Contacts of the helix formed by residues 279 - 285 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254D LYS* 4.3 13.0 - - + -
255D VAL 4.4 0.2 + - - -
256D MET* 4.0 28.5 - - + -
277D GLU* 3.9 21.3 - - - +
278D PRO* 1.3 79.0 - - - +
280D THR* 1.3 69.1 + - - +
281D ALA* 2.8 19.0 + - + +
282D SER* 3.0 15.7 + - - +
283D LEU* 3.3 14.1 + - - +
303D THR* 5.9 4.7 - - + +
330D GLY* 3.0 25.8 - - - +
331D SER 3.7 17.0 - - - +
332D ALA* 3.7 24.0 - - + +
355D THR* 5.6 3.8 - - + -
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Residues in contact with THR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ILE* 1.3 73.5 - - - +
281D ALA* 1.3 63.0 + - - +
283D LEU* 3.9 10.3 - - - +
284D GLY* 3.2 16.8 + - - -
330D GLY 3.2 6.9 + - - -
331D SER* 4.0 2.8 - - - +
357D GLY* 2.9 29.7 + - - +
360D GLU 4.0 1.8 - - - -
361D ARG* 3.2 39.0 - - - +
364D VAL* 3.8 20.4 - - + -
434D PHE* 3.3 24.0 - - + -
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Residues in contact with ALA 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D MET* 4.4 1.3 - - + -
279D ILE* 2.8 19.8 + - + +
280D THR* 1.3 76.0 - - - +
282D SER* 1.3 57.6 + - - +
284D GLY 3.2 0.2 + - - -
285D THR* 2.9 34.5 + - - +
303D THR* 5.8 0.7 - - + -
307D LEU* 3.4 23.2 - - + +
331D SER 5.3 0.6 + - - -
355D THR* 4.2 13.5 - - + -
356D ASN 5.1 1.4 + - - -
433D ILE* 3.6 17.5 - - + -
434D PHE* 3.5 12.2 - - - -
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Residues in contact with SER 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D VAL 3.0 19.8 + - - -
256D MET* 3.7 32.7 - - - +
279D ILE 3.0 20.4 + - - -
281D ALA* 1.3 74.8 - - - +
283D LEU* 1.3 56.7 + - - +
284D GLY 3.4 0.2 - - - -
285D THR 4.0 3.9 - - - +
307D LEU* 4.1 6.7 - - - -
308D SER 6.1 0.2 - - - -
313D THR* 4.2 2.9 - - - +
314D PRO* 3.3 26.0 - - - +
317D LEU* 3.5 21.9 - - - +
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Residues in contact with LEU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D PRO* 4.0 14.6 - - + -
279D ILE 3.3 21.9 + - - +
280D THR* 3.9 8.3 - - - +
282D SER* 1.3 76.4 - - - +
284D GLY* 1.3 54.3 + - - +
314D PRO* 3.5 10.9 - - - +
317D LEU* 3.9 19.5 - - + -
318D ASN* 3.0 41.5 + - - +
321D LEU* 3.8 18.2 - - + -
329D THR* 3.7 30.1 - - + -
361D ARG* 5.9 0.2 - - + -
364D VAL* 4.1 6.9 - - + +
365D ILE* 3.9 19.3 - - + -
368D LYS* 3.9 10.2 - - - +
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Residues in contact with GLY 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D THR 3.2 8.1 + - - -
281D ALA 3.2 2.6 + - - -
282D SER 3.4 0.2 - - - -
283D LEU* 1.3 78.2 - - - +
285D THR* 1.3 62.9 + - - +
314D PRO* 4.5 5.4 - - - -
364D VAL* 3.5 22.7 - - - -
368D LYS* 4.9 8.2 + - - +
434D PHE* 4.0 4.0 - - - -
437D MET* 3.2 22.5 - - - +
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Residues in contact with THR 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D ALA 2.9 23.2 + - - +
282D SER* 4.0 5.9 - - - +
284D GLY* 1.3 78.0 - - - +
286D ASP* 1.3 75.4 + - - +
289D HIS* 3.7 18.7 + - - -
301D PHE* 3.8 14.8 - - + -
307D LEU* 4.4 4.6 - - + +
313D THR* 5.8 0.3 - - - +
314D PRO* 3.4 18.3 - - - +
433D ILE* 3.7 37.3 + - + +
434D PHE* 4.1 7.0 - - + -
437D MET* 5.3 0.9 - - - -
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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