Contacts of the helix formed by residues 324 - 328 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C HIS* 5.6 1.0 + - - -
259C LYS* 3.9 7.0 - - - -
322C TRP 3.8 4.2 + - - -
323C VAL* 1.3 76.1 - - - +
325C GLY* 1.3 66.2 + - - -
326C ARG* 3.3 3.1 - - - -
327C TYR* 3.0 31.9 + - - +
328C SER* 3.1 11.8 + - - -
562C TYR 5.7 4.7 - - - -
564C GLN* 6.1 0.7 - - - -
5003C G6Q 4.7 1.8 - - - -
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Residues in contact with GLY 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLY* 3.2 18.8 - - - +
208C SER* 5.9 0.4 - - - -
259C LYS* 4.5 13.1 - - - +
319C PHE* 6.0 0.4 - - - -
323C VAL 3.7 2.0 + - - -
324C GLY* 1.3 70.4 - - - -
326C ARG* 1.3 57.4 + - - +
327C TYR 3.1 2.9 + - - -
328C SER* 2.7 29.3 + - - -
329C MET 4.9 0.3 + - - -
5003C G6Q 3.3 30.4 + - - -
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Residues in contact with ARG 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLY* 4.5 1.3 - - - -
324C GLY* 6.4 0.7 - - - -
325C GLY* 1.3 74.1 - - - +
327C TYR* 1.3 76.6 + - + +
328C SER 3.6 0.7 - - - -
404C TYR* 3.5 23.0 + - - -
407C GLN* 3.7 41.3 - - + +
408C LEU* 3.9 19.9 - - + +
411C GLU* 3.1 35.6 + - - +
412C SER* 2.7 25.3 + - - +
547C GLU* 4.5 0.5 - - - +
561C SER 3.0 22.0 + - - -
562C TYR* 3.4 11.8 - - - +
563C ASP 2.9 22.4 + - - -
564C GLN* 2.8 21.9 + - - -
5003C G6Q 2.9 19.4 + - - +
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Residues in contact with TYR 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C VAL* 5.9 0.2 - - + -
148C HIS* 3.6 46.4 - + + +
151C LEU* 4.1 0.3 - - - +
323C VAL* 3.9 4.5 - - - +
324C GLY* 3.0 24.5 + - - +
326C ARG* 1.3 104.3 - - + +
328C SER* 1.3 57.2 + - - +
329C MET 3.7 2.2 - - - -
330C TRP* 3.3 21.4 - - - +
404C TYR* 4.8 0.9 - - - -
408C LEU* 3.4 21.0 - - + +
412C SER* 2.9 16.3 + - - -
547C GLU* 3.7 35.7 + - + -
550C VAL* 3.7 15.8 - - - +
561C SER 3.9 0.4 + - - -
562C TYR* 3.4 38.0 + + - -
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Residues in contact with SER 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLY 3.1 15.8 + - - -
319C PHE* 4.6 5.4 - - - -
323C VAL* 3.7 16.6 - - - -
324C GLY 3.4 9.4 - - - -
325C GLY* 2.7 25.9 + - - -
326C ARG 3.6 0.6 - - - -
327C TYR* 1.3 75.7 - - - +
329C MET* 1.3 61.9 + - - +
330C TRP 3.0 6.9 + - - -
331C SER* 2.7 26.0 + - - -
333C ILE* 3.2 22.2 - - - +
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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
------------------------------------------------------------
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