Contacts of the strand formed by residues 261 - 268 (chain A) in PDB entry 4EJX
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 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A HIS* 4.1 47.0 + - - +
194A ILE* 3.6 7.2 - - - +
195A ASP* 2.7 66.9 + - - +
196A ARG 3.3 3.6 + - - -
259A GLU 4.1 7.4 + - - +
260A ASP* 1.3 66.9 - - - +
262A VAL* 1.3 59.4 + - - +
306A TYR* 4.3 28.7 - - + +
307A MET 4.0 3.8 - - - -
308A VAL* 4.8 8.1 - - + +
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Residues in contact with VAL 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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194A ILE* 4.9 0.2 - - - -
196A ARG* 3.4 17.0 - - + +
198A PHE* 3.6 30.5 - - + -
256A MET* 4.3 15.3 - - + -
260A ASP* 3.3 30.7 - - + +
261A ARG* 1.3 72.6 - - - +
263A LYS* 1.3 65.0 + - - +
264A TRP* 3.4 28.6 - - + +
306A TYR* 3.9 3.5 - - - -
307A MET* 2.9 44.0 + - + +
309A ALA* 4.5 4.7 - - + -
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Residues in contact with LYS 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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153A GLY* 6.0 3.1 - - - -
154A ASN 5.2 1.7 - - - +
155A CYS* 3.0 32.2 + - - +
191A GLU* 3.6 14.2 + - - +
194A ILE* 4.0 22.4 - - + -
196A ARG 2.9 11.9 + - - +
197A GLU* 3.8 2.7 - - + -
198A PHE 3.1 25.6 + - - +
261A ARG 4.0 1.2 + - - -
262A VAL* 1.3 76.9 - - - +
264A TRP* 1.3 62.8 + - - +
265A TYR* 2.8 49.9 + - + +
304A ASP* 4.5 9.0 - - - -
305A ALA 3.3 21.5 - - - +
306A TYR* 4.4 12.8 - - + -
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Residues in contact with TRP 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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198A PHE* 3.6 18.2 - + + -
200A VAL* 3.7 31.4 - - + -
254A LEU* 4.2 18.4 - - + -
256A MET* 3.6 38.6 - - + -
262A VAL* 3.4 30.2 + - + +
263A LYS* 1.3 78.5 - - - +
265A TYR* 1.3 62.6 + - - +
266A LEU* 3.3 17.6 - - + +
280A PHE* 3.5 37.2 - + + -
285A LEU* 4.4 6.1 - - + -
304A ASP* 3.3 2.4 - - - -
305A ALA* 2.6 46.5 + - + -
307A MET* 3.5 26.0 - - + +
317A LEU* 4.1 4.7 - - + -
333A PHE* 5.0 3.4 - + - -
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Residues in contact with TYR 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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79A LYS* 5.7 0.9 - - - -
155A CYS* 3.0 31.8 - - + +
157A THR* 3.2 35.4 - - + +
179A ILE* 3.9 32.8 - - + -
191A GLU* 3.1 10.7 + - - -
197A GLU* 4.3 18.6 + - + -
198A PHE 3.1 21.7 + - - +
199A VAL* 3.7 9.3 - - + +
200A VAL 2.9 23.3 + - - +
263A LYS* 2.8 52.0 + - + +
264A TRP* 1.3 70.1 - - - +
266A LEU* 1.3 60.7 + - - +
267A PHE* 3.8 8.3 - - + -
303A PHE 3.7 1.1 - - - -
304A ASP* 3.8 8.5 - - + -
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Residues in contact with LEU 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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200A VAL* 2.9 32.5 - - + +
202A PHE* 4.0 11.0 - - + -
264A TRP* 3.3 30.1 - - + +
265A TYR* 1.3 73.6 - - - +
267A PHE* 1.3 60.0 + - - +
278A ALA* 4.3 3.6 - - + -
280A PHE* 3.8 28.5 - - + -
295A ILE* 3.7 26.9 - - + -
297A LEU* 3.7 17.2 - - + +
303A PHE* 2.8 41.0 + - + +
304A ASP 4.7 0.9 - - - -
305A ALA* 3.8 6.7 - - + +
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Residues in contact with PHE 267 (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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74A LEU* 4.4 2.2 - - + -
157A THR* 3.4 29.6 - - + -
159A ILE* 3.6 24.2 - - + -
175A ILE* 4.8 9.2 - - + -
177A PRO* 3.5 40.8 - - + -
199A VAL* 3.6 19.1 - - + -
200A VAL 2.9 11.4 + - - -
201A MET* 3.3 55.1 - - + +
202A PHE 3.3 2.8 + - - -
265A TYR* 3.8 5.6 - - + -
266A LEU* 1.3 73.0 - - - +
268A GLY* 1.3 62.3 + - - +
269A MET* 5.6 2.2 - - + -
297A LEU* 3.6 5.8 - - - +
300A ALA 5.6 0.4 - - - -
301A THR 3.3 18.2 - - - +
302A LEU* 4.2 6.5 - - + -
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Residues in contact with GLY 268 (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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202A PHE 3.3 10.3 - - - -
267A PHE* 1.3 76.8 - - - +
269A MET* 1.3 57.3 + - - +
276A HIS* 4.8 1.6 - - - -
297A LEU* 3.7 20.5 - - - +
298A PHE* 3.0 17.4 + - - +
300A ALA* 2.7 30.5 + - - -
301A THR 3.6 6.7 + - - -
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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