Contacts of the helix formed by residues 390 - 398 (chain A) in PDB entry 2VIF
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 THR 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A PRO 5.6 0.9 - - - +
389A ILE* 1.3 75.9 - - - +
391A ARG* 1.3 65.6 + - - +
392A TRP* 3.3 27.0 + - + +
393A GLU* 2.9 37.8 + - - +
394A ALA* 2.9 22.5 + - - +
409A ARG* 4.1 3.1 - - - +
412A SER* 4.3 17.3 - - - +
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Residues in contact with ARG 391 (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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390A THR* 1.3 74.6 - - - +
392A TRP* 1.3 113.5 + - + +
394A ALA 3.4 0.5 + - - -
395A GLU* 3.0 62.4 + - - +
409A ARG* 3.6 29.9 - - - +
412A SER* 5.0 1.3 + - - -
430A HIS* 3.4 12.0 - - + +
566P ASN* 3.0 39.8 + - - +
567P ASN* 3.3 15.6 - - - +
568P PTR 3.9 22.2 + - + +
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Residues in contact with TRP 392 (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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390A THR* 3.2 24.3 + - + +
391A ARG* 1.3 127.1 - - + +
393A GLU* 1.3 67.8 + - + +
395A GLU* 3.2 14.9 + - - +
396A GLY* 3.2 17.3 + - - -
412A SER* 5.6 5.6 - - - -
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Residues in contact with GLU 393 (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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388A PRO 4.1 3.9 - - - +
389A ILE* 3.3 23.9 - - + +
390A THR* 2.9 46.9 + - - +
392A TRP* 1.3 76.6 - - + +
394A ALA* 1.3 61.3 + - - +
396A GLY* 3.0 4.8 + - - -
397A LYS* 3.0 35.8 + - - +
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Residues in contact with ALA 394 (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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389A ILE* 4.1 13.1 - - + +
390A THR 2.9 16.0 + - - +
391A ARG 3.6 4.9 - - - +
392A TRP 3.3 0.2 - - - -
393A GLU* 1.3 76.7 - - - +
395A GLU* 1.3 63.1 + - - +
397A LYS* 3.1 5.5 + - - +
398A LEU* 3.0 29.4 + - - +
407A LEU* 4.4 4.7 - - + -
409A ARG* 3.8 12.6 - - - +
421A SER* 3.6 30.7 - - - +
428A THR* 4.7 0.9 - - - -
430A HIS* 4.3 0.7 - - + -
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Residues in contact with GLU 395 (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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391A ARG* 3.0 39.3 + - - +
392A TRP* 3.5 17.0 - - - +
393A GLU 3.2 0.2 - - - -
394A ALA* 1.3 75.6 - - - +
396A GLY* 1.3 62.4 + - - +
398A LEU 3.4 1.6 + - - -
399A ALA* 3.1 23.4 + - - +
423A ARG* 5.2 0.5 + - - -
428A THR* 3.9 23.9 + - - +
430A HIS* 2.8 28.2 + - + +
567P ASN* 3.0 24.8 + - - +
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Residues in contact with GLY 396 (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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392A TRP 3.2 8.1 + - - -
393A GLU* 3.0 8.6 + - - -
395A GLU* 1.3 77.0 - - - +
397A LYS* 1.3 62.1 + - - +
399A ALA* 3.2 20.3 + - - +
400A ASN 4.9 0.3 + - - -
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Residues in contact with LYS 397 (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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386A TRP* 3.5 48.8 - - + -
389A ILE* 4.5 7.6 - - + -
393A GLU* 3.0 34.4 + - - +
394A ALA* 3.1 8.9 + - - +
396A GLY* 1.3 76.6 - - - +
398A LEU* 1.3 62.5 + - + +
399A ALA 3.4 0.6 + - - -
400A ASN 4.9 1.2 + - - -
401A VAL* 4.1 14.0 - - - +
407A LEU* 4.2 10.1 - - + -
491A VAL* 4.6 5.0 - - - +
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Residues in contact with LEU 398 (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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394A ALA 3.0 16.1 + - - +
395A GLU 3.7 1.8 - - - -
397A LYS* 1.3 80.1 - - - +
399A ALA* 1.3 62.8 + - - +
400A ASN 3.2 4.1 + - - -
401A VAL* 3.5 20.4 + - + +
405A SER 4.5 7.4 - - - +
406A PHE 4.6 0.4 - - - +
407A LEU* 4.0 19.5 - - + -
421A SER* 3.7 30.3 - - - +
422A PHE* 3.9 7.9 - - - +
423A ARG* 3.3 20.9 - - + -
428A THR* 3.6 34.8 - - + +
491A VAL* 3.5 32.5 - - + -
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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