Contacts of the helix formed by residues 302 - 310 (chain A) in PDB entry 2O2C
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 ASN 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A LYS 4.4 0.7 - - - +
260A THR* 3.2 31.2 + - - +
261A PHE* 4.3 2.7 - - + -
262A THR* 4.9 3.6 - - - +
300A SER* 3.2 4.8 + - - +
301A THR* 1.3 79.0 + - - +
303A ASN* 1.3 61.6 + - - +
304A GLN* 3.4 11.1 + - - +
305A LYS* 3.2 32.1 + - - +
306A VAL* 3.0 27.9 + - - +
316A MET* 3.8 2.9 - - - -
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Residues in contact with ASN 303 (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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301A THR 3.2 4.5 + - - +
302A ASN* 1.3 72.9 + - - +
304A GLN* 1.3 61.6 + - - +
306A VAL* 3.6 3.1 + - - +
307A LYS* 3.4 27.8 + - + +
313A GLU* 3.4 25.4 + - - +
316A MET* 3.6 14.7 - - - +
318A GLN* 2.9 41.1 + - - -
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Residues in contact with GLN 304 (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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302A ASN* 3.3 9.3 + - - +
303A ASN* 1.3 76.7 - - - +
305A LYS* 1.3 64.9 + - + +
307A LYS* 3.3 13.4 + - - +
308A GLU* 3.0 41.4 + - + +
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Residues in contact with LYS 305 (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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261A PHE* 3.6 35.5 - - + +
262A THR* 4.2 23.9 - - + +
302A ASN* 3.2 25.7 + - - +
304A GLN* 1.3 75.8 - - + +
306A VAL* 1.3 63.7 + - - +
308A GLU* 3.6 31.5 + - + +
309A PHE* 3.5 15.1 + - - +
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Residues in contact with VAL 306 (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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261A PHE* 3.9 21.5 - - + -
298A ALA* 3.6 24.0 - - + -
300A SER* 3.9 18.6 - - - -
302A ASN 3.0 19.5 + - - +
303A ASN 3.8 5.6 - - - +
304A GLN 3.3 0.4 - - - -
305A LYS* 1.3 75.6 - - - +
307A LYS* 1.3 64.5 + - + +
309A PHE* 3.5 12.0 + - - +
310A GLY 3.6 0.2 + - - -
311A ILE* 3.5 34.5 + - + +
312A ASP 5.2 0.7 - - - +
313A GLU* 6.1 0.7 - - - -
316A MET* 3.8 26.7 - - + -
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Residues in contact with LYS 307 (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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303A ASN 3.4 13.2 + - - +
304A GLN* 3.3 16.9 + - - +
306A VAL* 1.3 79.5 - - + +
308A GLU* 1.3 61.5 + - + +
310A GLY* 3.3 13.3 + - - -
311A ILE 4.0 17.6 + - - +
312A ASP* 6.1 0.4 - - - +
313A GLU* 4.4 29.6 - - + +
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Residues in contact with GLU 308 (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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274A ARG* 5.1 0.9 + - - -
304A GLN* 3.0 32.9 + - + +
305A LYS* 3.8 36.6 + - + +
306A VAL 3.3 0.4 - - - -
307A LYS* 1.3 75.6 - - + +
309A PHE* 1.3 61.7 + - - +
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Residues in contact with PHE 309 (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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256A VAL* 4.7 2.0 - - + -
261A PHE* 4.2 17.3 - + + -
267A ILE* 5.1 7.0 - - + -
270A ALA* 3.5 41.1 - - + -
271A LEU* 3.7 27.8 - - + -
274A ARG* 2.7 56.3 + - + +
292A VAL* 4.8 2.9 - - + +
296A PHE* 3.8 25.4 - + + -
305A LYS 3.5 9.8 + - - +
306A VAL 3.5 9.8 + - - +
307A LYS 3.2 0.4 - - - -
308A GLU* 1.3 79.4 - - - +
310A GLY* 1.3 57.8 + - - +
311A ILE* 3.6 25.4 - - + -
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Residues in contact with GLY 310 (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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292A VAL* 3.8 20.0 - - - +
293A ALA* 4.9 4.3 + - - +
306A VAL 3.6 0.2 + - - -
307A LYS 3.3 12.5 + - - -
308A GLU 3.4 0.6 - - - -
309A PHE* 1.3 79.7 - - - +
311A ILE* 1.3 64.9 + - - +
312A ASP* 4.0 5.2 + - - +
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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