Contacts of the strand formed by residues 256 - 264 (chain A) in PDB entry 3RJD
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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231A MET* 4.9 6.1 - - - -
254A ASP 3.4 3.7 + - - -
255A SER* 1.3 74.9 - - - +
257A LEU* 1.3 64.0 + - - -
258A TYR* 3.5 10.2 - - - -
277A GLU* 3.6 5.9 - - - +
278A LEU 3.1 31.6 + - - +
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Residues in contact with LEU 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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231A MET* 3.4 4.5 - - - +
232A GLY* 2.9 35.6 + - - +
256A GLY* 1.3 72.7 - - - -
258A TYR* 1.3 61.3 + - - +
259A TRP* 4.1 1.9 - - - -
275A GLU* 4.0 43.3 - - + +
276A LEU 3.9 1.1 - - - -
277A GLU* 3.9 30.1 - - + +
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Residues in contact with TYR 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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194A LEU* 3.6 18.2 - - + +
210A LEU* 3.6 17.0 - - + -
230A TYR 3.5 5.6 - - - +
231A MET* 3.8 17.9 - - + -
236A LEU* 3.5 29.6 - - + -
247A ILE* 4.0 21.7 - - + +
254A ASP* 2.5 46.3 + - - +
256A GLY 3.5 18.6 - - - -
257A LEU* 1.3 73.7 - - - +
259A TRP* 1.3 62.5 + - - +
274A PRO 4.2 0.2 - - - +
275A GLU* 3.4 0.7 - - - -
276A LEU* 2.6 44.0 + - + +
278A LEU* 3.7 28.5 - - + -
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Residues in contact with TRP 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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194A LEU* 3.6 8.1 - - - +
229A PHE* 4.0 1.4 - - - +
230A TYR* 3.0 82.4 + + + +
232A GLY 3.2 28.2 + - - +
233A SER* 5.7 1.8 - - - -
257A LEU 4.1 7.6 - - - -
258A TYR* 1.3 78.7 - - - +
260A CYS* 1.3 76.5 + - - +
261A GLU* 4.0 6.5 - - - -
272A ARG* 3.6 55.4 - - + -
273A SER* 3.6 20.9 - - - +
274A PRO 4.6 0.4 - - - -
275A GLU* 3.8 30.6 + - + -
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Residues in contact with CYS 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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192A PRO* 4.0 3.1 - - - -
194A LEU* 4.2 11.2 - - + +
212A CYS* 2.0 55.9 - - + -
228A SER 3.4 11.7 - - - +
229A PHE* 4.0 14.6 - - + -
259A TRP* 1.3 81.6 - - - +
261A GLU* 1.3 58.6 + - - +
272A ARG* 3.5 2.8 - - - -
273A SER* 2.8 49.4 + - - -
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Residues in contact with GLU 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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212A CYS* 4.4 2.8 - - - -
226A TYR 3.8 1.4 - - - +
227A PHE* 3.3 7.8 - - - +
228A SER* 3.0 40.5 + - - +
230A TYR* 2.9 35.2 + - + -
259A TRP* 4.0 3.3 - - - -
260A CYS* 1.3 74.4 - - - +
262A ALA* 1.3 60.1 + - - +
263A ALA* 5.5 1.3 - - + -
270A LEU* 4.3 30.1 - - + +
271A LYS 3.5 12.8 - - - +
272A ARG* 3.3 34.7 + - + +
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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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189A PHE* 3.4 26.0 - - + -
192A PRO* 3.9 19.2 - - + +
214A THR* 4.2 6.5 - - + -
225A LEU* 5.2 2.2 - - + -
226A TYR 3.8 3.4 - - - -
227A PHE* 4.1 24.9 - - + -
261A GLU* 1.3 72.5 - - - +
263A ALA* 1.3 60.2 + - - +
270A LEU* 3.2 1.8 - - - -
271A LYS 2.8 36.3 + - - -
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Residues in contact with ALA 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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189A PHE* 4.1 1.5 - - - -
225A LEU* 3.4 11.5 - - - +
226A TYR* 2.7 47.8 + - + +
239A ARG* 5.9 5.4 - - + -
261A GLU* 5.5 2.0 - - + -
262A ALA* 1.3 74.6 - - - +
264A THR* 1.3 67.8 + - - +
267A GLY* 5.0 4.9 - - - -
269A VAL 3.3 7.0 - - - +
270A LEU* 3.5 22.2 - - + -
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Residues in contact with THR 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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188A LEU* 4.3 20.4 - - + -
189A PHE* 4.0 20.9 - - + -
216A LEU* 5.9 2.2 - - + -
224A GLN 3.8 7.6 - - - +
225A LEU* 4.2 5.4 - - + -
226A TYR* 4.6 3.2 - - - +
239A ARG* 4.8 2.1 + - - -
263A ALA* 1.3 78.2 - - - +
265A GLU* 1.4 57.5 + - - +
266A ASP* 3.1 12.8 + - - -
267A GLY* 2.8 24.8 + - - -
268A ASN* 3.6 8.0 + - - +
269A VAL* 3.3 27.9 + - + +
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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