Contacts of the strand formed by residues 267 - 273 (chain A) in PDB entry 2O7R
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 ARG 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A PHE* 6.2 0.7 - - + -
195A LYS 3.1 10.8 + - - +
196A GLY* 3.0 24.1 - - - -
197A LEU 3.0 4.7 + - - -
265A GLY 4.2 7.4 - - - +
266A TRP* 1.3 75.6 - - - +
268A VAL* 1.3 63.2 + - - +
295A ASP* 2.7 42.1 + - + +
297A VAL* 3.2 27.1 - - - +
325A LYS 5.4 0.6 + - - -
326A PHE* 3.4 57.6 + - + +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.4 29.2 - - + +
199A LEU* 4.2 12.1 - - + -
261A ILE* 4.3 10.5 - - + -
266A TRP* 5.0 0.7 - - + -
267A ARG* 1.3 79.5 - - - +
269A MET* 1.3 64.4 + - - +
270A VAL* 4.0 15.3 - - + -
289A LEU* 3.9 27.4 - - + -
294A VAL* 3.8 23.6 - - + -
295A ASP 2.9 11.5 + - - +
296A VAL* 3.2 7.6 - - + +
297A VAL 2.8 24.3 + - - -
326A PHE* 4.0 2.9 - - - -
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Residues in contact with MET 269 (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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197A LEU 2.8 10.9 + - - +
198A VAL* 3.6 15.9 - - + -
199A LEU* 2.8 33.0 + - - +
268A VAL* 1.3 74.3 - - - +
270A VAL* 1.3 62.6 + - - +
271A VAL* 3.9 15.7 - - + -
297A VAL* 3.2 18.2 - - + +
319A PHE* 3.9 27.6 - - - -
322A ILE* 3.7 29.4 - - + +
323A LEU* 4.2 4.7 - - - -
326A PHE* 3.3 54.1 - - + -
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Residues in contact with VAL 270 (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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199A LEU* 3.5 18.4 - - + +
202A PRO* 4.3 19.7 - - + -
268A VAL* 4.0 17.7 - - + -
269A MET* 1.3 78.2 - - - +
271A VAL* 1.4 63.6 + - - +
282A GLN* 4.0 11.4 - - + +
285A LEU* 5.3 2.9 - - + -
286A ALA* 4.4 17.0 - - + +
289A LEU* 4.5 9.0 - - + -
296A VAL* 4.6 5.2 - - + -
297A VAL 3.0 7.6 + - - +
298A ALA* 3.4 4.7 - - - -
299A GLN 3.0 23.0 + - - -
300A PHE* 3.6 27.9 - - + -
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Residues in contact with VAL 271 (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 VAL* 6.2 0.7 - - + -
199A LEU 3.1 6.3 + - - +
200A ASP* 3.4 28.3 - - - +
201A GLU* 2.8 29.0 + - - -
202A PRO* 4.1 3.3 - - - +
269A MET* 3.9 26.0 - - + -
270A VAL* 1.4 78.9 - - - +
272A GLY* 1.3 58.0 + - - +
282A GLN* 4.3 0.3 - - - +
299A GLN* 3.2 27.4 - - + +
300A PHE* 3.9 6.0 - - - -
301A ASP* 6.1 0.2 - - - +
309A LYS* 4.0 11.4 - - - +
319A PHE* 4.1 21.3 - - + -
322A ILE* 6.0 1.3 - - + -
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Residues in contact with GLY 272 (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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201A GLU* 4.6 10.5 - - - -
271A VAL* 1.3 80.0 - - - +
273A CYS* 1.3 62.3 + - - +
276A ASP* 5.5 0.2 - - - -
282A GLN* 4.0 11.0 - - - -
299A GLN 3.2 5.0 + - - +
300A PHE* 3.3 18.3 - - - -
301A ASP* 3.1 23.4 + - - +
309A LYS* 5.9 2.0 - - - -
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Residues in contact with CYS 273 (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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201A GLU* 5.7 2.7 - - - -
272A GLY* 1.3 77.4 - - - +
274A HIS* 1.3 66.4 + - - +
275A GLY 3.2 3.6 + - - -
276A ASP* 3.2 19.7 + - - +
279A ILE* 3.4 20.5 - - - +
282A GLN* 4.7 1.0 + - - -
300A PHE* 5.9 0.2 - - - -
301A ASP* 3.3 21.5 - - + +
303A GLY 3.3 20.0 - - - +
304A GLY* 3.7 3.4 - - - -
305A TYR* 3.4 37.5 - - - -
306A HIS* 5.1 0.2 - - - -
308A VAL* 4.8 5.6 - - + -
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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