Contacts of the helix formed by residues 260 - 266 (chain C) in PDB entry 2A19
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 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258C THR* 3.0 17.2 + - - +
259C VAL* 1.3 78.1 - - - +
261C LYS* 1.3 67.0 + - - +
262C ARG* 3.7 4.3 + - - +
263C PHE* 3.2 17.0 + - + +
264C GLY* 3.4 17.2 + - - -
327C TRP* 2.8 30.3 + - - -
329C GLY* 3.6 24.8 - - - -
330C PHE 3.6 11.8 + - - +
331C ASP* 3.5 4.8 + - - +
363C PHE* 3.6 22.6 - - + -
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Residues in contact with LYS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C VAL 4.2 8.3 - - - +
260C ASP* 1.3 76.0 + - - +
262C ARG* 1.3 64.4 + - - +
264C GLY* 3.8 0.7 + - - -
265C MET* 3.2 32.9 + - + +
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Residues in contact with ARG 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ARG* 3.5 34.0 - - - +
266B ASP* 2.7 40.8 + - - -
260C ASP* 3.4 3.7 + - - +
261C LYS* 1.3 75.8 - - - +
263C PHE* 1.3 65.6 + - - +
265C MET* 3.2 4.7 + - - +
266C ASP* 3.0 49.5 + - - +
327C TRP* 3.3 62.6 - - + +
328C ASP 5.8 0.2 - - - +
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Residues in contact with PHE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C THR* 3.6 26.7 - - + +
260C ASP* 3.2 22.5 + - + +
261C LYS 3.5 0.4 - - - -
262C ARG* 1.3 79.0 - - - +
264C GLY* 1.3 57.0 + - - +
267C PHE* 3.0 44.0 + + + +
270C ILE* 3.7 36.5 - - + +
282C PHE* 3.8 32.1 - + + -
284C ALA* 4.3 0.9 - - + -
295C ILE* 3.7 39.5 - - + -
327C TRP* 3.8 15.9 - + + -
363C PHE* 3.9 13.9 - + - -
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Residues in contact with GLY 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C THR* 5.1 2.6 - - - +
260C ASP 3.4 13.1 + - - -
261C LYS 4.3 0.9 - - - -
262C ARG 3.3 0.4 - - - -
263C PHE* 1.3 79.1 - - - +
265C MET* 1.3 58.6 + - - +
267C PHE 3.1 7.3 - - - +
270C ILE* 4.9 6.3 - - - +
287C ARG* 2.9 30.4 + - - -
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Residues in contact with MET 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ARG* 5.9 0.7 - - - +
261C LYS* 3.2 25.7 + - + +
262C ARG* 3.2 7.5 + - - +
264C GLY* 1.3 76.2 - - - +
266C ASP* 1.3 67.4 + - - +
287C ARG* 3.3 16.2 + - - +
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Residues in contact with ASP 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ARG* 2.5 41.8 + - - -
326B CYS 5.2 1.5 - - - +
327B TRP* 5.4 2.5 - - - +
262C ARG* 3.0 24.8 + - - +
265C MET* 1.3 87.8 - - - +
267C PHE* 1.3 84.1 + - + +
286C HIS* 3.9 14.7 + - + -
287C ARG* 3.0 33.2 + - - +
327C TRP* 5.9 0.2 - - - -
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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