Contacts of the helix formed by residues 311 - 317 (chain A) 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 TRP 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL* 2.7 28.7 + - + -
124A PRO* 4.1 10.6 - - + +
299A GLU* 3.6 6.1 - - + +
303A GLY* 3.6 31.2 - - - -
304A GLY 4.2 3.4 - - - -
309A LYS* 3.5 7.9 - - - +
310A PHE* 1.3 96.2 - + + +
312A ALA* 1.3 65.4 + - - +
313A HIS* 3.5 33.4 - + + +
314A GLU* 3.1 41.3 + - + +
325A MET* 3.4 31.4 - - + -
327A PHE* 3.7 26.5 - + + -
331A MET* 3.8 24.0 - - + -
337A PHE* 3.9 14.6 - + - -
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A PRO* 3.7 16.6 - - + -
267A ILE* 5.0 3.6 - - + -
299A GLU* 2.9 16.0 + - - +
302A THR* 3.7 23.0 + - + -
307A THR* 3.5 29.7 + - + +
310A PHE 4.2 0.8 + - - -
311A TRP* 1.3 70.8 - - - +
313A HIS* 1.3 62.0 + - - +
314A GLU 3.1 1.2 + - - -
315A HIS* 3.1 25.9 + - + +
316A TRP* 4.4 3.3 + - - -
408A ARG* 5.0 1.9 + - - -
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Residues in contact with HIS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO* 3.6 25.1 - - + +
125A LYS 4.9 1.0 + - - -
127A MET* 5.5 1.6 - - + -
266A PRO* 4.5 0.4 - - - +
297A VAL* 4.4 6.3 - - + +
299A GLU* 2.8 25.6 + - - +
311A TRP* 3.1 14.6 - + + +
312A ALA* 1.3 77.2 - - - +
314A GLU* 1.3 68.0 + - + +
315A HIS 3.1 0.4 - - - -
316A TRP* 2.9 65.8 + - + +
317A GLY 4.1 0.9 + - - -
318A LEU 5.2 0.5 + - - -
321A PRO* 3.5 30.5 - - + +
322A ALA* 6.1 1.1 - - + -
325A MET* 3.4 30.0 - - + +
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO* 6.3 0.4 - - + -
309A LYS* 4.0 30.5 + - + +
310A PHE* 3.7 10.5 + - - +
311A TRP* 3.1 53.6 + - + +
313A HIS* 1.3 89.2 - - + +
315A HIS* 1.3 61.4 + - - +
316A TRP 3.1 0.2 - - - -
317A GLY* 3.1 15.9 + - - +
318A LEU 6.0 0.4 - - - +
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Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ASP* 3.2 14.9 - - - +
282A ARG* 4.5 1.7 + - - -
307A THR* 3.0 39.4 + - - -
308A GLY* 4.7 1.8 - - - -
309A LYS* 3.2 37.5 - - + +
312A ALA* 3.1 22.2 + - + +
313A HIS 3.1 0.8 - - - -
314A GLU* 1.3 77.4 - - - +
316A TRP* 1.3 61.5 + - + +
317A GLY* 3.3 1.4 + - - -
408A ARG* 3.4 52.2 + - + +
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Residues in contact with TRP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A VAL* 5.2 0.4 - - + -
266A PRO* 4.1 17.9 + - + +
278A ASP* 3.4 23.8 + - - -
281A PHE* 3.3 59.2 - + + +
282A ARG* 2.8 41.9 + - + +
295A PHE* 3.9 13.0 - + - -
297A VAL* 3.8 20.9 - - + -
312A ALA 4.4 4.4 + - - -
313A HIS* 2.9 45.7 + - + +
315A HIS* 1.3 78.6 - - + +
317A GLY* 1.3 60.0 + - - +
318A LEU* 3.4 22.8 + - + +
321A PRO* 3.7 25.4 - - + -
408A ARG* 5.3 1.4 - - - +
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 5.5 5.4 + - - -
313A HIS 4.1 0.4 + - - -
314A GLU 3.1 16.4 + - - -
315A HIS 3.2 2.3 - - - -
316A TRP* 1.3 77.4 - - - +
318A LEU* 1.3 63.6 + - - +
319A ASP* 4.0 3.6 + - - +
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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