Contacts of the strand formed by residues 629 - 645 (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 LEU 629 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B GLU* 3.6 4.0 - - - +
624B TYR* 2.9 65.6 + - + +
625B LEU* 5.4 3.8 - - + -
628B ARG* 1.3 78.9 + - - +
630B ASN* 1.3 67.9 + - - +
631B THR* 5.4 0.4 - - + -
677B ILE* 4.0 24.0 - - + -
678B SER 3.4 18.6 - - - +
679B GLY 3.7 11.7 - - - +
680B GLU 3.5 27.6 - - - +
681B LEU* 4.2 11.2 - - + -
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Residues in contact with ASN 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 2.9 28.4 + - - +
149B PRO* 4.3 3.9 - - - +
162B PRO* 4.2 30.5 - - + +
163B ARG* 4.7 3.0 - - - +
622B GLY 3.6 11.8 + - - +
623B GLU* 3.4 25.9 + - - +
624B TYR* 4.5 0.7 - - - -
627B GLY* 4.4 6.0 - - - +
629B LEU* 1.3 78.8 + - - +
631B THR* 1.3 67.7 + - - +
677B ILE* 3.3 6.6 - - - +
678B SER* 2.8 38.9 + - - +
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Residues in contact with THR 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B TYR* 4.7 1.2 - - - -
621B LYS* 3.5 6.1 - - - +
622B GLY* 3.0 33.3 + - - +
624B TYR* 2.9 37.9 + - + +
629B LEU* 5.4 1.1 - - + -
630B ASN* 1.3 81.5 - - - +
632B SER* 1.3 63.9 + - - +
676B GLU 3.2 9.6 - - - +
677B ILE* 3.9 24.7 - - + -
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Residues in contact with SER 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B TYR* 5.5 2.7 - - - -
620B ILE 3.3 8.1 - - - -
621B LYS* 3.7 25.1 - - - -
631B THR* 1.3 78.6 - - - +
633B LEU* 1.3 63.2 + - - +
634B ALA* 5.9 1.3 - - - -
674B GLU 4.4 1.8 + - - -
675B ALA* 3.2 3.9 - - - +
676B GLU* 2.9 53.5 + - - +
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Residues in contact with LEU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B TYR* 4.8 1.1 - - - -
619B GLY* 3.3 2.6 - - - -
620B ILE* 2.9 51.2 + - + +
632B SER* 1.3 75.9 - - - +
634B ALA* 1.3 73.4 + - - +
635B TYR* 6.0 1.6 - - + -
673B TYR* 5.8 4.3 - - + -
674B GLU 3.4 6.3 - - - +
675B ALA* 4.2 13.7 - - + +
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 4.5 7.0 - - - +
586B TYR* 3.6 22.2 - - - +
617B GLU* 4.0 13.7 - - + +
618B ILE 3.7 5.8 - - - +
619B GLY* 4.1 0.4 - - - -
632B SER* 5.9 2.0 - - - -
633B LEU* 1.3 82.9 - - - +
635B TYR* 1.3 60.8 + - - +
636B PHE* 4.8 3.4 - - + -
673B TYR* 3.1 10.4 - - - +
674B GLU* 2.8 43.1 + - + +
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Residues in contact with TYR 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B TYR 5.5 0.9 - - - -
617B GLU* 3.3 5.4 - - - +
618B ILE* 2.8 52.4 + - + +
633B LEU* 5.0 2.8 - - + +
634B ALA* 1.3 72.6 - - - +
636B PHE* 1.3 70.9 + - - +
637B GLU* 2.9 29.1 + - + -
671B LYS* 3.6 18.9 + - + +
672B GLY* 3.2 27.8 - - - -
673B TYR* 4.3 13.5 - + + -
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Residues in contact with PHE 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 3.7 55.0 - - + -
615B ASN* 4.2 5.6 - - - +
616B TYR 3.2 9.0 - - - +
617B GLU* 3.9 19.1 - - + +
634B ALA* 4.5 5.6 - - + -
635B TYR* 1.3 83.5 - - - +
637B GLU* 1.3 70.6 + - - +
638B ILE* 4.7 5.2 - - + -
670B THR* 4.0 16.6 - - + -
672B GLY* 3.0 52.1 + - - +
673B TYR* 3.4 30.1 - - - -
674B GLU* 4.2 5.6 - - + -
692B THR* 4.7 6.1 - - + -
693B HIS 3.8 10.8 - - - -
694B LYS* 4.8 1.8 - - + -
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Residues in contact with GLU 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B GLN 3.7 1.6 - - - +
615B ASN* 3.6 1.2 - - - -
616B TYR* 2.9 42.6 + - + +
635B TYR* 2.9 30.5 + - + -
636B PHE* 1.3 79.5 - - - +
638B ILE* 1.3 63.3 + - - +
639B HIS* 3.0 29.7 + - + +
669B LYS* 3.8 9.8 + - + +
670B THR 3.1 14.1 - - - +
671B LYS* 3.6 23.8 + - + +
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Residues in contact with ILE 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 4.1 26.0 - - + -
212B PHE* 3.7 35.3 - - + -
251B GLY* 4.4 15.9 - - - +
262B LEU* 4.2 17.5 - - + -
263B GLY 4.6 2.5 - - - +
614B GLN 3.3 10.1 - - - +
615B ASN* 4.0 20.9 - - + +
636B PHE* 4.7 4.0 - - + -
637B GLU* 1.3 75.6 - - - +
639B HIS* 1.3 69.9 + - - +
640B GLU 3.9 0.2 - - - -
668B ALA 3.5 1.0 - - - +
669B LYS* 3.0 9.0 - - - +
670B THR* 2.8 50.2 + - + +
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Residues in contact with HIS 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B GLY* 3.0 22.5 - - - -
614B GLN* 3.0 20.0 + - - +
616B TYR* 4.2 26.3 + + + -
637B GLU* 3.0 32.2 + - - +
638B ILE* 1.3 83.3 - - - +
640B GLU* 1.3 59.8 + - - +
641B GLU* 3.3 14.8 - - - +
667B LYS* 6.4 1.8 - - - -
668B ALA 3.5 4.7 - - - +
669B LYS* 3.5 34.6 - - + +
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Residues in contact with GLU 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PHE* 3.5 31.0 - - + -
262B LEU* 3.9 5.3 - - + +
611B ASP* 2.5 33.9 - - - +
612B GLU 3.2 16.4 - - - +
613B GLY* 4.2 1.3 - - - -
638B ILE 3.8 1.4 + - - -
639B HIS* 1.3 73.6 - - - +
641B GLU* 1.3 67.3 + - - +
643B ARG* 2.8 43.6 + - + +
667B LYS* 3.2 9.8 - - - +
668B ALA* 2.6 44.5 + - + +
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Residues in contact with GLU 641 (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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611B ASP* 4.0 1.0 - - - +
612B GLU* 2.8 53.7 + - + +
613B GLY* 3.7 2.8 - - - -
614B GLN* 2.1 46.3 + - - +
639B HIS* 3.3 18.1 - - - +
640B GLU* 1.3 76.1 - - - +
642B ASN* 1.3 74.0 + - - +
643B ARG 3.6 0.7 - - - -
666B ILE 4.1 2.9 - - - -
667B LYS* 4.4 20.1 - - + +
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Residues in contact with ASN 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B GLN* 3.4 15.9 + - - +
608B LEU* 5.0 2.4 - - + +
609B GLU* 3.0 45.9 + - + +
610B PRO 3.3 16.5 + - - +
611B ASP* 3.4 8.5 - - - +
612B GLU* 4.0 13.3 + - - -
641B GLU* 1.3 81.2 + - - +
643B ARG* 1.3 63.4 + - - +
644B ALA 3.3 3.5 + - - -
665B GLY* 4.0 19.1 - - - +
666B ILE 3.3 7.9 + - - +
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Residues in contact with ARG 643 (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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211B GLY 4.1 14.6 + - - -
212B PHE* 4.3 7.5 - - - -
611B ASP* 3.8 7.6 - - - +
640B GLU* 2.8 37.0 + - + +
641B GLU 3.6 1.8 - - - -
642B ASN* 1.3 70.0 - - - +
644B ALA* 1.3 70.3 + - - +
645B GLU* 3.2 10.2 + - - +
664B LYS 3.5 0.3 - - - +
665B GLY* 4.2 0.4 - - - -
666B ILE* 2.8 55.0 + - + +
668B ALA* 4.2 15.0 - - + +
696B ILE* 4.2 3.6 - - - +
698B ASP* 4.9 5.2 - - - -
704B VAL* 3.6 39.1 - - - +
705B SER* 4.5 2.6 + - - -
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Residues in contact with ALA 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B GLN* 3.8 12.2 + - - +
600B TYR* 3.8 33.6 - - + -
608B LEU* 3.6 28.5 - - + -
611B ASP* 4.3 1.6 + - - +
642B ASN 3.3 6.1 + - - -
643B ARG* 1.3 73.5 - - - +
645B GLU* 1.3 61.9 + - - +
663B TYR* 4.6 3.9 - - + -
664B LYS 3.8 0.2 - - - -
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Residues in contact with GLU 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B ARG* 3.2 9.9 + - + +
644B ALA* 1.3 75.4 - - - +
646B GLU* 1.3 64.7 + - + +
647B ASP 3.5 2.9 - - - +
663B TYR* 3.3 9.2 - - - +
664B LYS* 3.0 40.4 + - + +
666B ILE* 3.9 26.9 - - + +
698B ASP* 3.7 15.8 - - - +
702B LYS* 3.7 26.2 + - - -
704B VAL* 5.2 2.6 - - - +
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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
------------------------------------------------------------
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