Contacts of the helix formed by residues 303 - 311 (chain A) in PDB entry 2O8C
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 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A SER* 5.3 4.5 + - - -
188A GLU* 3.5 15.7 - - - +
192A ILE* 3.4 2.2 - - - +
302A LEU* 1.3 78.3 - - - +
304A ILE* 1.3 64.4 + - - +
305A ALA 3.2 2.7 - - - +
306A ALA* 3.3 28.5 + - + +
307A VAL* 3.4 18.2 + - - +
708A ILE 4.0 1.2 + - - -
709A LEU* 3.4 26.1 - - - +
710A ALA 3.5 8.9 + - - +
731A GLU* 4.5 9.5 - - - +
734A SER* 5.2 5.9 + - - -
735A ILE* 3.3 31.1 - - - +
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Residues in contact with ILE 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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188A GLU* 3.5 43.2 + - + +
192A ILE* 4.2 12.8 - - + -
216A ILE* 3.8 13.9 - - + +
219A ARG* 3.2 53.8 - - + +
220A GLY* 4.1 13.7 - - - -
303A ASP* 1.3 74.8 - - - +
305A ALA* 1.3 59.9 + - - +
307A VAL* 3.7 6.4 + - + +
308A ARG* 3.5 31.9 + - - +
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Residues in contact with ALA 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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219A ARG* 5.2 3.5 - - - +
303A ASP* 3.2 1.4 - - - +
304A ILE* 1.3 76.5 - - - +
306A ALA* 1.3 59.7 + - - +
307A VAL 3.3 0.9 - - - -
308A ARG* 3.4 14.1 + - + +
309A ALA* 3.0 27.4 + - - +
710A ALA* 4.0 7.7 - - - +
712A VAL* 4.8 18.8 - - - +
731A GLU* 3.2 32.2 + - - +
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Residues in contact with ALA 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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302A LEU* 4.6 7.2 - - + -
303A ASP* 3.3 25.9 + - + +
304A ILE 3.3 0.4 - - - -
305A ALA* 1.3 78.3 - - - +
307A VAL* 1.3 62.7 + - - +
309A ALA* 3.5 1.1 + - - +
310A LEU* 3.4 30.9 + - - +
312A LEU* 5.3 0.4 - - - -
708A ILE* 3.4 28.9 - - + +
710A ALA* 4.0 21.4 - - + +
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Residues in contact with VAL 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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192A ILE* 3.8 29.6 - - + -
302A LEU* 4.3 4.9 - - + -
303A ASP 3.4 14.8 - - - +
304A ILE* 3.8 9.0 - - + +
306A ALA* 1.3 78.4 - - - +
308A ARG* 1.3 61.1 + - + +
310A LEU 3.5 1.0 + - - -
311A ASN* 2.9 23.6 + - - -
312A LEU* 3.2 49.7 + - + +
313A PHE* 4.8 11.9 - - + +
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Residues in contact with ARG 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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219A ARG* 4.6 23.6 - - - +
220A GLY 5.3 1.2 - - - +
304A ILE* 3.5 23.3 + - + +
305A ALA* 3.4 15.6 + - + +
306A ALA 3.3 0.2 - - - -
307A VAL* 1.3 78.9 - - + +
309A ALA* 1.3 63.5 + - - +
311A ASN* 3.5 13.2 + - - +
680A ARG* 4.9 2.8 + - - -
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Residues in contact with ALA 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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305A ALA 3.0 17.1 + - - +
306A ALA* 3.7 10.5 - - - +
307A VAL 3.3 0.4 - - - -
308A ARG* 1.3 80.2 - - - +
310A LEU* 1.3 64.8 + - + +
311A ASN* 5.0 1.2 - - - +
639A HIS* 5.4 2.1 + - - -
680A ARG* 3.2 50.8 + - + +
710A ALA* 4.5 5.8 - - + -
712A VAL* 3.9 18.2 - - + -
746A ILE* 5.7 1.1 - - + -
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Residues in contact with LEU 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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302A LEU* 5.5 2.2 - - + -
306A ALA 3.4 20.1 + - - +
307A VAL 4.3 0.4 - - - +
309A ALA* 1.3 81.2 - - + +
311A ASN* 1.3 71.3 + - - +
312A LEU* 4.2 13.5 - - + -
326A LEU* 4.4 6.6 - - - +
639A HIS* 4.9 8.1 + - - -
641A CYS* 5.2 2.1 - - - -
680A ARG* 3.3 32.3 - - + +
683A GLY* 3.4 35.4 - - - +
684A VAL* 3.8 19.2 - - + +
687A LEU* 3.8 22.7 - - + -
708A ILE* 4.6 12.1 - - + -
746A ILE* 4.3 9.2 - - + -
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Residues in contact with ASN 311 (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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307A VAL 2.9 10.2 + - - -
308A ARG* 3.5 11.1 + - - +
309A ALA 3.3 3.7 - - - +
310A LEU* 1.3 81.5 - - - +
312A LEU* 1.3 59.6 + - - +
313A PHE 4.4 1.4 + - - -
314A GLN* 3.4 28.6 + - - +
323A SER* 3.6 23.3 + - - +
324A GLN 3.3 26.5 + - - +
325A SER* 3.7 4.3 + - - +
326A LEU* 3.0 24.3 + - - +
639A HIS* 6.3 1.1 - - + -
641A CYS* 6.2 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