Contacts of the helix formed by residues 389 - 395 (chain D) in PDB entry 2VK8
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 389 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387D GLU 4.0 0.7 - - - -
388D THR* 1.3 79.6 - - - +
390D THR* 1.3 66.4 + - - -
391D SER 3.1 4.5 + - - -
392D ALA* 3.3 5.1 + - - +
393D PHE* 3.3 20.2 - - - -
476D ILE* 3.7 25.8 - - - +
549D LEU* 4.3 0.7 - - - -
1564D TPP 3.6 16.4 - - - -
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Residues in contact with THR 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D GLN* 2.9 35.5 + - - +
371D TRP* 4.1 1.0 - - - -
389D GLY* 1.3 71.0 - - - -
391D SER* 1.3 57.2 + - - +
393D PHE 3.3 0.9 + - - -
394D GLY* 2.8 28.6 + - - -
469D LEU* 3.9 5.4 - - - +
475D THR* 3.9 14.8 - - - +
544D ASP 4.0 1.1 - - - +
545D ALA* 3.9 16.8 - - + -
546D PRO* 3.7 6.8 - - - +
549D LEU* 3.8 24.0 - - + +
1564D TPP 2.6 36.2 + - - +
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Residues in contact with SER 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D TRP* 3.6 16.1 - - - -
386D ALA* 3.8 3.2 - - - +
387D GLU* 3.4 14.6 - - - -
389D GLY 3.1 0.8 - - - -
390D THR* 1.3 79.3 + - - +
392D ALA* 1.3 57.9 + - - +
394D GLY* 3.7 0.2 - - - -
395D ILE* 2.9 33.4 + - - +
441D PHE* 3.6 32.2 + - - +
442D ILE* 4.1 4.4 + - - -
443D GLY* 4.4 2.2 + - - -
469D LEU* 3.3 24.1 - - - +
1564D TPP 4.6 0.7 + - - -
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Residues in contact with ALA 392 (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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246D PRO* 5.8 0.2 - - - +
386D ALA* 4.0 10.5 - - - +
387D GLU 2.9 28.5 + - - +
388D THR* 3.9 11.7 - - - +
389D GLY 3.3 4.0 + - - +
391D SER* 1.3 73.0 - - - +
393D PHE* 1.3 69.9 + - + +
395D ILE* 3.4 15.6 - - - +
396D ASN* 3.9 9.7 + - - +
408D SER* 3.7 21.0 + - - +
410D VAL* 5.8 3.7 - - + +
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Residues in contact with PHE 393 (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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267D LEU* 5.9 1.8 - - + -
292D PHE* 3.9 46.9 - + + -
388D THR* 5.9 1.8 - - + -
389D GLY 3.3 15.7 - - - +
390D THR 3.3 5.7 + - - +
391D SER 3.2 0.4 - - - -
392D ALA* 1.3 84.3 - - + +
394D GLY* 1.3 63.9 + - - +
396D ASN* 3.4 14.6 - - - +
397D GLN* 3.2 6.6 - - - +
476D ILE* 3.8 12.6 - - + -
546D PRO* 3.9 4.5 - - + -
548D ASN* 3.1 36.7 + - + +
549D LEU* 3.6 47.8 - - + -
552D GLN* 3.8 26.7 - - + -
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Residues in contact with GLY 394 (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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371D TRP* 3.3 50.1 - - - +
390D THR 2.8 11.9 + - - -
393D PHE* 1.3 73.7 - - - +
395D ILE* 1.3 59.2 + - - +
396D ASN 3.1 2.7 - - - -
397D GLN* 2.9 23.5 + - - +
546D PRO* 3.6 7.8 - - - +
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Residues in contact with ILE 395 (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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249D LYS* 3.4 16.0 - - + -
371D TRP* 3.9 9.9 - - + -
374D LEU* 3.7 21.3 - - + -
384D VAL* 3.8 21.8 - - + +
386D ALA* 3.8 20.2 - - + -
391D SER 2.9 15.2 + - - +
392D ALA* 3.4 16.2 - - - +
394D GLY* 1.3 77.7 - - - +
396D ASN* 1.3 67.4 + - - +
398D THR* 3.0 32.9 + - - +
400D PHE* 4.0 19.3 - - + -
408D SER* 4.9 9.9 - - - +
441D PHE* 5.2 2.0 - - + -
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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