Contacts of the strand formed by residues 294 - 298 (chain B) in PDB entry 1OHV
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 ALA 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 3.6 33.4 - - + +
150B TRP* 3.6 7.0 - - + -
260B ALA 2.9 8.8 + - - +
261B GLY* 3.1 1.4 - - - -
262B ILE 2.7 32.2 + - - +
288B SER* 3.4 1.3 + - - -
293B CYS* 1.3 73.3 - - - +
295B PHE* 1.3 56.6 + - - +
296B LEU 3.7 0.2 + - - -
323B ASP* 3.4 9.2 - - + -
342B PHE* 3.5 31.4 - - + -
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Residues in contact with PHE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 4.1 13.7 - - + -
264B VAL* 3.8 24.9 - - + -
281B PHE* 4.4 4.5 - + - -
284B LEU* 3.8 32.8 - - + -
285B ARG* 3.4 40.8 - - + +
288B SER* 3.5 21.8 - - - +
293B CYS 3.4 0.2 + - - -
294B ALA* 1.3 70.7 - - - +
296B LEU* 1.3 62.2 + - - +
297B VAL* 3.6 20.0 - - + -
316B TRP* 3.9 10.8 - + - -
321B PRO 3.3 27.6 - - - -
322B ALA* 3.5 2.8 - - - +
323B ASP* 2.7 33.7 + - - +
324B VAL* 3.2 9.9 + - - +
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Residues in contact with LEU 296 (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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140B ASN* 4.4 2.7 - - - +
143B ALA* 3.9 15.0 - - + -
144B PHE* 3.5 38.8 - - + -
147B ILE* 3.9 23.8 - - + -
182B ILE* 5.5 1.1 - - + -
262B ILE 2.7 17.2 + - - +
263B ILE* 3.2 17.3 - - + +
264B VAL* 3.1 25.6 + - - +
294B ALA 3.7 0.2 + - - -
295B PHE* 1.3 72.8 - - - +
297B VAL* 1.3 71.9 + - - +
324B VAL* 3.4 14.8 - - + +
326B THR* 3.9 27.6 - - + +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 3.6 5.8 - - + +
266B PRO* 3.7 29.4 - - + -
295B PHE* 3.6 32.8 - - + -
296B LEU* 1.3 75.3 - - - +
298B ASP* 1.3 60.0 + - - +
299B GLU* 3.8 15.3 - - + +
313B HIS* 4.4 4.3 - - + +
316B TRP* 3.8 17.7 - - + -
322B ALA* 3.7 18.6 - - + -
324B VAL 2.9 12.6 + - - +
325B MET* 3.2 13.0 - - + +
326B THR 3.0 23.7 + - - -
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Residues in contact with ASP 298 (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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140B ASN* 2.8 14.1 + - - -
190B HIS* 2.7 32.8 + - + +
263B ILE* 4.2 6.7 - - + -
264B VAL 3.0 15.4 + - - +
265B GLU* 3.8 6.6 - - + +
266B PRO* 3.2 18.9 - - - +
296B LEU 3.9 1.2 + - - -
297B VAL* 1.3 68.1 - - - +
299B GLU* 1.3 59.3 + - - +
300B VAL* 3.0 30.7 + - - +
301B GLN 5.0 0.3 + - - -
302B THR* 4.0 1.7 + - - +
326B THR* 3.5 9.4 - - - +
600B PLP 2.7 28.9 + - - +
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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