Contacts of the strand formed by residues 507 - 512 (chain B) in PDB entry 2W93
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 507 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B LEU 5.2 0.2 - - - -
499B LEU* 3.9 15.5 - - + -
500B PRO* 3.6 33.5 - - + +
504B ALA* 3.4 41.1 - - + -
505B LYS* 4.0 5.8 + - - -
506B ASP* 1.3 78.9 + - - +
508B GLU* 1.3 78.9 + - - +
509B THR* 3.9 19.5 - - + -
532B LYS* 3.7 6.8 - - - +
533B ILE* 3.3 25.8 - - + +
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Residues in contact with GLU 508 (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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499B LEU* 4.1 2.1 - - - +
507B TYR* 1.3 77.8 - - - +
509B THR* 1.3 66.1 + - - +
510B HIS* 2.7 38.8 + - + +
526B SER* 4.8 6.6 + - - -
527B PHE* 4.3 4.2 - - - +
532B LYS* 3.2 36.4 + - + +
533B ILE 3.1 5.5 + - - +
534B ARG* 3.0 35.2 + - + +
535B MET 3.0 23.0 + - - -
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Residues in contact with THR 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LEU* 3.5 47.6 + - + +
499B LEU* 4.2 11.0 - - + -
507B TYR* 3.9 21.4 - - + -
508B GLU* 1.3 79.0 - - - +
510B HIS* 1.3 75.1 + - - +
535B MET* 3.3 8.5 - - + +
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Residues in contact with HIS 510 (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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496B LEU* 3.7 9.6 - - - +
508B GLU* 2.7 40.9 + - + +
509B THR* 1.3 83.1 + - - +
511B ARG* 1.3 61.2 + - - +
512B VAL* 5.2 0.2 - - + -
521B LEU* 3.3 46.0 - - + +
527B PHE* 4.1 15.3 - + + -
534B ARG* 4.8 2.2 - - + -
535B MET 3.0 11.6 + - - +
536B ILE* 3.3 6.6 - - + -
537B GLU 2.9 24.6 + - - -
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Residues in contact with ARG 511 (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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494B ASP* 4.8 8.9 + - - -
495B HIS 5.8 0.6 - - - +
496B LEU* 3.6 26.5 - - + +
510B HIS* 1.3 75.4 - - - +
512B VAL* 1.3 73.0 + - - +
513B ALA* 5.1 2.5 - - + +
517B GLU* 3.9 9.8 - - - +
537B GLU* 2.9 37.9 + - + +
539B MET* 4.0 26.3 - - + +
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Residues in contact with VAL 512 (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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365B LEU* 3.7 16.3 - - + +
510B HIS* 5.2 0.4 - - + -
511B ARG* 1.3 81.5 - - - +
513B ALA* 1.3 60.6 + - - +
514B THR 3.8 0.2 - - - -
517B GLU* 3.5 31.6 - - + +
518B TRP* 3.9 17.5 - - + +
521B LEU* 3.9 25.8 - - + -
536B ILE* 4.0 6.5 - - + -
537B GLU 2.9 9.3 + - - +
538B VAL* 3.5 26.9 - - + -
539B MET* 2.9 26.2 + - - +
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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