Contacts of the strand formed by residues 664 - 682 (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 LYS 664 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B ASP* 5.2 2.7 - - + -
608B LEU* 4.0 7.9 - - - -
643B ARG 3.5 1.2 - - - +
644B ALA* 3.8 0.9 - - - -
645B GLU* 3.0 38.8 + - - +
647B ASP* 3.7 37.2 - - + +
663B TYR* 1.3 75.0 - - - +
665B GLY* 1.3 61.2 - - - +
666B ILE* 3.8 24.4 + - + +
699B ASP* 4.7 5.5 + - - -
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Residues in contact with GLY 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B LEU* 3.8 15.5 - - - +
642B ASN* 4.0 23.7 - - - +
643B ARG 3.5 7.6 - - - -
664B LYS* 1.3 74.5 - - - +
666B ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B GLU 3.9 0.3 - - - -
642B ASN 3.3 8.1 + - - -
643B ARG* 2.8 49.4 + - + +
645B GLU* 3.9 24.2 - - + +
664B LYS* 3.8 34.5 - - + +
665B GLY* 1.3 78.4 - - - +
667B LYS* 1.3 72.7 + - - +
698B ASP* 3.4 31.2 - - - +
699B ASP* 3.3 26.0 - - + +
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Residues in contact with LYS 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B HIS* 6.4 1.8 - - - -
640B GLU 3.2 13.2 - - - +
641B GLU* 4.4 21.1 - - + -
642B ASN 5.5 0.2 - - - +
643B ARG* 5.2 0.2 - - - -
666B ILE* 1.3 87.2 - - - +
668B ALA* 1.3 64.3 + - - +
698B ASP 3.8 0.2 - - - -
699B ASP* 2.9 40.0 + - - +
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Residues in contact with ALA 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PHE* 6.2 0.2 - - - -
638B ILE 3.5 0.2 - - - +
639B HIS* 3.5 3.3 - - - +
640B GLU* 2.6 62.9 + - + +
643B ARG* 4.2 14.1 - - - +
667B LYS* 1.3 78.7 - - - +
669B LYS* 1.3 60.5 + - - +
696B ILE* 4.5 9.4 - - + -
697B ARG 3.3 15.0 - - - +
698B ASP* 4.6 1.8 - - - +
699B ASP 4.4 1.3 - - - +
704B VAL* 5.9 0.9 - - + -
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Residues in contact with LYS 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLU* 3.8 11.4 + - + +
638B ILE 3.0 2.2 - - - +
639B HIS* 3.5 47.1 - - + +
668B ALA* 1.3 74.7 - - - +
670B THR* 1.3 65.7 + - - +
671B LYS* 3.9 23.0 + - + +
695B ILE 3.7 1.7 - - - +
696B ILE* 3.2 5.3 - - - -
697B ARG* 2.9 36.3 + - + +
698B ASP 5.3 0.2 - - - -
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Residues in contact with THR 670 (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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210B ARG* 3.0 35.9 + - + +
212B PHE* 3.6 7.6 - - - -
636B PHE* 4.0 22.0 - - + -
637B GLU* 3.1 9.4 - - - +
638B ILE* 2.8 45.2 + - - +
669B LYS* 1.3 71.7 - - - +
671B LYS* 1.3 61.6 + - - +
694B LYS* 4.3 13.0 - - + -
695B ILE 3.6 6.3 - - - +
696B ILE* 3.4 23.0 - - + +
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Residues in contact with LYS 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B TYR* 3.6 22.3 + - - +
637B GLU* 3.6 19.4 + - + -
669B LYS* 3.9 28.8 - - + +
670B THR* 1.3 74.5 - - - +
672B GLY* 1.3 57.3 + - - +
693B HIS* 4.6 2.8 - - - -
694B LYS* 3.5 1.9 - - - +
695B ILE* 3.0 37.0 + - + +
697B ARG* 6.3 4.0 - - + +
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Residues in contact with GLY 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B TYR* 3.2 14.2 - - - -
636B PHE* 3.0 46.9 + - - +
671B LYS* 1.3 75.0 - - - +
673B TYR* 1.3 63.9 + - - -
693B HIS* 3.3 20.6 - - - -
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Residues in contact with TYR 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B LEU* 5.8 4.5 - - + -
634B ALA 3.1 16.8 - - - +
635B TYR* 4.3 15.3 - + + -
636B PHE* 3.4 5.1 - - - -
672B GLY* 1.3 76.6 - - - +
674B GLU* 1.3 68.8 + - - +
675B ALA* 5.6 0.9 - - + -
691B TYR* 4.2 20.9 + + - -
692B THR* 3.5 2.1 - - - +
693B HIS* 2.8 75.3 + + + +
711B ASP* 5.2 0.3 + - - -
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Residues in contact with GLU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 4.0 6.0 + - - +
194B GLY* 3.7 5.0 - - - -
210B ARG* 3.2 25.1 + - - +
250B LYS* 2.8 36.4 + - - +
632B SER* 4.0 2.4 + - - +
633B LEU* 3.4 2.6 - - - -
634B ALA* 2.8 43.0 + - + +
636B PHE* 4.2 8.3 - - + -
673B TYR* 1.3 79.5 - - - +
675B ALA* 1.3 60.8 + - - +
676B GLU* 3.5 17.0 - - + +
691B TYR 3.1 8.5 - - - +
692B THR* 2.4 34.6 + - - +
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Residues in contact with ALA 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B SER 3.2 10.8 - - - +
633B LEU* 4.4 15.7 - - + -
673B TYR* 5.6 1.9 - - + -
674B GLU* 1.3 75.3 - - - +
676B GLU* 1.3 61.6 + - - +
690B GLY* 3.1 2.6 - - - -
691B TYR* 2.6 46.1 + - + +
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Residues in contact with GLU 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE 4.0 7.4 - - - +
170B THR* 2.7 33.2 + - - +
193B PRO* 4.4 9.7 - - + +
250B LYS* 3.0 22.7 + - - -
631B THR* 3.2 6.4 - - - +
632B SER* 2.9 51.9 + - - +
674B GLU* 3.5 18.7 - - + +
675B ALA* 1.3 76.3 - - - +
677B ILE* 1.3 65.1 + - - +
688B GLN* 5.3 0.5 - - - +
689B ALA 3.1 13.9 - - - +
690B GLY* 3.6 4.8 - - - -
692B THR* 5.2 0.2 + - - -
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Residues in contact with ILE 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B LEU* 4.0 19.1 - - + -
630B ASN 3.3 13.5 - - - +
631B THR* 3.9 16.6 - - + -
676B GLU* 1.3 77.9 - - - +
678B SER* 1.3 66.6 + - - +
681B LEU* 4.0 22.0 - - + -
687B VAL* 4.2 10.8 - - + -
688B GLN* 3.5 1.9 - - - +
689B ALA* 2.8 55.7 + - + +
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Residues in contact with SER 678 (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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147B TYR 3.5 18.6 - - - -
148B THR* 3.4 15.9 + - - -
149B PRO* 4.6 5.7 - - - +
171B VAL 6.1 0.2 - - - -
629B LEU* 3.4 6.3 - - - +
630B ASN* 2.8 43.6 + - - +
676B GLU 5.7 0.2 - - - -
677B ILE* 1.3 75.9 - - - +
679B GLY* 1.3 59.8 + - - +
687B VAL* 3.3 7.9 - - - -
688B GLN* 4.7 12.6 - - - -
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Residues in contact with GLY 679 (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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146B SER* 4.3 0.2 - - - -
147B TYR 4.1 1.6 + - - -
148B THR* 3.7 11.8 - - - -
628B ARG 3.4 9.6 - - - -
629B LEU* 3.7 3.1 - - - -
678B SER* 1.3 75.8 - - - +
680B GLU* 1.3 63.6 + - - -
681B LEU 3.4 1.4 + - - -
686B GLN* 3.6 19.1 - - - -
687B VAL* 2.9 37.2 + - - +
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Residues in contact with GLU 680 (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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625B LEU* 4.1 21.2 - - + +
628B ARG* 2.9 66.3 + - + +
629B LEU* 3.5 22.6 - - - +
679B GLY* 1.3 68.5 - - - -
681B LEU* 1.3 59.3 + - - +
682B ALA 3.2 21.2 - - - +
683B PRO* 3.5 30.2 - - - +
685B TRP 3.6 2.0 - - - +
686B GLN* 3.5 20.9 - - - +
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Residues in contact with LEU 681 (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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625B LEU* 5.6 3.0 - - - +
629B LEU* 4.2 8.7 - - + -
677B ILE* 4.0 18.8 - - + -
679B GLY 3.4 3.2 + - - -
680B GLU* 1.3 73.2 - - - +
682B ALA* 1.3 62.8 + - - +
685B TRP* 3.0 54.6 + - + +
687B VAL* 3.1 51.8 - - + +
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Residues in contact with ALA 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B LEU* 5.9 2.0 - - - -
680B GLU* 3.2 17.4 - - - +
681B LEU* 1.3 80.1 - - - +
683B PRO* 1.4 81.1 - - + +
684B GLY 3.0 2.9 + - - +
685B TRP* 3.0 35.2 + - + -
719B TYR* 6.0 1.6 - - + -
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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