Contacts of the helix formed by residues 281 - 292 (chain A) in PDB entry 2V5E
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 ASN 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ASN 4.4 4.5 - - - +
277A CYS* 4.4 6.0 - - - +
279A LYS* 3.3 13.8 - - + +
280A GLU* 1.3 79.0 - - - +
282A TYR* 1.3 65.4 + - - +
283A ALA* 3.0 15.0 + - - +
284A ASP* 2.7 45.5 + - + +
285A CYS* 3.3 18.7 + - - +
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Residues in contact with TYR 282 (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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274A VAL 4.6 0.5 + - - -
275A SER* 2.7 50.3 + - - -
277A CYS* 3.6 19.7 - - - -
281A ASN* 1.3 72.0 + - - +
283A ALA* 1.3 57.8 + - - +
285A CYS* 3.1 5.2 + - - +
286A LEU* 2.9 37.6 + - + +
340A ASN* 3.5 16.3 + - + +
341A ALA* 3.5 34.1 - - + +
344A ALA* 3.6 28.9 - - + -
349A SER* 5.8 1.8 - - - -
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Residues in contact with ALA 283 (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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209A TYR* 4.3 5.0 + - - -
281A ASN* 3.0 10.7 + - - +
282A TYR* 1.3 78.6 - - - +
284A ASP* 1.3 59.8 + - - +
286A LEU* 3.5 8.0 + - - +
287A LEU* 3.0 28.6 + - - +
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Residues in contact with ASP 284 (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 ASN* 3.2 36.2 + - + +
279A LYS* 6.1 2.6 - - + -
281A ASN* 2.7 41.9 + - + +
282A TYR 3.3 0.2 - - - -
283A ALA* 1.3 75.4 - - - +
285A CYS* 1.3 59.2 + - - +
287A LEU* 3.7 16.6 - - + +
288A ALA* 3.0 21.7 + - - +
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Residues in contact with CYS 285 (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 ASN* 3.5 17.1 - - - +
267A CYS* 2.1 59.2 - - - -
281A ASN 3.3 8.2 + - - +
282A TYR* 3.1 11.0 + - - +
284A ASP* 1.3 76.3 - - - +
286A LEU* 1.3 59.8 + - - +
288A ALA 3.2 0.5 + - - -
289A TYR* 2.8 26.7 + - - +
337A CYS* 4.2 8.3 - - - -
338A LEU* 3.8 28.5 - - - -
341A ALA* 4.4 4.7 - - + -
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Residues in contact with LEU 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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209A TYR* 3.6 28.8 - - + -
213A PHE* 4.1 15.7 - - + -
282A TYR* 2.9 28.8 + - + +
283A ALA* 3.9 4.3 - - - +
285A CYS* 1.3 67.9 - - - +
287A LEU* 1.3 55.3 + - - +
289A TYR* 3.8 2.9 - - - +
290A SER* 2.8 41.1 + - - -
338A LEU* 4.5 5.6 - - + -
341A ALA* 3.6 42.6 - - + +
342A ILE* 3.8 19.1 - - + -
345A PHE* 3.9 20.4 - - + -
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Residues in contact with LEU 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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209A TYR* 3.2 16.7 + - - +
259A ARG* 5.6 0.7 - - - -
262A ASP* 6.2 0.7 - - - +
266A ASN* 5.9 2.2 - - - +
283A ALA 3.0 18.4 + - - +
284A ASP* 3.7 18.6 - - - +
286A LEU* 1.3 75.1 - - - +
288A ALA* 1.3 58.2 + - - +
290A SER* 3.4 3.6 + - - +
291A GLY* 3.0 25.5 + - - -
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Residues in contact with ALA 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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259A ARG* 4.2 8.1 - - - +
262A ASP* 3.5 21.3 - - + +
263A PHE* 3.5 34.1 - - + +
266A ASN* 3.9 2.9 - - + +
284A ASP 3.0 19.2 + - - +
285A CYS 3.2 4.5 + - - +
287A LEU* 1.3 78.9 - - - +
289A TYR* 1.3 63.2 + - - +
291A GLY* 3.4 9.1 + - - -
292A LEU* 3.5 15.6 + - - +
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Residues in contact with TYR 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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212A LEU* 4.8 10.3 - - + -
213A PHE* 3.7 29.8 - + - -
263A PHE* 3.7 28.4 - + + -
285A CYS 2.8 17.0 + - - +
286A LEU* 3.8 3.1 - - - +
288A ALA* 1.3 73.1 - - - +
290A SER* 1.3 70.2 + - - +
291A GLY 3.0 1.1 - - - -
292A LEU* 3.0 23.1 + - + +
293A ILE* 4.1 5.3 + - + +
299A PRO* 3.4 41.6 + - + +
300A ASN* 3.8 6.9 + - - -
301A TYR* 4.7 3.9 + + - -
309A VAL* 3.1 46.5 - - + +
332A PHE* 4.8 3.8 - + - -
338A LEU* 3.8 20.4 - - + -
342A ILE* 5.0 2.7 - - + -
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Residues in contact with SER 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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200A PHE* 4.1 22.4 - - - +
209A TYR* 3.5 25.3 + - - -
212A LEU* 3.9 22.0 - - - -
213A PHE* 4.4 1.3 - - - -
286A LEU 2.8 26.0 + - - -
287A LEU* 3.4 6.9 + - - +
289A TYR* 1.3 74.8 - - - +
291A GLY* 1.3 58.1 + - - +
293A ILE* 3.0 38.9 + - - +
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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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197A ARG* 5.5 0.2 - - - +
200A PHE* 5.8 2.5 - - - -
259A ARG* 2.8 49.1 + - - +
287A LEU* 3.0 21.1 + - - -
288A ALA 3.6 4.9 - - - -
289A TYR 3.0 0.8 - - - -
290A SER* 1.3 76.6 + - - +
292A LEU* 1.3 59.1 + - - +
293A ILE 3.2 3.4 + - - +
295A THR* 4.0 4.9 - - - +
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Residues in contact with LEU 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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256A CYS 4.7 2.2 - - - +
259A ARG* 3.7 9.6 - - + +
260A LEU* 3.6 33.7 - - + +
263A PHE* 4.0 22.2 - - + -
288A ALA 3.5 9.8 + - - +
289A TYR* 3.0 13.5 + - + +
291A GLY* 1.3 75.1 - - - +
293A ILE* 1.3 59.0 + - - +
294A GLY 3.3 0.2 + - - -
295A THR* 2.7 41.2 + - - +
297A MET* 4.1 16.6 - - + +
298A THR 3.6 6.1 + - - -
299A PRO* 3.8 15.0 - - + -
332A PHE* 3.8 31.9 - - + -
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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