Contacts of the strand formed by residues 256 - 266 (chain A) in PDB entry 2P0R
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 TYR 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ALA* 3.8 8.4 - - - +
231A GLY* 3.3 5.9 - - - -
232A CYS* 3.1 39.7 + - - +
234A ILE* 5.2 0.2 - - + -
249A GLY 4.4 1.9 + - - -
250A LEU* 3.6 9.3 - - + +
251A ILE* 2.9 51.4 + - - +
254A HIS* 3.3 34.5 + + - -
255A ALA* 1.3 75.6 - - - +
257A SER* 1.3 59.4 + - - +
276A ILE* 3.4 29.8 - - + -
277A ARG 3.6 4.0 - - - -
278A ASN* 3.7 33.7 + - + -
279A PRO* 4.1 0.2 - - - -
283A VAL 4.9 1.0 + - - -
317A PHE* 3.9 18.8 - + - -
328A PHE* 3.7 24.7 - + - -
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Residues in contact with SER 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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101A ALA* 2.6 35.3 + - - +
104A ALA* 3.4 14.4 - - - +
105A SER* 3.5 12.3 - - - -
230A LEU 3.8 5.2 - - - -
231A GLY* 4.5 0.4 - - - -
256A TYR* 1.3 72.4 - - - +
258A VAL* 1.3 59.6 + - - +
259A THR* 3.7 17.6 + - - +
276A ILE* 3.4 4.0 - - - +
277A ARG* 2.7 43.5 + - - +
279A PRO* 5.4 0.9 - - - +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 4.0 5.0 + - - -
108A LEU* 4.3 2.6 - - - +
220A LEU* 5.8 1.1 - - + -
224A LEU* 3.9 13.8 - - + +
230A LEU* 2.9 40.5 + - + +
231A GLY* 3.8 18.4 - - - +
232A CYS* 3.6 19.1 - - + -
257A SER* 1.3 72.5 - - - +
259A THR* 1.3 61.3 + - - +
260A GLY 4.4 5.6 - - - +
261A ILE* 5.0 4.5 - - + -
274A ILE* 3.7 32.5 - - + -
275A ARG 3.7 3.1 - - - +
276A ILE* 3.6 16.6 - - + -
324A PHE* 4.8 1.8 - - + -
331A VAL* 5.0 4.0 - - + -
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Residues in contact with THR 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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86A ARG* 4.1 11.7 - - - -
104A ALA* 5.4 3.1 - - + +
108A LEU* 3.4 30.0 - - + +
224A LEU* 3.9 7.0 - - - +
257A SER* 3.8 25.8 - - - +
258A VAL* 1.3 76.2 - - - +
260A GLY* 1.3 59.4 + - - +
275A ARG* 2.9 44.7 + - - +
276A ILE 4.2 0.3 + - - -
277A ARG* 3.8 9.0 - - + -
316A GLU* 2.8 28.7 + - - +
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Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 3.4 9.3 - - - +
258A VAL* 4.4 0.9 - - - +
259A THR* 1.3 80.2 + - - +
261A ILE* 1.3 68.7 + - - +
262A ASP 4.3 0.2 - - - -
274A ILE* 3.5 5.0 - - - +
275A ARG* 2.7 48.2 + - - -
318A TRP* 4.3 4.7 - - - -
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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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217A TYR* 3.4 37.5 - - + +
220A LEU* 4.1 19.5 - - + -
221A GLU* 3.5 45.8 - - + +
224A LEU* 3.5 15.0 - - + +
230A LEU* 5.6 0.7 - - + -
258A VAL* 5.0 4.5 - - + -
260A GLY* 1.3 74.1 - - - +
262A ASP* 1.3 67.8 + - - +
263A GLN* 4.2 0.8 + - - +
273A LEU 4.0 1.3 - - - -
274A ILE* 3.5 37.2 - - + -
318A TRP* 4.6 0.6 - - - -
321A PHE* 5.0 0.2 - - + -
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Residues in contact with ASP 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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217A TYR* 2.8 10.7 + - - -
261A ILE* 1.3 75.4 - - - +
263A GLN* 1.3 86.6 + - - +
273A LEU* 2.6 42.7 + - - +
306A ARG* 2.8 34.7 + - - +
307A LEU* 3.7 13.3 - - + +
318A TRP* 3.6 23.1 - - + -
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Residues in contact with GLN 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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217A TYR* 1.8 49.1 + - - +
221A GLU* 4.7 10.9 + - - +
261A ILE* 4.2 3.4 + - - +
262A ASP* 1.3 100.1 + - - +
264A VAL* 1.3 66.6 + - - +
270A ARG* 3.2 46.2 + - + +
271A ILE 3.3 11.0 - - - +
272A GLU* 4.3 3.8 - - - -
273A LEU* 4.3 2.7 - - - +
306A ARG* 3.1 24.3 + - - -
307A LEU* 4.1 2.1 - - - +
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Residues in contact with VAL 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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263A GLN* 1.3 73.0 - - - +
265A SER* 1.3 64.4 + - - +
266A PHE 3.7 0.2 + - - -
269A GLN 3.6 0.2 - - - +
270A ARG* 3.6 5.3 - - - -
271A ILE* 2.8 34.7 + - + +
273A LEU* 3.4 20.9 - - + -
289A TRP* 3.4 32.3 - - + -
296A TRP* 5.2 0.2 - - + -
299A VAL* 4.5 9.9 - - + -
303A GLU* 4.0 24.0 - - + +
307A LEU* 3.0 36.1 - - + -
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Residues in contact with SER 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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264A VAL* 1.3 78.2 - - - +
266A PHE* 1.3 61.2 + - - +
267A ARG 4.4 0.2 - - - -
268A GLY* 3.9 17.5 - - - -
269A GLN 3.3 10.8 + - - -
270A ARG* 4.6 1.3 - - - +
298A SER 4.7 4.7 - - - +
299A VAL* 4.7 9.0 - - - +
303A GLU* 4.0 11.2 + - - +
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Residues in contact with PHE 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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264A VAL 3.7 0.6 + - - -
265A SER* 1.3 74.1 + - - +
267A ARG* 1.3 110.3 + - + +
269A GLN* 2.8 25.6 + - - +
271A ILE* 3.4 27.6 - - + +
289A TRP* 3.6 30.1 - + + -
295A GLU* 3.7 35.9 - - + -
298A SER* 3.4 27.8 - - - -
299A VAL* 5.4 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