Contacts of the helix formed by residues 263 - 274 (chain A) in PDB entry 4J1R
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 VAL 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ILE* 4.5 4.5 - - + -
261A SER* 3.2 4.5 + - - +
262A GLY* 1.3 75.7 - - - +
264A ASP* 1.3 64.5 + - - +
265A GLN 3.1 1.6 - - - -
266A LEU* 3.0 20.7 + - + +
267A VAL* 3.6 4.7 + - + +
291A PHE* 4.0 18.6 - - + -
293A PHE* 3.7 26.0 - - + -
61B VAL* 4.3 11.0 - - + +
62B ILE* 3.5 15.5 - - - +
63B GLY* 3.4 41.5 - - - +
64B ASN* 4.0 6.5 - - + +
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Residues in contact with ASP 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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259A GLY* 3.4 3.9 - - - -
260A ASP* 2.5 42.9 + - + +
261A SER* 2.9 27.0 + - - +
263A VAL* 1.3 76.9 - - - +
265A GLN* 1.3 61.8 + - - +
267A VAL* 2.9 29.7 + - - +
268A GLU* 3.1 25.2 + - - +
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Residues in contact with GLN 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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220A ARG* 3.1 37.3 + - + +
221A TYR* 3.2 11.6 + - - -
223A ARG* 4.5 5.7 + - + +
228A ILE* 3.6 18.2 - - + -
257A PHE* 2.9 45.5 - - - +
259A GLY* 3.0 21.5 + - - -
261A SER 3.1 17.7 + - - +
262A GLY 3.6 9.6 - - - +
264A ASP* 1.3 77.1 - - - +
266A LEU* 1.3 60.9 + - - +
268A GLU* 3.4 2.6 + - - +
269A ILE* 3.1 31.9 + - + +
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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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225A PRO* 4.8 10.1 - - + +
228A ILE* 3.9 28.1 - - + +
229A PHE* 3.7 36.3 - - + -
263A VAL 3.0 12.5 + - - +
265A GLN* 1.3 76.9 - - - +
267A VAL* 1.3 59.7 + - - +
269A ILE* 3.1 11.5 + - + +
270A ILE* 2.8 43.3 + - + +
276A PRO* 6.4 1.3 - - + -
291A PHE* 4.0 25.4 - - + -
293A PHE* 3.7 25.4 - - + -
323A TYR* 5.5 3.8 - - + -
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Residues in contact with VAL 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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263A VAL* 3.8 4.9 - - + +
264A ASP* 3.2 33.0 - - - +
266A LEU* 1.3 75.4 - - - +
268A GLU* 1.3 58.9 + - - +
270A ILE* 3.2 14.0 + - + +
271A LYS* 2.8 44.4 + - + +
293A PHE* 4.0 24.7 - - + -
296A ILE* 6.5 0.7 - - + -
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Residues in contact with GLU 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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256A ILE 5.0 1.1 - - - +
257A PHE* 3.6 28.9 - - + -
258A PRO* 3.9 38.4 - - - +
259A GLY* 4.0 3.6 - - - -
260A ASP* 5.3 1.4 - - - +
264A ASP* 3.1 27.6 + - - +
265A GLN 3.6 7.0 - - - +
266A LEU 3.2 0.2 - - - -
267A VAL* 1.3 77.4 - - - +
269A ILE* 1.3 62.4 + - - +
271A LYS* 3.5 39.5 + - - +
272A VAL* 3.7 7.3 - - - +
144B ARG* 5.8 0.9 + - - -
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Residues in contact with ILE 269 (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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223A ARG 4.2 8.3 - - - +
225A PRO* 4.3 7.9 - - + -
228A ILE* 3.9 22.7 - - + -
241A TRP* 3.6 24.0 - - + -
257A PHE* 3.8 24.7 - - + -
265A GLN* 3.1 22.1 + - - +
266A LEU* 3.3 11.7 - - + +
268A GLU* 1.3 76.1 - - - +
270A ILE* 1.3 59.9 + - - +
272A VAL* 3.1 5.9 + - - +
273A LEU* 2.8 38.2 + - + +
323A TYR* 3.6 29.4 - - + +
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Residues in contact with ILE 270 (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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266A LEU* 2.8 29.2 + - + +
267A VAL* 3.2 12.8 + - + +
269A ILE* 1.3 69.1 - - + +
271A LYS* 1.3 58.6 + - + +
272A VAL 2.9 6.5 + - - -
274A GLY* 2.6 55.2 + - - +
275A THR* 3.8 26.7 - - + +
276A PRO* 4.5 7.6 - - + -
293A PHE* 3.9 31.6 - - + -
294A PRO 5.2 0.2 - - - +
296A ILE* 4.1 23.8 - - + +
323A TYR* 3.6 6.5 - - - +
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Residues in contact with LYS 271 (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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267A VAL* 2.8 34.0 + - + +
268A GLU* 3.7 36.1 + - - +
269A ILE 3.3 0.4 - - - -
270A ILE* 1.3 73.9 - - + +
272A VAL* 1.3 61.3 + - + +
296A ILE* 5.5 10.7 - - + +
297A LYS 5.4 1.8 - - - +
299A HIS* 4.0 23.3 + - - +
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Residues in contact with VAL 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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256A ILE* 4.9 9.6 - - + +
257A PHE* 3.7 27.1 - - + -
268A GLU 3.7 5.8 - - - +
269A ILE 3.1 6.2 + - - +
270A ILE 2.9 0.8 + - - -
271A LYS* 1.3 84.7 - - + +
273A LEU* 1.3 73.3 + - + +
274A GLY 3.3 1.3 - - - -
298A ALA* 3.7 1.4 - - - +
299A HIS* 3.1 33.2 + - + +
301A TRP* 4.5 16.9 - - + -
304A VAL* 4.0 29.6 - - + -
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Residues in contact with LEU 273 (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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241A TRP* 3.7 26.9 - - + -
257A PHE* 4.8 3.6 - - + -
269A ILE* 2.8 16.5 + - + +
272A VAL* 1.3 79.8 - - + +
274A GLY* 1.3 61.1 + - - +
275A THR 4.8 1.7 - - - +
298A ALA* 3.4 15.5 - - - +
301A TRP* 3.5 37.9 - - + +
321A LEU* 3.7 22.0 - - + +
323A TYR* 3.4 46.2 - - + +
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Residues in contact with GLY 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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270A ILE* 2.6 33.0 + - - -
272A VAL 3.3 3.0 + - - -
273A LEU* 1.3 72.7 - - - +
275A THR* 1.3 60.0 - - - -
296A ILE 3.1 15.9 - - - -
297A LYS 3.9 1.8 - - - -
298A ALA* 3.7 12.7 - - - +
323A TYR* 2.6 29.5 + - - -
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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