Contacts of the strand formed by residues 294 - 298 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ILE* 3.6 33.2 - - + +
150D TRP* 3.7 8.5 - - + -
260D ALA 2.8 9.0 + - - +
261D GLY* 3.1 1.2 - - - -
262D ILE 2.7 32.6 + - - +
288D SER* 3.4 1.2 + - - -
293D CYS* 1.3 71.7 - - - +
295D PHE* 1.3 57.2 + - - +
296D LEU 3.7 0.2 + - - -
323D ASP* 3.4 9.6 - - + -
342D PHE* 3.5 32.1 - - + -
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Residues in contact with PHE 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ILE* 4.1 13.0 - - + -
264D VAL* 3.8 26.2 - - + -
281D PHE* 4.5 4.3 - + - -
284D LEU* 3.8 32.3 - - + -
285D ARG* 3.4 40.6 - - + +
288D SER* 3.5 22.2 - - - +
293D CYS 3.4 0.4 + - - -
294D ALA* 1.3 71.1 - - - +
296D LEU* 1.3 60.4 + - - +
297D VAL* 3.6 18.8 - - + -
316D TRP* 3.9 11.0 - + - -
321D PRO 3.4 26.7 - - - -
322D ALA* 3.5 2.8 - - - +
323D ASP* 2.7 33.7 + - - +
324D VAL* 3.2 9.4 + - - +
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Residues in contact with LEU 296 (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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140D ASN* 4.4 2.9 - - - +
143D ALA* 3.9 15.3 - - + -
144D PHE* 3.5 38.6 - - + -
147D ILE* 3.9 23.3 - - + -
182D ILE* 5.5 1.3 - - + -
262D ILE 2.8 16.9 + - - +
263D ILE* 3.2 17.3 - - + +
264D VAL* 3.2 25.1 + - - +
294D ALA 3.7 0.6 + - - -
295D PHE* 1.3 71.3 - - - +
297D VAL* 1.3 73.9 + - - +
324D VAL* 3.3 15.7 - - + +
326D THR* 3.9 27.1 - - + +
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Residues in contact with VAL 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 3.6 6.1 - - + +
266D PRO* 3.7 29.6 - - + -
295D PHE* 3.6 32.5 - - + -
296D LEU* 1.3 74.1 - - - +
298D ASP* 1.3 60.5 + - - +
299D GLU* 3.8 15.3 - - + +
313D HIS* 4.4 4.3 - - + +
316D TRP* 3.8 18.6 - - + -
322D ALA* 3.7 17.3 - - + -
324D VAL 2.9 11.7 + - - +
325D MET* 3.2 13.0 - - + +
326D THR 3.0 24.3 + - - -
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Residues in contact with ASP 298 (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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140D ASN* 2.8 15.4 + - - -
190D HIS* 2.8 30.6 + - + +
263D ILE* 4.2 7.6 - - + -
264D VAL 2.9 13.9 + - - +
265D GLU* 3.8 6.9 - - + +
266D PRO* 3.2 18.8 - - - +
296D LEU 3.9 1.2 + - - -
297D VAL* 1.3 70.0 - - - +
299D GLU* 1.3 58.6 + - - +
300D VAL* 2.9 30.5 + - - +
301D GLN 5.0 0.3 + - - -
302D THR* 4.0 1.6 + - - +
326D THR* 3.4 8.5 - - - +
600D PLP 2.7 31.2 + - - +
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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