Contacts of the helix formed by residues 284 - 289 (chain B) in PDB entry 2V90
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 LEU 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B GLN* 3.8 41.1 - - + +
258B GLY 5.1 1.3 - - - +
260B GLY* 3.9 27.4 - - - -
281B ASP* 3.7 22.6 + - + +
282B PRO 3.2 4.9 - - - +
283B GLY* 1.3 82.2 - - - +
285B PRO* 1.3 80.8 - - + +
286B ALA 3.2 2.4 + - - -
287B LYS* 3.2 5.2 + - - +
288B LYS* 3.0 22.2 + - - +
338D SER* 3.7 28.7 - - - +
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Residues in contact with PRO 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.4 13.2 - - + +
253B GLU 3.0 38.4 - - - +
255B GLY* 4.4 5.8 - - - +
258B GLY 3.8 17.5 - - - +
259B PHE* 3.6 13.0 - - - +
284B LEU* 1.3 93.6 - - + +
286B ALA* 1.3 62.2 + - - +
288B LYS* 3.1 9.3 + - + -
289B ALA* 2.8 19.9 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LEU* 3.7 12.5 - - + +
259B PHE 2.7 22.6 + - - +
260B GLY 3.8 10.3 - - - +
261B PHE* 3.8 19.5 - - + -
280B VAL* 3.9 9.9 - - + -
285B PRO* 1.3 71.4 - - - +
287B LYS* 1.3 65.0 + - - +
289B ALA* 3.1 12.0 + - - +
291B MET* 3.1 36.0 + - + +
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B VAL* 3.4 30.3 + - + +
281B ASP 3.1 23.6 + - - +
282B PRO* 3.9 16.1 - - + +
283B GLY 4.2 2.0 - - - +
284B LEU 3.2 5.8 + - - +
286B ALA* 1.3 77.2 - - - +
288B LYS* 1.3 59.8 + - + +
290B GLY* 2.9 21.8 + - - -
291B MET 4.0 9.0 + - - +
292B GLN* 6.2 0.6 - - - +
336D GLU* 4.0 14.1 - - - +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLY* 3.9 16.4 - - - +
284B LEU 3.0 19.8 + - - +
285B PRO* 3.1 8.3 + - + +
287B LYS* 1.3 75.9 - - + +
289B ALA* 1.3 56.0 + - - +
290B GLY 3.3 2.0 - - - -
333D ALA 4.7 12.1 - - - +
334D ASP* 4.2 27.2 + - + +
336D GLU* 2.9 29.6 + - + +
337D THR* 3.0 24.0 + - - +
311F GLU* 4.9 5.1 + - - -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ARG* 3.8 1.0 + - - -
250B LEU* 3.1 36.5 - - + +
251B HIS 4.5 6.5 - - - +
252B LEU* 2.9 36.3 - - + -
285B PRO 2.8 4.3 + - - +
286B ALA 3.1 3.3 + - - +
288B LYS* 1.3 76.3 - - - +
290B GLY* 1.3 59.5 + - - +
291B MET* 3.4 1.3 - - - +
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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