Contacts of the strand formed by residues 563 - 578 (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 ILE 563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554B TYR* 3.8 2.9 - - + +
555B ARG* 3.6 2.6 - - - -
556B VAL* 3.2 54.6 + - + +
560B ASN* 6.1 0.2 - - + -
561B PRO 3.3 11.2 + - - +
562B THR* 1.3 72.5 - - - +
564B ARG* 1.3 66.7 + - - +
565B GLU* 5.9 0.9 - - + -
595B PRO* 3.8 28.7 - - + -
596B GLN 3.4 21.5 - - - +
598B SER* 3.8 28.5 - - - +
601B ARG* 6.1 1.1 - - - +
607B LEU* 3.5 26.5 - - + -
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Residues in contact with ARG 564 (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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527B ARG* 3.5 24.4 - - - +
553B ASP* 3.0 26.9 + - - -
554B TYR 3.4 4.0 + - - -
555B ARG* 3.4 43.5 - - + +
562B THR* 4.0 13.6 + - + +
563B ILE* 1.3 81.0 - - - +
565B GLU* 1.3 73.5 + - - +
566B SER* 3.5 24.4 + - - +
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Residues in contact with GLU 565 (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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552B VAL* 3.7 3.6 - - - +
553B ASP* 3.4 4.6 - - - -
554B TYR* 2.9 47.9 + - + +
563B ILE* 5.6 1.1 - - + +
564B ARG* 1.3 80.8 - - - +
566B SER* 1.3 64.0 + - - +
568B ARG* 3.1 32.5 + - + +
593B PHE* 4.5 13.0 - - + -
595B PRO* 4.4 13.0 - - + -
609B GLU* 5.6 0.9 - - - +
610B PRO* 3.6 35.7 - - + +
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Residues in contact with SER 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ASP* 2.5 28.6 + - - -
564B ARG* 3.5 21.8 + - - +
565B GLU* 1.3 71.5 + - - +
567B GLY* 1.3 65.5 + - - +
568B ARG* 3.4 8.2 + - - +
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Residues in contact with GLY 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B VAL* 4.9 13.2 - - - +
552B VAL 3.2 13.6 + - - -
553B ASP* 4.4 3.2 + - - +
566B SER* 1.3 72.5 - - - +
568B ARG* 1.3 64.6 + - - +
569B PHE* 3.7 3.5 + - - +
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Residues in contact with ARG 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B ARG 3.4 1.6 - - - +
551B VAL* 3.4 4.0 - - - -
552B VAL* 2.9 32.4 + - - +
565B GLU* 3.1 30.5 + - + +
566B SER 3.4 2.6 - - - +
567B GLY* 1.3 77.5 - - - +
569B PHE* 1.3 60.0 + - - +
593B PHE* 3.8 41.5 - - + +
609B GLU* 3.8 28.3 - - - +
610B PRO* 4.0 18.2 - - - +
612B GLU* 3.3 35.2 + - - -
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Residues in contact with PHE 569 (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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533B MET* 4.9 10.8 - - + -
548B GLY 4.4 4.5 - - - -
549B GLY* 4.3 9.0 - - - -
550B ARG 3.4 20.2 - - - -
551B VAL* 4.3 14.1 - - + +
567B GLY 3.7 3.7 + - - +
568B ARG* 1.3 76.3 - - - +
570B ILE* 1.3 73.3 + - - +
571B PRO* 3.8 36.7 - - + +
591B ASP* 4.1 4.3 - - - +
593B PHE* 5.5 1.0 - - - -
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Residues in contact with ILE 570 (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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254B GLY* 3.7 33.7 - - - +
255B LEU* 4.2 6.1 - - + +
258B GLY 4.2 7.6 - - - +
549B GLY* 3.1 5.9 - - - -
550B ARG* 2.8 40.9 + - + +
552B VAL* 3.7 26.5 - - + -
569B PHE* 1.3 79.6 - - - +
571B PRO* 1.4 66.4 - - - +
591B ASP* 3.2 42.6 - - + +
592B ILE* 5.1 0.2 - - - -
593B PHE* 4.0 24.7 - - + +
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Residues in contact with PRO 571 (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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255B LEU* 6.0 0.2 - - - +
548B GLY 3.9 3.4 - - - +
569B PHE* 3.8 31.8 - - + +
570B ILE* 1.4 92.9 - - - +
572B TYR* 1.3 62.4 - - - +
573B VAL* 4.2 6.7 - - + -
589B TYR* 3.6 36.4 - - + +
590B THR* 4.3 0.9 - - - -
591B ASP* 3.7 28.2 + - + +
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Residues in contact with TYR 572 (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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155B ALA* 4.5 2.3 - - - +
156B THR* 3.8 25.2 - - + +
166B PRO* 3.4 28.1 - - + +
167B GLN* 2.9 30.6 + - + -
255B LEU* 3.8 39.3 - - + -
534B THR* 4.8 6.7 - - + -
546B PHE* 3.9 26.5 - + + -
547B LEU* 3.4 2.9 - - - -
548B GLY 2.8 43.8 + - - +
571B PRO* 1.3 74.5 - - - +
573B VAL* 1.3 70.9 + - - +
588B SER* 5.7 1.8 - - - -
589B TYR 3.9 1.6 - - - -
590B THR* 3.5 26.7 - - + -
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Residues in contact with VAL 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B LEU* 6.0 2.7 - - + -
546B PHE 3.3 4.7 - - - +
547B LEU* 3.8 26.9 - - + -
571B PRO* 4.2 6.0 - - + -
572B TYR* 1.3 87.4 - - - +
574B GLY* 1.3 63.6 + - - +
588B SER* 3.3 4.3 - - - -
589B TYR* 2.8 53.0 + - + +
590B THR* 5.2 0.3 - - - +
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Residues in contact with GLY 574 (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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166B PRO* 4.8 3.8 - - - -
545B LEU* 3.8 2.9 - - - +
546B PHE* 2.6 51.4 + - - +
572B TYR* 5.5 0.2 - - - -
573B VAL* 1.3 81.1 - - - +
575B ALA* 1.3 56.9 + - - +
587B ALA 3.0 14.8 - - - -
588B SER* 3.8 6.5 - - - -
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Residues in contact with ALA 575 (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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166B PRO* 4.2 3.2 - - - +
543B LEU* 4.5 11.0 - - + -
544B ASN 3.3 10.8 - - - +
545B LEU* 4.5 18.2 - - + -
546B PHE* 4.7 0.4 - - - -
574B GLY* 1.3 73.7 - - - +
576B VAL* 1.3 63.6 + - - +
577B TYR* 6.4 0.2 - - + -
586B TYR* 3.2 6.4 - - - +
587B ALA* 2.9 35.1 + - + +
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Residues in contact with VAL 576 (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* 4.0 14.1 - - + +
164B GLU* 3.7 27.8 - - - +
166B PRO* 4.7 4.5 - - + -
536B ARG* 5.5 2.0 - - - +
542B ASP 3.2 3.8 - - - +
543B LEU* 3.5 2.5 - - - -
544B ASN* 2.9 41.2 + - + +
546B PHE* 3.7 17.3 - - + -
575B ALA* 1.3 77.3 - - - +
577B TYR* 1.3 60.8 + - - +
578B ASP* 4.2 6.6 - - - +
584B SER* 3.8 26.0 - - - +
585B VAL 3.6 4.7 - - - +
586B TYR* 3.9 10.5 - - + +
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Residues in contact with TYR 577 (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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540B THR* 6.0 2.2 - - + -
542B ASP* 2.9 34.7 + - + -
543B LEU* 4.2 22.9 - - + -
575B ALA 4.3 0.2 - - - -
576B VAL* 1.3 74.0 - - - +
578B ASP* 1.3 77.4 + - - +
579B LEU* 4.0 18.8 - - + +
584B SER* 3.2 2.6 - - - -
585B VAL* 2.9 47.0 + - + +
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Residues in contact with ASP 578 (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* 4.8 7.4 + - - -
541B ASP 3.4 18.9 - - - +
542B ASP* 2.8 41.2 + - - +
544B ASN* 5.5 4.0 + - - -
576B VAL* 4.2 8.0 - - - +
577B TYR* 1.3 90.7 - - - +
579B LEU* 1.3 61.2 + - - +
580B ASN 4.2 11.4 - - - +
583B TYR 4.8 0.2 - - - -
584B SER* 2.8 25.4 + - - +
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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