Contacts of the strand formed by residues 507 - 512 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496D LEU 5.1 0.7 - - - -
499D LEU* 4.0 10.5 - - + -
500D PRO* 3.7 33.0 - - + +
504D ALA* 3.7 37.9 - - + -
505D LYS 4.0 8.4 + - - -
506D ASP* 1.3 77.6 + - - +
508D GLU* 1.3 68.0 + - - +
509D THR* 3.9 31.9 - - + -
532D LYS* 3.9 8.7 + - - +
533D ILE* 3.3 23.8 - - + +
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Residues in contact with GLU 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D LEU* 4.1 1.4 - - - +
507D TYR* 1.3 74.3 - - - +
509D THR* 1.3 65.2 + - - +
510D HIS* 2.8 35.5 + - + +
526D SER* 5.3 4.3 + - - -
527D PHE* 4.3 4.0 - - - -
532D LYS* 3.7 24.6 + - + +
533D ILE 3.0 6.9 + - - +
534D ARG* 3.0 42.8 + - + +
535D MET 3.0 23.6 + - - +
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Residues in contact with THR 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D LEU* 3.5 45.7 + - + +
499D LEU* 4.1 11.7 - - + -
507D TYR* 3.9 24.3 - - + -
508D GLU* 1.3 78.2 - - - +
510D HIS* 1.3 76.3 + - - +
535D MET* 3.3 10.5 - - + +
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Residues in contact with HIS 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D LEU* 3.7 9.1 - - - +
508D GLU* 2.8 37.7 + - + +
509D THR* 1.3 87.1 + - - +
511D ARG* 1.3 55.0 + - - +
512D VAL* 4.9 0.4 - - + -
521D LEU* 3.5 49.4 - - + +
527D PHE* 4.0 10.5 - + - -
534D ARG* 4.8 2.2 - - + -
535D MET 3.0 7.5 + - - +
536D ILE* 3.3 11.1 - - + -
537D GLU 2.8 31.0 + - - -
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Residues in contact with ARG 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D ASP* 5.1 6.1 + - - -
496D LEU* 3.7 25.5 - - + +
510D HIS* 1.3 74.3 - - - +
512D VAL* 1.3 71.1 - - - +
513D ALA* 5.1 2.7 - - + +
517D GLU* 3.8 13.4 - - - +
537D GLU* 2.9 35.9 + - + +
539D MET* 3.8 26.5 - - + +
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Residues in contact with VAL 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D LEU* 3.7 16.3 - - + +
510D HIS* 4.9 0.2 - - + -
511D ARG* 1.3 83.6 - - - +
513D ALA* 1.3 60.8 + - - +
517D GLU* 3.9 28.9 - - + +
518D TRP* 3.9 24.2 - - + +
521D LEU* 3.9 29.2 - - + -
536D ILE* 4.0 7.6 - - + -
537D GLU 2.9 8.4 + - - +
538D VAL* 3.6 18.3 - - + -
539D MET* 3.0 25.8 + - - +
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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