Contacts of the helix formed by residues 324 - 328 (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 GLY 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A HIS* 5.5 1.6 + - - -
259A LYS* 4.1 5.6 - - - -
321A ASP 5.3 0.2 - - - -
322A TRP 3.8 4.6 + - - -
323A VAL* 1.3 74.1 - - - +
325A GLY* 1.3 61.4 + - - -
326A ARG* 3.3 3.1 - - - -
327A TYR* 2.9 38.1 + - - +
328A SER* 3.1 11.3 + - - -
562A TYR 5.7 4.7 - - - -
5001A G6Q 4.4 1.8 - - - -
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Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLY* 3.3 18.3 - - - +
208A SER* 6.0 0.2 - - - -
259A LYS* 4.6 12.8 - - - +
319A PHE* 5.9 0.9 - - - -
323A VAL 3.7 2.0 + - - -
324A GLY* 1.3 70.0 - - - -
326A ARG* 1.3 57.2 + - - +
327A TYR 3.1 2.9 + - - -
328A SER* 2.6 28.7 + - - -
5001A G6Q 3.4 28.6 + - - -
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLY* 4.5 1.3 - - - -
324A GLY* 5.1 0.7 - - - -
325A GLY* 1.3 71.9 - - - +
327A TYR* 1.3 75.5 + - + +
328A SER 3.7 0.9 - - - -
404A TYR* 3.6 23.4 + - - -
407A GLN* 3.5 43.7 - - + +
408A LEU* 3.8 19.3 - - - +
411A GLU* 3.0 33.3 + - - +
412A SER* 2.8 23.6 + - - +
547A GLU* 4.6 0.3 - - - +
561A SER 3.0 21.0 + - - -
562A TYR* 3.4 12.0 - - - +
563A ASP 2.9 23.0 + - - -
564A GLN* 2.8 21.9 + - - -
5001A G6Q 3.0 19.1 + - - +
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Residues in contact with TYR 327 (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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148A HIS* 3.5 50.1 - + + +
151A LEU* 4.1 0.9 - - - +
323A VAL* 4.1 4.2 - - - +
324A GLY* 2.9 22.8 + - - +
326A ARG* 1.3 101.1 - - + +
328A SER* 1.3 58.3 + - - +
329A MET 3.7 2.5 - - - -
330A TRP* 3.3 19.3 - - - -
404A TYR* 4.8 1.6 - - - -
408A LEU* 3.4 20.0 - - + -
412A SER* 2.9 20.4 + - - -
547A GLU* 3.7 34.4 + - + +
550A VAL* 3.7 16.1 - - - +
562A TYR* 3.5 36.2 + + - -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLY 3.1 15.6 + - - -
208A SER* 5.4 0.2 + - - -
319A PHE* 4.6 3.6 - - - -
323A VAL* 3.7 18.2 - - - -
324A GLY 3.5 8.3 - - - -
325A GLY* 2.6 26.8 + - - -
326A ARG 3.7 0.6 - - - -
327A TYR* 1.3 76.7 - - - +
329A MET* 1.3 61.5 + - - +
330A TRP 3.0 6.4 + - - -
331A SER* 2.8 23.1 + - - +
333A ILE* 3.2 25.4 - - - +
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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
------------------------------------------------------------
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