Contacts of the helix formed by residues 285 - 299 (chain A) in PDB entry 2V3V
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 PRO 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A ARG 4.9 0.2 - - - +
284A VAL* 1.4 94.7 - - + +
286A VAL* 1.3 63.1 + - - +
287A GLU* 3.4 24.9 - - + +
288A GLN* 3.1 38.4 + - + +
289A ILE 4.0 0.9 + - - -
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Residues in contact with VAL 286 (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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275A PRO* 3.7 35.7 - - + -
276A GLU* 4.0 20.0 - - + +
279A ALA* 3.4 23.3 - - + -
284A VAL 3.4 1.2 + - - -
285A PRO* 1.3 71.3 - - - +
287A GLU* 1.3 66.6 + - - +
289A ILE* 3.1 20.8 + - + +
290A TYR* 3.4 20.9 - - + -
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Residues in contact with GLU 287 (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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216A MET* 4.2 2.2 - - - +
285A PRO* 3.4 17.8 - - + +
286A VAL* 1.3 91.5 + - - +
288A GLN* 1.3 61.6 + - + +
290A TYR* 3.8 11.6 - - + +
291A GLY* 2.8 27.9 + - - -
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Residues in contact with GLN 288 (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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216A MET* 3.5 33.7 - - + +
217A HIS 3.2 22.2 + - - +
218A VAL* 3.6 25.5 - - + +
219A ALA 4.4 0.7 + - - -
228A PHE* 3.9 3.2 - - + -
284A VAL* 3.7 22.6 - - + +
285A PRO* 3.1 31.9 + - + +
286A VAL 3.1 0.8 - - - -
287A GLU* 1.3 76.0 - - + +
289A ILE* 1.3 64.8 + - - +
292A ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 289 (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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228A PHE* 3.4 26.7 - - + +
231A SER* 3.8 34.5 - - - +
232A MET* 4.1 6.1 - - + +
235A VAL* 4.2 8.5 - - + -
275A PRO* 3.4 36.6 - - + +
278A VAL* 3.9 15.3 - - + -
279A ALA* 3.8 22.0 - - + +
284A VAL* 4.6 4.9 - - + -
286A VAL 3.1 9.9 + - - +
288A GLN* 1.3 79.3 - - - +
290A TYR* 1.3 61.1 + - - +
292A ALA* 4.1 1.4 - - - +
293A ALA* 3.2 22.9 + - - +
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Residues in contact with TYR 290 (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 TRP* 4.1 13.7 - + - -
235A VAL* 3.7 25.4 - - + -
238A ASN* 5.9 0.4 - - - -
239A GLU* 3.7 14.8 - - - -
275A PRO* 3.7 16.2 - - + +
276A GLU* 2.9 20.5 + - - -
286A VAL* 3.4 42.0 - - + -
287A GLU* 3.4 10.4 + - - +
289A ILE* 1.3 74.2 - - - +
291A GLY* 1.3 60.6 + - - +
293A ALA* 3.5 1.0 + - - +
294A ARG* 2.9 71.8 + - - +
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Residues in contact with GLY 291 (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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201A ILE* 4.9 0.8 - - - +
216A MET* 3.7 16.6 - - - -
287A GLU 2.8 17.9 + - - -
290A TYR* 1.3 78.3 - - - +
292A ALA* 1.3 55.1 + - - +
294A ARG* 4.0 5.1 - - - +
295A ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 292 (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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171A PHE* 4.8 1.2 - - + -
201A ILE* 4.1 35.6 - - + +
216A MET* 4.0 2.7 - - - +
228A PHE* 4.2 10.1 - - + -
232A MET* 3.9 22.9 - - + +
288A GLN 3.0 18.6 + - - +
289A ILE 4.1 2.2 - - - +
291A GLY* 1.3 70.8 - - - +
293A ALA* 1.3 60.9 + - - +
295A ALA* 3.4 1.7 + - - +
296A PHE* 2.9 32.4 + - - +
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Residues in contact with ALA 293 (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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232A MET* 3.6 39.9 - - - +
235A VAL* 3.6 20.9 - - + -
236A ILE* 3.9 7.5 - - + +
241A LEU* 5.2 0.4 - - - -
289A ILE 3.2 17.0 + - - +
290A TYR 3.8 0.4 - - - +
292A ALA* 1.3 78.1 - - - +
294A ARG* 1.3 59.0 + - - +
296A PHE* 3.5 2.9 - - - +
297A ALA* 2.9 32.1 + - - +
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Residues in contact with ARG 294 (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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235A VAL* 4.5 3.8 - - + -
239A GLU* 2.8 43.1 + - - +
241A LEU* 4.2 13.9 - - + -
290A TYR* 2.9 49.5 + - - +
291A GLY* 4.0 4.9 - - - +
293A ALA* 1.3 72.3 - - - +
295A ALA* 1.3 59.9 + - - +
298A GLU* 2.7 57.9 + - - +
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Residues in contact with ALA 295 (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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169A CYS* 3.7 14.6 - - - -
199A LYS* 3.9 28.5 - - + +
201A ILE* 4.0 17.3 - - + -
291A GLY 2.9 22.3 + - - +
292A ALA 3.7 3.8 - - - +
294A ARG* 1.3 73.8 - - - +
296A PHE* 1.3 61.5 + - - +
298A GLU* 5.3 0.9 - - - -
299A SER* 2.6 30.1 + - - -
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Residues in contact with PHE 296 (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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169A CYS* 3.9 6.6 - - - -
171A PHE* 3.9 16.2 - + + -
232A MET* 4.1 18.2 - - + -
236A ILE* 4.4 11.2 - - + -
292A ALA 2.9 19.1 + - - +
293A ALA* 3.5 5.2 - - - +
295A ALA* 1.3 77.3 - - - +
297A ALA* 1.3 60.6 + - - +
299A SER 4.1 0.5 + - - -
302A THR* 2.7 40.3 + - + -
304A SER* 3.5 21.3 - - - -
326A LEU* 3.4 46.7 - - + -
327A HIS* 3.3 26.9 - + - -
330A THR* 3.7 10.8 - - - -
332A GLN* 3.4 11.5 + - + -
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Residues in contact with ALA 297 (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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236A ILE* 4.0 17.5 - - + -
241A LEU* 3.7 43.3 - - + +
293A ALA 2.9 20.2 + - - +
296A PHE* 1.3 77.3 - - - +
298A GLU* 1.3 63.6 + - - +
299A SER 3.3 1.7 + - - +
330A THR* 4.2 7.9 - - + -
332A GLN* 4.0 9.4 + - - +
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Residues in contact with GLU 298 (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 LEU* 4.1 26.7 - - + +
294A ARG* 2.7 48.6 + - - +
295A ALA* 4.8 0.4 - - - +
297A ALA* 1.3 71.9 - - - +
299A SER* 1.3 61.2 - - - +
300A ALA* 3.8 1.2 + - - -
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Residues in contact with SER 299 (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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168A THR* 3.3 20.4 + - - +
169A CYS* 3.2 13.0 - - - +
199A LYS* 4.6 8.3 + - - +
295A ALA* 2.6 24.5 + - - -
297A ALA 3.3 2.2 - - - +
298A GLU* 1.3 80.0 - - - +
300A ALA* 1.3 59.8 + - - +
301A ALA 3.3 1.1 - - - -
302A THR* 3.5 17.5 - - - -
332A GLN* 2.9 24.8 + - - -
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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