Contacts of the helix formed by residues 351 - 360 (chain B) in PDB entry 3OVS
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 ASP 351 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B PRO* 4.6 7.6 - - + +
348B GLN* 3.2 15.8 + - + +
350B GLU* 1.3 74.5 - - - +
352B GLU* 1.3 64.4 + - - +
353B ARG* 3.2 4.7 + - - +
354B ASN* 2.7 40.6 + - + +
355B VAL* 3.0 22.2 + - - +
15D C 5.5 0.7 - - - -
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Residues in contact with GLU 352 (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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193A ARG* 4.9 6.2 - - - +
243A ARG* 3.2 61.3 + - - +
247A GLU* 5.4 2.4 - - - +
350B GLU 2.7 7.4 + - - +
351B ASP* 1.3 71.0 + - - +
353B ARG* 1.3 65.6 + - + +
355B VAL* 3.5 6.2 + - - +
356B LYS* 3.2 27.8 + - + +
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Residues in contact with ARG 353 (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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351B ASP* 3.2 5.8 + - - +
352B GLU* 1.3 81.9 - - + +
354B ASN* 1.3 64.1 + - - +
356B LYS* 3.1 22.7 + - + +
357B LYS* 3.2 21.4 + - + +
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Residues in contact with ASN 354 (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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347B PRO* 3.6 5.1 - - + +
351B ASP* 2.7 39.4 + - - +
353B ARG* 1.3 79.1 - - - +
355B VAL* 1.3 60.1 + - - +
357B LYS* 4.0 9.0 + - - +
358B PHE* 3.1 28.6 + - - +
15D C 2.7 50.8 + - + +
16D A 4.1 7.2 - - - +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 4.2 11.4 - - + +
243A ARG* 4.9 2.7 - - - +
347B PRO* 3.8 10.1 - - + -
348B GLN 3.7 18.8 - - - +
349B PHE 3.9 11.0 - - - +
351B ASP 3.0 15.9 + - - +
352B GLU* 3.6 10.1 - - - +
353B ARG 3.2 0.2 - - - -
354B ASN* 1.3 77.2 - - - +
356B LYS* 1.3 58.1 + - + +
358B PHE* 3.3 1.9 + - + +
359B LEU* 2.9 48.0 + - + +
374B TRP* 3.5 34.5 - - + +
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Residues in contact with LYS 356 (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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247A GLU* 3.4 31.1 + - - +
352B GLU* 3.2 18.2 + - + +
353B ARG* 3.1 14.8 + - + +
355B VAL* 1.3 78.0 - - + +
357B LYS* 1.3 58.1 + - + +
359B LEU* 3.7 4.8 - - - +
360B SER* 2.9 33.7 + - - -
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Residues in contact with LYS 357 (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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353B ARG* 3.2 20.0 + - + +
354B ASN* 4.0 9.0 + - - +
356B LYS* 1.3 79.0 - - + +
358B PHE* 1.3 63.2 + - - +
360B SER* 2.7 23.6 + - - +
361B ARG* 3.6 13.2 - - - +
15D C 3.5 41.7 + - - +
16D A 3.8 21.1 + - - -
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Residues in contact with PHE 358 (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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344B ARG* 4.0 11.2 - - + -
345B MET 4.2 3.8 - - - -
346B GLY* 3.4 31.4 - - - -
347B PRO* 3.7 14.8 - - + -
354B ASN 3.1 20.0 + - - +
355B VAL* 3.7 3.1 - - - +
357B LYS* 1.3 77.3 - - - +
359B LEU* 1.3 73.3 + - + +
360B SER 3.4 0.5 + - - -
361B ARG* 3.6 3.1 + - - +
363B ARG* 2.4 42.3 + - - -
367B PRO* 4.6 5.6 - - + -
374B TRP* 4.2 9.4 - + + -
375B TRP 3.9 11.7 - - - -
376B ALA* 3.6 34.5 - - + -
15D C 3.3 40.4 + - - +
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Residues in contact with LEU 359 (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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240A HIS* 3.4 34.3 - - + +
355B VAL* 2.9 33.4 + - + +
356B LYS* 3.7 4.3 - - - +
358B PHE* 1.3 84.6 - - + +
360B SER* 1.3 58.6 + - - +
361B ARG 3.3 6.2 + - - +
363B ARG* 5.6 0.7 - - - +
366B ARG* 4.9 10.8 - - - +
367B PRO* 3.8 28.2 - - + +
374B TRP* 3.7 32.8 - - + -
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Residues in contact with SER 360 (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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356B LYS* 2.9 17.4 + - - -
357B LYS* 2.7 23.8 + - - +
359B LEU* 1.3 77.0 - - - +
361B ARG* 1.3 65.3 + - - +
362B ASN* 3.7 10.1 + - - +
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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