Contacts of the strand formed by residues 293 - 295 (chain H) in PDB entry 3EXF
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 VAL 293 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E GLN* 2.7 38.8 - - - +
354E TRP* 4.0 9.4 - - + -
281F GLU* 4.2 8.1 - - + -
259H LEU 3.1 8.6 + - - +
260H VAL* 3.3 9.6 - - + +
261H THR* 2.7 34.0 + - - +
276H CYS* 5.3 0.2 - - - -
291H PRO* 4.8 6.3 - - + +
292H ALA* 1.3 81.3 - - - +
294H ARG* 1.3 63.0 + - - +
322H ALA* 4.1 26.0 - - + +
326H THR* 3.4 28.9 - - + +
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Residues in contact with ARG 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349E ARG* 3.1 29.8 + - - +
351E ALA 3.9 0.2 - - - +
352E ASN* 3.9 15.6 - - - +
353E GLN* 4.4 2.4 + - - +
274F GLU* 2.9 31.5 + - - -
277F ALA* 3.6 15.4 - - - +
278F ARG* 3.9 2.8 - - - +
281F GLU* 2.8 41.2 + - - +
261H THR* 3.4 17.7 - - - +
263H GLU* 5.7 0.2 + - - -
267H PRO* 3.3 40.2 + - - +
272H GLY* 3.3 29.8 - - - +
273H ALA* 4.2 3.8 - - - +
276H CYS* 4.3 8.3 - - - -
293H VAL* 1.3 76.4 - - - +
295H VAL* 1.3 61.6 + - - +
296H THR* 4.4 10.3 - - + +
322H ALA* 5.7 0.4 - - - -
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Residues in contact with VAL 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E ALA 3.1 12.1 - - - +
352E ASN* 4.6 2.7 - - + -
260H VAL* 4.1 12.3 - - + -
261H THR* 2.9 11.0 + - - +
262H VAL* 3.4 16.6 - - + -
263H GLU* 3.0 24.6 + - - +
294H ARG* 1.3 72.3 - - - +
296H THR* 1.3 61.0 + - - +
314H PRO* 3.4 29.8 - - + -
318H ASP* 3.9 13.5 - - + +
319H ILE* 4.0 17.3 - - + +
322H ALA* 3.8 29.2 - - + -
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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
------------------------------------------------------------
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