Contacts of the strand formed by residues 271 - 276 (chain A) in PDB entry 1OPO
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 GLU 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A SER 3.9 0.2 - - - +
267A VAL* 3.7 6.5 - - - +
268A ASN* 3.3 59.8 + - - +
269A GLY 3.2 1.2 - - - -
270A ASN* 1.3 79.3 - - - +
272A LEU* 1.3 63.3 + - - +
273A GLN* 3.5 24.4 - - - +
331A LYS* 2.7 40.0 + - + +
333A THR* 3.7 22.2 - - + -
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Residues in contact with LEU 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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265A PRO* 4.5 4.3 - - + -
266A SER 3.3 13.7 - - - +
267A VAL* 3.9 20.0 - - + -
270A ASN 4.0 0.9 + - - +
271A GLU* 1.3 75.3 - - - +
273A GLN* 1.3 80.1 + - - +
274A LEU* 4.3 16.6 - - + -
286A VAL* 5.8 0.4 - - + -
330A LEU 3.7 1.0 - - - +
331A LYS* 3.5 4.0 - - - +
332A ILE* 2.8 64.6 + - + +
334A LYS* 6.5 1.3 - - + -
341A LEU* 4.5 22.0 - - + +
343A TRP* 4.5 16.2 - - + +
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Residues in contact with GLN 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL 3.7 1.2 - - - +
265A PRO* 3.2 4.5 - - - +
266A SER* 2.8 60.9 + - - +
268A ASN* 5.3 3.2 - - - +
271A GLU* 3.5 24.8 + - - +
272A LEU* 1.3 76.2 - - - +
274A LEU* 1.3 65.0 + - - +
275A ARG* 3.8 0.7 - - + -
300A ILE* 5.9 1.6 - - - +
329A ILE* 4.1 34.1 - - + +
330A LEU 3.5 3.1 - - - -
331A LYS* 3.9 20.6 - - + +
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Residues in contact with LEU 274 (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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263A VAL* 4.0 26.7 - - + -
264A VAL 3.9 1.1 - - - -
265A PRO* 3.8 22.2 - - + -
272A LEU* 4.3 11.2 - - + -
273A GLN* 1.3 80.5 - - - +
275A ARG* 1.3 62.3 + - - +
276A VAL* 3.5 5.1 + - - +
284A ILE* 4.4 12.3 - - + -
286A VAL* 4.9 0.7 - - + -
329A ILE* 3.5 3.4 - - - -
330A LEU* 2.9 53.2 + - + +
332A ILE* 4.2 19.1 - - + -
343A TRP* 4.0 38.4 - - + +
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Residues in contact with ARG 275 (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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263A VAL* 3.2 5.3 - - - -
264A VAL* 2.8 83.4 + - - +
266A SER* 6.3 1.8 - - - -
273A GLN* 3.8 1.9 - - + -
274A LEU* 1.3 69.2 - - - +
276A VAL* 1.3 63.1 + - - +
277A VAL* 3.3 14.0 + - - +
327A GLY* 3.9 25.6 - - - +
328A GLN 3.5 9.6 - - - +
329A ILE* 4.1 16.2 - - + -
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Residues in contact with VAL 276 (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 TYR 4.3 3.8 - - - +
263A VAL* 3.8 19.5 - - + -
274A LEU 4.3 5.4 - - - +
275A ARG* 1.3 68.1 - - - +
277A VAL* 1.3 62.5 + - - +
278A ALA* 3.4 22.7 + - - +
282A TRP* 3.8 26.5 - - + +
284A ILE* 4.7 13.2 - - + -
304A ILE* 5.6 4.0 - - + -
321A LEU* 5.3 7.6 - - + -
323A THR* 4.1 9.0 - - + +
325A MET 4.7 0.3 - - - +
326A GLU* 3.9 0.5 - - - -
327A GLY* 2.9 27.2 + - - -
328A GLN* 2.8 25.7 + - + +
330A LEU* 5.4 3.1 - - + +
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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