Contacts of the helix formed by residues 257 - 267 (chain A) in PDB entry 2O9C
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 SER 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLU* 2.7 30.7 + - - -
29A ILE* 4.1 5.3 + - - +
254A ARG* 4.5 0.2 - - - +
255A ALA 3.8 1.2 + - - -
256A THR* 1.3 73.6 - - - +
258A PRO* 1.4 71.3 - - - +
259A MET* 3.2 14.2 + - - +
260A HIS* 3.0 4.0 + - - +
261A MET* 2.9 19.6 + - - +
328A LBV 3.0 46.2 + - - +
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Residues in contact with PRO 258 (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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12A LEU* 6.4 2.2 - - + -
27A GLU* 3.6 14.4 - - - +
256A THR 3.4 7.0 - - - +
257A SER* 1.4 82.4 - - - +
259A MET* 1.3 61.5 + - + +
261A MET* 3.2 12.4 + - + +
262A GLN* 3.0 24.1 + - - +
265A ARG* 4.9 1.9 + - - -
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Residues in contact with MET 259 (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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19A ILE* 3.8 36.6 - - + +
20A THR* 4.6 5.4 - - - -
21A THR* 4.6 9.6 - - - -
24A CYS* 4.8 0.2 - - + -
27A GLU* 4.4 6.7 + - - +
257A SER* 3.2 11.0 + - - +
258A PRO* 1.3 79.1 - - + +
260A HIS* 1.3 58.6 + - - +
262A GLN* 3.4 22.2 + - - +
263A TYR* 3.1 24.1 + - - +
328A LBV 3.3 56.2 - - + +
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Residues in contact with HIS 260 (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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224A THR* 4.7 0.4 - - - -
256A THR* 3.8 18.8 - - + -
257A SER* 3.0 9.1 + - - +
259A MET* 1.3 76.9 - - - +
261A MET* 1.3 67.7 + - - +
263A TYR* 3.1 16.0 + + - +
264A LEU* 2.9 51.7 + - + +
328A LBV 2.8 108.6 + + + +
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Residues in contact with MET 261 (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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224A THR* 3.3 27.1 - - + -
226A ASP 3.6 10.5 - - - +
227A THR* 3.4 32.3 - - - +
228A ARG 4.8 0.2 - - - -
229A ALA 3.6 18.8 - - - +
256A THR* 3.8 21.5 - - - +
257A SER 2.9 18.4 + - - +
258A PRO* 3.2 14.8 + - + +
260A HIS* 1.3 77.6 - - - +
262A GLN* 1.3 57.4 + - - +
264A LEU* 3.2 9.5 + - - +
265A ARG* 3.0 49.8 + - - +
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Residues in contact with GLN 262 (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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258A PRO 3.0 16.3 + - - +
259A MET* 3.7 24.1 - - - +
261A MET* 1.3 75.8 - - - +
263A TYR* 1.3 58.9 + - - +
265A ARG* 3.2 24.4 + - - +
266A ASN* 2.8 53.6 + - - +
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Residues in contact with TYR 263 (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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203A PHE* 4.2 4.7 - - - -
207A ASP* 2.8 27.5 + - + -
259A MET 3.1 13.6 + - - +
260A HIS* 3.1 27.9 + + - +
262A GLN* 1.3 75.8 - - - +
264A LEU* 1.3 63.7 + - - +
266A ASN* 3.2 19.1 + - - +
267A MET* 3.2 44.3 + - + +
328A LBV 3.1 76.7 - + + +
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Residues in contact with LEU 264 (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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224A THR* 4.1 10.5 - - - +
227A THR* 3.7 25.4 - - + -
260A HIS* 2.9 52.2 + - + +
261A MET* 3.6 9.6 - - - +
262A GLN 3.2 0.2 - - - -
263A TYR* 1.3 72.5 - - - +
265A ARG* 1.3 67.0 + - - +
267A MET* 3.0 30.2 + - + +
269A VAL* 3.0 32.7 + - + +
272A SER* 3.7 34.1 - - - +
290A HIS* 4.6 2.7 - - - +
328A LBV 5.3 1.3 - - - +
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Residues in contact with ARG 265 (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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227A THR* 2.9 35.4 + - - +
228A ARG* 3.7 52.4 + - - +
258A PRO 4.9 1.4 + - - -
261A MET* 3.0 33.6 + - - +
262A GLN* 3.2 35.3 + - - +
264A LEU* 1.3 75.7 - - - +
266A ASN* 1.3 59.6 + - - +
268A GLY* 2.9 20.1 + - - -
269A VAL 4.4 4.9 - - - +
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Residues in contact with ASN 266 (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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262A GLN* 2.8 39.4 + - - +
263A TYR* 3.5 9.9 - - - +
264A LEU 3.2 0.4 - - - -
265A ARG* 1.3 78.3 - - - +
267A MET* 1.3 59.7 + - + +
268A GLY 3.3 1.0 + - - -
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Residues in contact with MET 267 (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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198A PHE* 4.2 24.0 - - + -
203A PHE* 6.3 0.7 - - - -
263A TYR* 3.2 41.6 + - + +
264A LEU* 3.0 27.1 + - + +
266A ASN* 1.3 75.3 - - + +
268A GLY* 1.3 60.5 + - - +
269A VAL* 3.8 9.0 - - + +
290A HIS* 3.6 21.5 - - + +
328A LBV 3.6 27.8 - - - +
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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