Contacts of the helix formed by residues 399 - 414 (chain A) in PDB entry 2VKT
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 CYS 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A GLY* 4.2 5.8 - - - -
373A PHE* 5.3 6.1 - - - -
398A VAL* 1.3 70.1 - - + +
400A LEU* 1.3 70.6 + - - +
402A MET* 2.8 21.7 + - - +
403A GLN* 3.1 13.8 + - - -
479A ARG 3.9 15.9 - - - -
480A HIS* 4.0 12.3 - - - -
523A VAL 2.5 16.5 + - - -
524A GLN* 3.3 35.5 - - - +
526A HIS* 3.7 29.4 - - + -
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Residues in contact with LEU 400 (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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370A PRO 5.4 0.4 - - - +
371A GLY* 4.5 0.9 - - - -
372A GLY 3.7 26.7 - - - +
373A PHE* 4.5 2.9 - - + -
374A GLY 3.5 30.1 - - - +
378A THR* 5.1 2.0 - - - +
381A LYS* 4.6 14.1 - - - +
398A VAL 3.1 1.4 + - - +
399A CYS* 1.3 84.1 - - - +
401A GLY* 1.3 55.3 + - - +
403A GLN* 3.4 26.1 + - + +
404A LEU* 3.0 48.2 + - + +
421A SER* 6.0 0.7 - - - +
423A GLU* 4.3 7.0 - - - +
424A PHE* 4.0 23.3 - - + -
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Residues in contact with GLY 401 (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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369A VAL* 3.8 32.1 - - - -
370A PRO 4.4 3.0 + - - -
385A ILE* 4.1 4.9 - - - +
395A PHE* 4.4 0.2 - - - -
397A GLY* 3.9 10.9 - - - -
398A VAL 3.0 12.8 + - - -
400A LEU* 1.3 76.4 - - - +
402A MET* 1.3 61.9 + - - +
404A LEU* 3.6 4.9 + - - +
405A ALA* 3.2 21.7 + - - +
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Residues in contact with MET 402 (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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397A GLY 3.8 7.5 - - - -
399A CYS 2.8 10.9 + - - +
401A GLY* 1.3 73.5 - - - +
403A GLN* 1.3 69.6 + - + +
405A ALA* 3.2 8.3 + - - +
406A VAL* 3.1 30.4 + - + +
484A VAL* 4.1 20.6 - - + -
509A MET 3.7 11.2 - - - +
510A GLU 3.9 13.7 - - - +
511A ILE 4.3 1.3 - - - -
512A ILE* 4.1 14.8 - - + -
522A GLY* 3.5 11.7 - - - +
523A VAL 3.3 30.5 - - - +
524A GLN* 3.6 43.3 - - + -
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Residues in contact with GLN 403 (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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399A CYS* 3.1 22.2 + - - +
400A LEU* 3.6 28.0 - - + +
401A GLY 3.3 0.2 - - - -
402A MET* 1.3 83.5 - - + +
404A LEU* 1.3 60.2 + - - +
406A VAL* 3.3 9.1 + - - +
407A ILE* 3.2 29.2 + - + +
421A SER* 5.1 0.5 + - - -
423A GLU* 4.2 4.0 - - - +
433A VAL* 3.8 22.9 - - + +
480A HIS* 4.8 3.0 - - - +
482A PHE* 3.5 38.4 + - - +
483A GLU* 5.7 1.3 - - - -
484A VAL* 6.0 2.2 - - + +
524A GLN* 3.1 28.2 + - - +
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Residues in contact with LEU 404 (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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369A VAL* 5.1 0.4 - - + -
378A THR* 3.9 29.8 - - + +
381A LYS* 3.8 38.8 - - + -
382A LEU* 3.4 22.8 - - + +
385A ILE* 3.9 15.5 - - + -
400A LEU* 3.0 43.5 + - + +
401A GLY* 4.0 4.5 - - - +
403A GLN* 1.3 74.8 - - - +
405A ALA* 1.3 57.9 + - - +
407A ILE* 3.3 15.7 + - + +
408A GLU* 2.9 25.6 + - - +
424A PHE* 4.7 5.8 - - + -
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Residues in contact with ALA 405 (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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385A ILE* 3.8 17.2 - - + +
395A PHE* 4.2 11.0 - - + -
401A GLY 3.2 13.6 + - - +
402A MET* 3.2 11.2 + - - +
404A LEU* 1.3 75.4 - - - +
406A VAL* 1.3 62.0 + - - +
408A GLU* 3.5 2.5 + - - +
409A PHE* 3.2 23.6 + - - +
497A LEU* 4.9 0.9 - - - +
512A ILE* 4.2 13.2 - - + -
520A PHE* 4.1 25.7 - - + -
522A GLY* 5.9 0.2 - - - -
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Residues in contact with VAL 406 (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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402A MET* 3.1 28.5 + - + +
403A GLN* 3.5 10.5 - - - +
404A LEU 3.2 0.2 - - - -
405A ALA* 1.3 74.7 - - - +
407A ILE* 1.3 64.1 + - - +
409A PHE* 3.3 4.7 + - - +
410A ALA* 3.1 21.5 + - - +
432A LEU* 3.9 23.3 - - + -
433A VAL* 5.0 2.9 - - + -
484A VAL* 4.3 20.9 - - + -
492A PHE* 4.2 16.3 - - + -
497A LEU* 4.5 10.5 - - + -
499A PHE* 4.6 3.4 - - + -
512A ILE* 3.8 28.3 - - + -
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Residues in contact with ILE 407 (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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382A LEU* 4.4 8.1 - - + -
403A GLN* 3.2 16.0 + - + +
404A LEU* 3.3 22.6 + - + +
406A VAL* 1.3 75.1 - - - +
408A GLU* 1.3 60.4 + - - +
410A ALA* 3.2 2.6 + - - +
411A ARG* 2.9 62.3 + - - +
419A ALA 3.6 8.5 - - - +
420A ASP* 4.1 9.2 - - - +
421A SER* 4.0 33.0 - - - +
424A PHE* 5.9 0.9 - - + -
432A LEU* 3.8 15.7 - - + -
433A VAL* 4.1 13.9 - - + -
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Residues in contact with GLU 408 (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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382A LEU* 4.0 25.4 - - + +
385A ILE* 4.0 15.1 - - + +
386A SER* 2.5 35.8 + - - +
389A ARG* 2.5 45.3 + - - -
404A LEU 2.9 17.6 + - - +
405A ALA 3.9 5.2 - - - +
407A ILE* 1.3 76.5 - - - +
409A PHE* 1.3 58.7 + - - +
411A ARG* 3.8 6.0 - - - +
412A ASN* 2.8 39.1 + - - +
520A PHE* 5.6 0.2 - - - -
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Residues in contact with PHE 409 (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 ARG* 4.3 9.0 - - - -
405A ALA 3.2 16.3 + - - +
406A VAL 3.6 4.3 - - - +
407A ILE 3.1 0.4 - - - -
408A GLU* 1.3 83.3 + - - +
410A ALA* 1.3 59.8 + - - +
413A CYS* 2.8 63.9 + - + +
414A LEU* 3.2 24.7 + - + -
492A PHE* 3.9 19.3 - + - -
495A ASN* 4.1 12.6 - - + -
496A ASP* 4.0 12.3 - - + -
497A LEU* 3.7 40.6 - - + -
514A LEU* 3.6 29.2 - - + -
520A PHE* 6.3 2.2 - + + -
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Residues in contact with ALA 410 (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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406A VAL 3.1 8.0 + - - +
407A ILE 3.2 3.8 + - - +
409A PHE* 1.3 75.1 - - - +
411A ARG* 1.3 57.9 + - - +
414A LEU* 3.1 16.1 + - - +
415A ASN 2.9 27.4 + - - -
416A LEU* 3.2 21.7 + - + -
419A ALA* 3.9 10.3 - - + -
432A LEU* 3.6 31.9 - - + -
492A PHE* 4.4 7.4 - - + -
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Residues in contact with ARG 411 (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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379A LEU* 6.1 1.4 - - - +
382A LEU* 3.7 26.6 - - - +
407A ILE* 2.9 31.0 + - - +
408A GLU* 3.8 7.0 - - - +
410A ALA* 1.3 79.0 - - - +
412A ASN* 1.3 68.2 + - - +
415A ASN* 3.4 6.1 - - - +
416A LEU 3.5 19.0 + - - +
417A LYS* 3.1 47.8 + - - +
418A ASP* 5.0 2.0 + - - +
419A ALA* 2.8 29.4 + - + +
420A ASP* 3.6 23.6 + - - -
425A ARG* 4.9 5.1 - - - +
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Residues in contact with ASN 412 (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 SER* 3.8 7.3 + - - -
389A ARG* 4.0 17.2 + - - +
408A GLU* 2.8 40.2 + - - +
411A ARG* 1.3 91.2 - - - +
413A CYS* 1.3 64.9 + - - +
415A ASN* 4.0 9.7 - - - +
417A LYS* 3.9 10.8 + - - +
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Residues in contact with CYS 413 (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 ARG* 3.6 36.8 - - - -
409A PHE* 2.8 54.8 + - + +
412A ASN* 1.3 74.6 - - - +
414A LEU* 1.3 58.5 + - - +
415A ASN* 3.4 6.4 + - - -
495A ASN* 3.8 12.7 - - - +
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Residues in contact with LEU 414 (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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409A PHE* 3.2 11.3 + - + -
410A ALA* 3.1 18.5 + - + +
413A CYS* 1.3 75.1 - - - +
415A ASN* 1.3 70.1 + - - +
416A LEU* 3.3 15.5 + - + +
491A GLN* 3.3 34.5 - - + +
492A PHE* 3.7 41.5 - - + -
495A ASN* 3.5 37.9 - - + +
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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
------------------------------------------------------------
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