Contacts of the helix formed by residues 310 - 319 (chain C) in PDB entry 2OB1
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 GLU 310 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C VAL* 4.5 3.3 - - + +
308C LEU* 3.1 9.1 - - - +
309C ASP* 1.3 98.1 - - + +
311C LEU* 1.3 65.1 + - - +
312C GLU* 3.2 5.5 + - - +
313C GLU* 3.1 48.6 + - + +
314C LEU* 3.3 9.9 + - - +
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C TRP* 3.8 31.2 - - + -
290C PHE* 4.5 8.1 - - + -
308C LEU* 3.7 30.7 + - + +
309C ASP 3.8 2.4 + - - -
310C GLU* 1.3 74.2 - - - +
312C GLU* 1.3 58.2 + - - +
314C LEU* 3.0 9.4 + - + +
315C LYS* 3.0 25.8 + - - +
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Residues in contact with GLU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C GLU* 3.2 3.5 - - - +
311C LEU* 1.3 78.6 - - - +
313C GLU* 1.3 58.4 + - + +
315C LYS* 3.4 24.1 + - - +
316C VAL* 3.0 45.4 + - + +
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C VAL* 4.5 12.3 - - + +
310C GLU* 3.1 42.1 + - + +
312C GLU* 1.3 76.4 - - + +
314C LEU* 1.3 65.4 + - - +
316C VAL* 3.5 6.8 + - - +
317C MET* 3.1 29.3 + - + +
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C VAL* 3.8 22.8 - - + +
76C TYR* 3.5 39.0 - - + -
80C LEU* 5.0 1.3 - - + -
287C TRP* 4.2 9.6 - - + -
290C PHE* 4.1 21.1 - - + -
308C LEU* 3.6 33.2 - - + -
310C GLU 3.3 6.6 + - - +
311C LEU* 3.0 9.9 + - + +
313C GLU* 1.3 79.6 - - - +
315C LYS* 1.3 56.5 + - - +
317C MET* 3.2 1.4 + - - -
318C GLN* 2.8 62.7 + - + +
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C TRP* 3.5 55.7 - - + +
311C LEU 3.0 9.8 + - - +
312C GLU* 3.7 29.0 + - - +
313C GLU 3.3 0.2 - - - -
314C LEU* 1.3 78.0 - - - +
316C VAL* 1.3 59.0 + - + +
319C THR* 2.9 47.6 + - + +
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Residues in contact with VAL 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C PHE* 4.6 6.1 - - + -
312C GLU* 3.0 40.3 + - + +
313C GLU* 3.9 6.5 - - - +
314C LEU 3.3 0.2 - - - -
315C LYS* 1.3 76.6 - - + +
317C MET* 1.3 60.2 + - + +
319C THR* 3.4 5.3 + - - -
320C HIS* 2.5 46.2 + - + -
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Residues in contact with MET 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PHE* 6.3 0.7 - - + -
73C VAL* 4.2 18.4 - - + -
243C PHE* 3.9 26.5 - - + -
313C GLU* 3.1 20.8 + - + +
314C LEU 3.7 2.9 - - - +
316C VAL* 1.3 80.5 - - + +
318C GLN* 1.3 70.6 + - - +
320C HIS* 3.1 19.0 + - - +
321C TYR* 3.3 37.9 - - + +
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Residues in contact with GLN 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C VAL* 4.7 2.2 + - - +
77C GLY* 3.3 31.7 - - - +
80C LEU* 3.7 13.7 - - + +
231C TYR* 4.7 2.0 + - - -
286C MET* 2.9 54.6 + - + +
287C TRP* 3.6 25.1 - - + +
314C LEU* 2.8 43.5 + - + +
317C MET* 1.3 81.5 + - - +
319C THR* 1.3 64.4 + - - +
320C HIS 3.1 1.8 - - - -
321C TYR* 3.2 22.0 + - - +
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Residues in contact with THR 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ILE* 3.5 18.2 - - - +
285C ASP* 3.6 24.9 - - - +
287C TRP* 3.4 27.8 - - + -
315C LYS* 2.9 43.8 + - + +
316C VAL* 3.4 12.8 + - - -
318C GLN* 1.3 76.2 - - - +
320C HIS* 1.3 65.8 + - - +
321C TYR 3.4 0.4 - - - -
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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