + - - +
635B TYR* 3.9 1.6 - - - +
636B PHE* 3.2 4.7 - - - -
637B GLU* 2.9 45.9 + - + +
639B HIS* 4.2 32.9 + + + +
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Residues in contact with GLU 617 (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* 5.2 2.4 - - - +
168B SER* 3.0 28.9 + - - -
210B ARG* 3.4 24.9 + - - -
250B LYS 4.4 0.9 - - - +
586B TYR* 2.7 31.9 + - + +
587B ALA* 3.0 6.1 - - - +
588B SER* 2.7 49.2 + - - +
615B ASN* 3.7 16.9 + - - +
616B TYR* 1.3 74.7 - - - +
618B ILE* 1.3 63.9 + - - +
634B ALA* 4.0 5.3 - - + +
635B TYR 3.3 15.3 - - - +
636B PHE* 3.9 7.7 - - + +
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Residues in contact with ILE 618 (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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585B VAL* 5.9 6.7 - - + -
586B TYR* 3.4 15.3 - - - +
587B ALA* 3.6 15.7 - - + -
617B GLU* 1.3 77.0 - - - +
619B GLY* 1.3 56.6 + - - +
634B ALA* 3.7 1.2 - - - +
635B TYR* 2.8 52.1 + - + +
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Residues in contact with GLY 619 (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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585B VAL* 3.2 7.3 - - - +
586B TYR* 2.8 56.7 + - - +
618B ILE* 1.3 77.3 - - - +
620B ILE* 1.3 57.0 + - - -
633B LEU* 3.3 13.5 - - - -
634B ALA* 4.1 1.1 - - - -
635B TYR 4.7 0.2 - - - -
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Residues in contact with ILE 620 (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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579B LEU* 4.3 18.8 - - + -
583B TYR* 4.3 25.4 - - + -
584B SER 3.4 11.4 - - - +
585B VAL* 4.1 13.2 - - + +
619B GLY* 1.3 75.0 - - - +
621B LYS* 1.3 65.1 - - - +
622B GLY 4.4 0.2 - - - -
632B SER* 3.3 2.9 - - - -
633B LEU* 2.9 62.0 + - + +
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Residues in contact with LYS 621 (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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162B PRO* 2.8 35.0 + - + +
163B ARG* 3.8 26.6 - - + +
165B THR 2.8 19.0 + - - +
167B GLN 3.1 18.6 + - - -
168B SER* 5.5 1.8 - - - +
169B ILE* 4.3 11.1 - - - +
582B THR 3.7 1.0 - - - +
583B TYR* 3.4 7.8 - - - -
584B SER* 2.8 39.3 + - - +
586B TYR* 3.9 26.7 - - + -
620B ILE* 1.3 77.0 - - - +
622B GLY* 1.3 61.0 - - - +
631B THR 3.5 5.8 - - - +
632B SER* 3.7 21.5 - - - -
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Residues in contact with GLY 622 (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* 5.1 1.1 - - - +
582B THR 3.7 2.5 - - - -
583B TYR* 3.6 21.8 - - - -
621B LYS* 1.3 76.6 - - - +
623B GLU* 1.3 61.5 + - - +
624B TYR* 3.7 3.8 - - - -
630B ASN* 3.6 8.1 + - - -
631B THR* 3.0 47.4 + - - +
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Residues in contact with GLU 623 (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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161B THR* 4.2 18.7 + - - +
162B PRO* 4.8 0.9 - - - +
163B ARG* 3.6 46.9 + - + +
581B ASP 4.5 1.9 - - - +
582B THR* 3.3 23.2 + - - +
622B GLY* 1.3 73.7 - - - +
624B TYR* 1.3 67.2 + - - +
626B ASP* 4.9 1.3 - - - -
627B GLY* 3.9 29.7 + - - +
629B LEU 3.6 5.2 - - - -
630B ASN* 3.4 16.8 + - - +
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Residues in contact with TYR 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B THR* 3.5 28.5 - - + -
583B TYR* 3.0 24.8 + - - -
622B GLY* 3.7 1.1 - - - -
623B GLU* 1.3 79.9 - - - +
625B LEU* 1.3 78.4 + - + +
626B ASP 3.1 3.6 + - - -
627B GLY 3.3 0.7 + - - -
628B ARG 3.2 15.2 + - - -
629B LEU* 2.9 48.6 + - + +
631B THR* 2.9 44.4 + - + +
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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