Contacts of the strand formed by residues 256 - 263 (chain A) in PDB entry 1RQ7
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ILE* 4.4 13.0 - - - -
255A GLN* 1.3 79.3 - - - +
257A VAL* 1.3 64.3 + - - +
288A ASN* 3.5 7.2 - - - -
308A ILE 3.7 0.7 - - - +
309A ALA* 3.6 0.2 - - - -
310A ALA* 2.8 43.0 + - - +
311A GLY* 4.9 0.2 - - - -
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Residues in contact with VAL 257 (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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214A ILE* 3.6 5.9 - - - +
251A MET* 4.3 22.7 - - + +
254A ALA* 4.0 24.2 - - + +
256A GLY* 1.3 79.3 - - - +
258A LEU* 1.3 65.8 + - - +
259A MET* 4.7 4.0 - - + +
279A VAL* 4.8 2.5 - - + -
283A ALA* 5.2 1.8 - - + -
287A ALA* 5.1 3.6 - - + -
288A ASN 3.0 7.6 + - - +
289A ILE* 3.2 29.1 - - + -
290A ILE 3.0 24.4 + - - +
307A VAL* 3.6 29.2 - - + -
308A ILE 3.2 5.6 - - - +
309A ALA* 4.6 1.3 - - - -
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Residues in contact with LEU 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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193A GLY 6.1 0.2 - - - -
194A ILE* 4.2 20.0 - - + -
197A LEU* 3.8 31.6 - - + -
206A VAL* 4.4 7.2 - - + -
211A VAL* 4.4 7.6 - - + -
214A ILE* 4.4 17.0 - - + +
215A MET* 4.1 29.8 - - + -
257A VAL* 1.3 73.2 - - - +
259A MET* 1.3 62.1 + - - +
260A SER* 5.5 0.9 - - - +
290A ILE* 3.6 30.3 - - + +
306A THR 3.7 1.0 - - - +
307A VAL* 3.6 1.7 - - - -
308A ILE* 2.8 45.5 + - + +
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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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197A LEU* 4.9 0.2 - - - +
257A VAL* 4.7 7.9 - - + -
258A LEU* 1.3 78.6 - - - +
260A SER* 1.3 63.6 + - - +
261A ILE* 3.8 32.8 - - + -
272A ILE* 5.5 1.6 - - + +
275A ALA* 4.7 10.3 - - + +
276A ALA* 5.2 2.7 - - + -
279A VAL* 3.6 28.5 - - + -
289A ILE* 5.0 0.4 - - + -
290A ILE 2.9 13.3 + - - +
291A PHE* 3.4 34.2 - - + -
292A GLY 3.0 27.7 + - - +
305A VAL* 4.0 12.8 - - + -
306A THR 3.2 3.1 - - - +
307A VAL* 3.5 26.2 - - + -
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Residues in contact with SER 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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193A GLY* 3.1 31.9 + - - -
197A LEU* 3.9 11.4 - - - +
258A LEU* 5.8 0.7 - - - -
259A MET* 1.3 77.1 - - - +
261A ILE* 1.3 61.9 + - - +
262A ALA* 5.0 0.9 + - - +
292A GLY 3.5 5.6 - - - -
294A VAL* 3.6 19.9 - - - +
304A ARG 3.7 1.3 + - - +
305A VAL* 3.2 4.7 - - - +
306A THR* 2.8 41.1 + - - +
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Residues in contact with ILE 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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234A SER* 3.8 24.7 - - - +
259A MET* 3.8 15.9 - - + -
260A SER* 1.3 75.2 + - - +
262A ALA* 1.3 65.6 + - - +
267A LEU* 4.3 13.9 - - + +
272A ILE* 4.4 21.1 - - + -
275A ALA* 4.0 16.4 - - + -
292A GLY 3.1 14.3 + - - +
293A THR* 3.2 19.1 - - + -
294A VAL 3.0 20.3 + - - +
303A VAL* 4.5 6.3 - - + -
304A ARG 3.5 3.1 - - - +
305A VAL* 3.8 24.2 - - + -
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Residues in contact with ALA 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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260A SER* 5.4 1.3 - - - +
261A ILE* 1.3 74.1 - - - +
263A GLY* 1.3 58.1 + - - +
267A LEU* 4.4 2.7 - - - -
294A VAL* 3.4 33.4 - - + -
296A ASP* 4.7 3.1 - - + -
299A LEU* 3.8 14.8 - - + +
303A VAL* 3.0 10.1 - - - +
304A ARG* 2.8 49.0 + - + +
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Residues in contact with GLY 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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262A ALA* 1.3 75.7 - - - +
264A GLY* 1.3 67.9 + - - +
267A LEU* 4.1 9.2 - - - +
294A VAL 3.1 7.8 + - - +
295A ILE* 3.7 0.2 - - - -
296A ASP 3.0 25.9 + - - -
299A LEU* 4.0 3.7 - - - +
302A GLU 4.0 13.9 - - - -
303A VAL* 4.0 11.0 - - - -
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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