Contacts of the helix formed by residues 334 - 339 (chain D) in PDB entry 2VKM
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 GLY 334 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ASP 3.1 17.7 - - - -
231D THR* 3.1 11.9 - - - -
233D ASN 3.2 12.0 + - - -
234D LEU* 4.5 1.6 - - - +
332D VAL 3.2 8.1 + - - -
333D MET* 1.3 77.0 - - - +
335D ALA* 1.3 66.6 + - - -
336D VAL 3.2 3.1 - - - -
337D ILE* 3.0 4.1 + - - +
338D MET* 2.9 21.6 + - - +
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Residues in contact with ALA 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D TYR* 4.7 2.9 - - + -
154D LEU* 5.0 4.9 - - + -
228D ASP 4.1 1.2 + - - -
229D SER* 5.2 1.0 - - - +
231D THR 2.8 9.1 + - - +
232D THR 3.4 5.1 + - - +
307D ARG* 3.4 27.1 - - - +
334D GLY* 1.3 70.6 - - - -
336D VAL* 1.3 56.4 + - - +
338D MET* 4.2 8.1 - - - +
339D GLU* 2.8 46.4 + - + +
1386D BSD 3.4 23.3 - - + -
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Residues in contact with VAL 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D THR 3.1 15.8 + - - +
234D LEU* 3.7 22.4 - - + +
300D ILE* 3.7 16.2 - - + +
304D GLN* 3.4 44.5 - - - +
305D TYR* 3.7 20.4 - - + -
307D ARG* 4.3 4.4 - - - -
323D ALA* 3.3 39.3 - - + +
334D GLY 3.2 0.6 + - - -
335D ALA* 1.3 76.9 - - - +
337D ILE* 1.3 62.4 + - - +
339D GLU* 4.1 2.1 + - - -
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Residues in contact with ILE 337 (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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227D VAL* 6.3 0.2 - - + -
234D LEU* 3.9 22.0 - - + -
283D ILE* 6.3 0.2 - - + -
285D LEU* 3.9 22.0 - - + -
298D ILE* 4.1 15.7 - - + -
300D ILE* 3.9 31.2 - - + -
333D MET* 3.8 44.4 - - + -
334D GLY 3.0 7.8 + - - +
336D VAL* 1.3 78.2 - - - +
338D MET* 1.3 62.9 + - + +
340D GLY* 3.0 18.9 + - - -
341D PHE* 3.2 22.2 - - + -
354D PHE* 4.5 6.5 - - + -
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Residues in contact with MET 338 (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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152D LEU* 3.7 37.0 - - + +
154D LEU* 3.9 26.2 + - + +
227D VAL* 4.0 17.9 - - + -
228D ASP 4.2 3.4 - - - +
229D SER* 3.7 33.0 - - - -
333D MET 4.3 4.7 - - - +
334D GLY 2.9 15.8 + - - +
335D ALA* 4.2 1.8 - - - +
337D ILE* 1.3 80.1 - - + +
339D GLU* 1.3 57.0 + - - +
340D GLY 3.1 0.9 - - - -
341D PHE 2.9 25.7 - - - +
343D VAL* 4.1 25.0 - - + +
345D PHE* 3.9 17.0 - - + -
354D PHE* 5.9 0.2 - - + -
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Residues in contact with GLU 339 (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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10D SER* 3.2 6.1 + - - -
14D TYR* 2.8 31.4 + - + +
154D LEU* 3.4 27.6 - - + +
156D GLY* 4.0 14.0 + - - +
303D GLN 5.4 1.2 - - - +
304D GLN* 4.5 17.2 - - + +
307D ARG* 2.4 41.7 + - - -
335D ALA* 2.8 27.5 + - + +
336D VAL 4.6 2.9 - - - +
337D ILE 3.2 0.4 + - - -
338D MET* 1.3 72.8 - - - +
340D GLY* 1.3 60.4 + - - +
341D PHE 4.7 0.2 - - - -
357D SER* 4.4 2.4 - - - -
359D CYS* 4.8 0.5 - - - +
360D HIS* 3.5 20.1 + - - +
361D VAL* 4.9 0.7 + - + +
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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