Contacts of the helix formed by residues 279 - 285 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A LYS* 3.9 24.0 - - + -
256A MET* 3.2 39.5 - - + -
277A GLU* 3.8 21.3 - - - +
278A PRO* 1.3 77.8 - - - +
280A THR* 1.3 66.1 + - - +
281A ALA* 4.3 7.9 - - + +
282A SER* 3.0 19.4 + - - +
283A LEU* 3.1 16.0 + - - +
303A THR* 5.7 4.7 - - + -
330A GLY 3.3 19.3 - - - +
331A SER 4.0 9.2 - - - +
332A ALA* 4.1 21.3 - - + +
355A THR* 5.9 1.6 - - + -
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Residues in contact with THR 280 (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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279A ILE* 1.3 70.9 - - - +
281A ALA* 1.3 70.8 + - - +
283A LEU* 3.1 7.7 + - - +
284A GLY 2.9 18.0 + - - -
330A GLY 3.3 7.7 + - - -
331A SER* 4.0 2.4 - - - +
357A GLY* 2.9 29.1 + - - -
360A GLU* 4.0 1.1 - - + -
361A ARG* 3.4 27.5 - - - +
364A VAL* 3.8 30.1 - - + -
434A PHE* 3.4 27.2 - - + -
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Residues in contact with ALA 281 (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 MET* 4.4 6.5 - - + -
279A ILE* 3.3 8.9 - - + +
280A THR* 1.3 81.3 - - - +
282A SER* 1.3 57.3 + - - +
285A THR* 2.9 30.3 + - - +
303A THR* 5.4 0.9 - - + -
307A LEU* 3.2 25.8 - - + -
331A SER 5.3 1.6 + - - +
355A THR* 4.1 13.2 - - + -
356A ASN 5.0 1.8 + - - -
433A ILE* 3.7 19.3 - - + -
434A PHE* 3.6 12.5 - - - -
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Residues in contact with SER 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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255A VAL 3.0 21.5 + - - -
256A MET* 3.9 22.2 - - - -
278A PRO* 4.1 1.0 - - - +
279A ILE* 3.0 23.0 + - - +
281A ALA* 1.3 78.6 - - - +
283A LEU* 1.3 58.1 + - - +
284A GLY 3.5 0.2 + - - -
285A THR 3.8 3.6 - - - +
307A LEU* 3.7 7.0 - - - +
313A THR* 4.4 2.6 - - - +
314A PRO* 3.4 25.3 - - - +
317A LEU* 3.4 26.2 - - - +
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Residues in contact with LEU 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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278A PRO* 4.0 22.0 - - + -
279A ILE 3.1 24.2 + - - +
280A THR* 3.1 5.4 + - - +
282A SER* 1.3 76.2 - - - +
284A GLY* 1.3 57.6 + - - +
314A PRO* 3.5 8.1 - - - +
317A LEU* 4.1 13.7 - - + -
318A ASN* 3.1 40.7 + - - +
321A LEU* 3.6 22.7 - - + -
329A THR* 4.1 25.8 - - + -
361A ARG* 5.8 1.1 - - + -
364A VAL* 3.9 11.6 - - + +
365A ILE* 4.2 13.2 - - + -
368A LYS* 3.8 12.0 - - - +
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Residues in contact with GLY 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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280A THR 2.9 12.4 + - - -
283A LEU* 1.3 79.9 - - - +
285A THR* 1.3 61.7 + - - +
314A PRO* 4.3 5.9 - - - +
364A VAL* 3.7 15.9 - - - -
368A LYS* 4.4 11.9 + - - -
434A PHE* 4.1 5.4 - - - -
437A MET* 3.4 23.1 - - - +
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Residues in contact with THR 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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281A ALA* 2.9 23.9 + - - +
282A SER* 3.8 6.2 - - - +
284A GLY* 1.3 78.9 - - - +
286A ASP* 1.3 73.5 + - - +
289A HIS* 4.1 12.1 + - - -
301A PHE* 3.8 19.7 - - + -
307A LEU* 4.6 4.8 - - + +
313A THR* 5.5 1.4 - - - +
314A PRO* 3.4 17.6 - - - +
433A ILE* 3.6 30.9 + - + +
434A PHE* 3.8 14.1 - - + -
437A MET* 5.1 2.5 - - - -
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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