Contacts of the strand formed by residues 313 - 316 (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 HIS 313 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D GLU* 5.1 1.8 + - - -
310D HIS* 3.0 64.7 + + - +
312D ASP* 1.3 105.6 + - - +
314D MET* 1.3 74.4 + - - +
315D LYS* 4.6 5.9 - - + +
320D THR* 4.5 12.8 - - + -
321D PHE 3.6 13.7 - - - +
322D PRO* 4.0 6.1 - - + -
323D GLY 3.9 4.3 - - - +
324D VAL 3.0 15.5 + - - +
603D PY0 4.6 2.9 - - - -
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Residues in contact with MET 314 (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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200D VAL* 3.9 12.1 - - + -
204D ILE* 4.0 13.2 - - + -
307D VAL* 4.0 16.6 - - + -
308D GLU 3.3 18.8 - - - +
309D PHE* 3.7 42.8 - - + -
313D HIS* 1.3 83.7 - - - +
315D LYS* 1.3 61.0 + - - +
316D ILE* 5.1 1.6 - - + -
320D THR* 3.6 2.6 - - - -
321D PHE* 2.8 45.3 + - + -
324D VAL* 3.5 29.2 - - + +
326D MET* 4.2 8.1 - - - -
329D VAL* 4.1 11.2 - - + -
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Residues in contact with LYS 315 (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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306D ILE 4.5 0.7 - - - +
307D VAL* 3.5 2.9 - - - +
308D GLU* 2.8 69.4 + - + +
313D HIS* 4.6 7.6 - - + +
314D MET* 1.3 74.4 - - - +
316D ILE* 1.3 63.2 + - - +
317D ARG 3.3 24.0 - - - +
318D ASN* 4.1 18.2 + - - +
319D ALA 3.2 11.7 - - - +
320D THR* 4.0 14.8 - - - +
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Residues in contact with ILE 316 (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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199A GLU* 4.1 1.6 - - - +
200D VAL* 3.8 34.1 - - + +
203D THR* 3.9 21.1 - - - +
204D ILE* 3.8 10.1 - - + -
207D LEU* 3.6 30.3 - - + -
306D ILE 3.6 2.5 - - - -
307D VAL* 4.3 14.1 - - + +
314D MET* 5.1 1.3 - - + -
315D LYS* 1.3 78.8 - - - +
317D ARG* 1.3 75.9 + - + +
318D ASN 3.0 0.7 + - - -
319D ALA* 2.8 30.0 + - + +
321D PHE* 3.9 25.1 - - + -
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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