Contacts of the helix formed by residues 302 - 310 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259B LYS 4.3 0.9 - - - +
260B THR* 3.0 31.1 + - - +
261B PHE* 4.1 2.5 - - + -
262B THR* 4.6 4.2 - - - +
300B SER* 3.2 6.5 + - - +
301B THR* 1.3 78.2 + - - +
303B ASN* 1.3 62.4 + - - +
304B GLN* 3.5 11.3 + - - +
305B LYS* 3.2 33.1 + - - +
306B VAL* 3.3 25.1 + - - +
316B MET* 3.9 3.6 - - - -
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Residues in contact with ASN 303 (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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301B THR 3.2 5.4 + - - +
302B ASN* 1.3 71.3 + - - +
304B GLN* 1.3 61.0 + - - +
306B VAL* 3.5 3.5 + - - +
307B LYS* 3.2 23.6 + - - +
313B GLU* 5.3 9.4 + - - +
316B MET* 3.6 19.8 - - - +
318B GLN* 2.6 45.8 + - - +
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Residues in contact with GLN 304 (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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302B ASN* 3.3 8.8 + - - +
303B ASN* 1.3 79.6 - - - +
305B LYS* 1.3 59.6 + - + +
307B LYS* 2.9 46.0 + - - +
308B GLU* 3.0 56.7 + - - +
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Residues in contact with LYS 305 (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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261B PHE* 3.6 25.6 - - + +
262B THR* 4.2 21.5 - - + -
302B ASN* 3.2 32.1 + - - +
304B GLN* 1.3 76.5 - - + +
306B VAL* 1.3 63.2 + - - +
308B GLU* 3.3 32.1 + - + +
309B PHE* 3.3 22.2 + - - +
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Residues in contact with VAL 306 (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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261B PHE* 3.9 14.8 - - + -
298B ALA* 3.8 22.4 - - + -
300B SER* 3.9 18.6 - - - -
302B ASN 3.3 17.4 + - - +
303B ASN 3.7 6.1 - - - +
304B GLN 3.3 0.4 - - - -
305B LYS* 1.3 76.2 - - - +
307B LYS* 1.3 64.3 + - - +
309B PHE* 3.3 9.2 + - - +
310B GLY 3.4 0.2 + - - -
311B ILE* 3.3 44.8 + - + +
312B ASP 4.8 0.7 - - - +
313B GLU* 6.0 0.9 - - - -
316B MET* 3.8 28.5 - - + -
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Residues in contact with LYS 307 (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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303B ASN 3.2 11.8 + - - +
304B GLN* 2.9 46.3 + - - +
306B VAL* 1.3 80.4 - - - +
308B GLU* 1.3 58.7 + - - +
310B GLY* 3.1 18.9 + - - -
311B ILE 4.0 10.5 - - - +
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Residues in contact with GLU 308 (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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274B ARG* 5.2 1.2 + - - -
304B GLN* 3.0 46.9 + - - +
305B LYS* 3.3 40.1 + - + +
307B LYS* 1.3 78.9 - - - +
309B PHE* 1.3 59.0 + - - +
310B GLY 3.4 0.2 - - - -
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Residues in contact with PHE 309 (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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256B VAL* 4.8 1.8 - - + -
261B PHE* 4.0 17.9 - + + -
267B ILE* 4.8 9.2 - - + -
270B ALA* 3.5 44.9 - - + -
271B LEU* 3.9 25.4 - - + -
274B ARG* 2.7 55.9 + - + +
292B VAL* 5.1 1.9 - - + +
296B PHE* 4.1 21.5 - + - -
305B LYS 3.3 13.2 + - - +
306B VAL 3.5 9.4 - - - +
307B LYS 3.2 0.8 - - - -
308B GLU* 1.3 78.0 - - - +
310B GLY* 1.3 58.9 + - - +
311B ILE* 3.8 23.6 - - + -
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Residues in contact with GLY 310 (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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292B VAL* 4.0 17.9 - - - +
293B ALA* 5.3 2.4 + - - +
307B LYS 3.1 13.1 + - - -
308B GLU 3.4 0.4 - - - -
309B PHE* 1.3 79.6 - - - +
311B ILE* 1.3 64.3 + - - +
312B ASP* 3.8 7.6 + - - +
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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