Contacts of the helix formed by residues 279 - 285 (chain B) in PDB entry 2VM8
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 ILE 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LYS* 4.0 11.0 - - + -
255B VAL 4.0 0.4 + - - -
256B MET* 3.9 25.8 - - + -
277B GLU* 3.7 24.7 - - - +
278B PRO* 1.3 78.5 - - - +
280B THR* 1.3 66.7 - - - +
281B ALA* 3.9 21.5 - - + -
282B SER* 2.9 16.6 + - - -
283B LEU* 3.0 17.3 + - - +
303B THR* 5.9 6.1 - - + +
330B GLY 2.8 23.1 - - - +
331B SER 3.4 22.0 - - - +
332B ALA* 3.8 15.5 - - + +
355B THR* 5.6 2.2 - - + -
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Residues in contact with THR 280 (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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279B ILE* 1.3 71.3 - - - +
281B ALA* 1.3 63.9 + - - +
283B LEU* 3.3 8.5 + - - +
284B GLY* 2.9 22.7 + - - -
330B GLY 2.9 11.6 + - - -
331B SER* 3.7 5.2 - - - +
357B GLY* 3.1 31.7 + - - +
360B GLU 3.9 9.4 - - - +
361B ARG* 3.4 32.2 - - - +
364B VAL* 4.0 9.8 - - + +
365B ILE* 6.4 0.4 - - - -
434B PHE* 3.4 23.0 - - + -
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B MET* 4.2 1.1 - - + -
279B ILE* 3.3 21.7 - - + +
280B THR* 1.3 76.8 - - - +
282B SER* 1.3 58.0 + - - +
285B THR* 3.0 27.9 + - - +
303B THR* 5.8 0.7 - - + -
307B LEU* 3.6 35.0 - - + +
331B SER 5.2 0.4 + - - -
355B THR* 4.2 6.1 - - + -
356B ASN 5.1 1.6 + - - +
433B ILE* 3.9 16.2 - - + -
434B PHE* 3.6 12.7 - - - -
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL 2.7 25.7 + - - -
256B MET* 3.4 33.6 - - - +
278B PRO* 4.1 0.3 - - - +
279B ILE* 2.9 21.1 + - - +
281B ALA* 1.3 76.4 - - - +
283B LEU* 1.3 58.1 + - - +
285B THR 4.0 4.2 - - - +
307B LEU* 4.6 2.5 - - - -
308B SER 6.1 0.4 - - - +
313B THR* 4.4 2.5 - - - +
314B PRO* 3.5 24.4 - - - +
317B LEU* 3.3 20.5 - - - +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PRO* 3.9 15.9 - - + -
279B ILE 3.0 25.0 + - - +
280B THR* 3.8 6.7 - - - +
282B SER* 1.3 76.0 - - - +
284B GLY* 1.3 58.1 + - - +
314B PRO* 3.7 3.5 - - - +
317B LEU* 4.0 27.1 - - + +
318B ASN* 3.0 47.1 + - - +
321B LEU* 4.0 7.0 - - + -
329B THR* 3.9 29.4 - - + -
361B ARG* 6.0 0.2 - - + -
364B VAL* 4.1 7.9 - - + -
365B ILE* 4.0 17.5 - - + -
368B LYS* 3.2 15.1 - - - +
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Residues in contact with GLY 284 (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 THR 2.9 12.6 + - - -
283B LEU* 1.3 80.9 - - - +
285B THR* 1.3 63.9 + - - +
364B VAL* 3.6 20.4 - - - -
368B LYS* 4.3 13.1 + - - -
434B PHE* 4.3 6.3 - - - -
437B MET* 3.2 24.6 - - - +
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Residues in contact with THR 285 (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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281B ALA 3.0 20.9 + - - +
282B SER* 4.0 3.3 - - - +
283B LEU 3.9 0.4 - - - -
284B GLY* 1.3 79.6 - - - +
286B ASP* 1.3 75.7 + - - +
289B HIS* 3.6 18.4 + - - -
301B PHE* 4.3 11.0 - - + -
307B LEU* 3.9 13.4 - - + +
313B THR* 5.6 0.9 - - - -
314B PRO* 3.2 21.6 - - - +
433B ILE* 3.7 25.3 + - + +
434B PHE* 4.2 11.7 - - + -
437B MET* 5.3 2.2 - - - -
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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