Contacts of the helix formed by residues 398 - 416 (chain A) in PDB entry 2VGL
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 ASP 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A HIS* 4.1 6.2 + - - +
367A LYS* 2.5 31.0 + - - -
396A MET 3.7 3.1 - - - +
397A CYS* 1.3 74.8 - - - +
399A ARG* 1.3 61.4 + - + +
400A SER* 2.7 19.6 + - - -
401A ASN* 2.6 22.2 + - - +
402A ALA* 2.6 36.8 + - - +
435A TYR* 3.6 18.4 - - + +
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A ASP* 1.3 76.5 - - + +
400A SER* 1.3 64.0 + - - +
402A ALA* 3.7 9.5 + - - +
403A GLN* 4.8 4.2 + - - +
435A TYR* 3.7 29.8 - - + +
437A VAL* 6.0 8.7 - - + +
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Residues in contact with SER 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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367A LYS* 3.4 18.0 + - - +
398A ASP* 2.7 24.0 + - - -
399A ARG* 1.3 81.2 - - - +
401A ASN* 1.3 65.0 + - - +
403A GLN* 4.4 5.0 + - - +
404A GLN* 4.9 2.8 + - - +
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Residues in contact with ASN 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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367A LYS* 4.3 16.2 - - - +
370A ILE* 3.8 17.6 - - + +
396A MET* 2.7 32.3 + - - +
398A ASP* 2.6 25.4 + - - +
400A SER* 1.3 85.1 + - - +
402A ALA* 1.3 67.7 + - - +
403A GLN 3.2 0.2 - - - -
404A GLN* 2.7 22.6 + - - +
405A ILE* 2.9 35.0 + - + +
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Residues in contact with ALA 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 CYS* 3.7 17.7 - - - -
398A ASP 2.6 21.3 + - - +
399A ARG* 4.2 5.8 - - - +
400A SER 3.4 2.2 - - - -
401A ASN* 1.3 69.3 - - - +
403A GLN* 1.3 60.3 + - + +
405A ILE* 4.6 0.7 - - - -
406A VAL* 2.9 39.8 + - + +
431A LEU* 5.3 1.6 - - + +
435A TYR* 3.8 29.6 - - + +
436A ALA* 5.5 0.4 - - - +
441A TRP* 5.4 3.8 - - - +
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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 ARG 4.8 3.8 + - - +
400A SER 4.4 3.9 + - - +
401A ASN 2.8 2.4 + - - -
402A ALA* 1.3 73.0 - - + +
404A GLN* 1.3 69.4 + - - +
406A VAL* 4.1 0.3 - - - +
407A ALA* 3.0 24.6 + - - +
437A VAL* 5.6 6.5 - - - +
438A ASP* 4.8 9.5 + - - -
441A TRP* 4.3 49.2 - - + +
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Residues in contact with GLN 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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370A ILE* 3.7 32.0 - - + +
371A GLU* 5.3 10.8 - - - +
374A ILE* 3.5 23.0 - - - +
400A SER 4.9 2.3 + - - +
401A ASN* 2.7 17.2 + - - +
403A GLN* 1.3 77.7 - - - +
405A ILE* 1.3 61.2 + - - +
407A ALA* 3.2 11.7 + - - +
408A GLU* 3.2 32.2 + - + +
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Residues in contact with ILE 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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370A ILE* 3.7 21.5 - - + -
374A ILE* 4.9 4.3 - - - -
393A LEU* 3.7 25.8 - - + +
396A MET* 4.6 3.6 - - + -
397A CYS* 3.2 28.0 - - + +
401A ASN* 2.9 39.7 + - + +
402A ALA* 3.9 3.6 - - - +
404A GLN* 1.3 75.8 - - - +
406A VAL* 1.3 53.1 + - - +
408A GLU* 3.1 6.9 + - - +
409A MET* 2.7 64.0 + - + +
431A LEU* 4.2 9.4 - - + -
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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 ALA* 2.9 25.9 + - + +
405A ILE* 1.3 72.6 - - - +
407A ALA* 1.3 64.9 + - - +
409A MET* 3.7 8.3 - - - +
410A LEU* 3.0 28.1 + - + +
428A VAL* 4.4 10.5 - - + -
431A LEU* 4.2 30.5 - - + -
432A ALA* 4.7 8.3 - - + +
441A TRP* 3.7 24.5 - - + +
445A THR* 3.6 30.7 - - + -
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Residues in contact with ALA 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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403A GLN 3.0 20.8 + - - +
404A GLN* 3.2 6.7 + - - +
406A VAL* 1.3 77.8 - - - +
408A GLU* 1.3 62.3 + - + +
410A LEU* 3.5 7.5 + - - +
411A SER* 2.9 27.1 + - - -
441A TRP* 4.9 8.7 - - + -
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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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374A ILE* 3.4 45.9 - - + +
377A LEU* 6.3 1.6 - - + -
378A LYS* 4.9 13.6 + - - +
393A LEU* 6.3 1.6 - - + -
404A GLN* 3.3 29.5 + - + +
405A ILE 3.1 6.1 + - - +
407A ALA* 1.3 77.9 - - + +
409A MET* 1.3 58.7 + - - +
411A SER* 3.5 12.1 + - - -
412A TYR* 2.7 36.8 + - - +
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Residues in contact with MET 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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377A LEU* 6.0 5.6 - - + -
390A VAL* 4.3 22.7 - - + +
393A LEU* 4.1 24.0 - - + +
394A TYR* 4.5 4.5 - - - +
405A ILE* 2.7 37.7 + - + +
406A VAL* 3.7 7.0 - - - +
408A GLU* 1.3 75.9 - - - +
410A LEU* 1.3 57.3 + - - +
412A TYR* 3.3 6.3 + - - +
413A LEU* 2.9 30.3 + - - +
424A ILE* 3.9 20.1 - - + +
427A LYS* 4.4 13.0 - - + -
428A VAL* 3.8 27.1 - - + -
431A LEU* 3.8 26.2 - - + -
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Residues in contact with LEU 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* 3.0 27.4 + - + +
407A ALA* 3.8 6.3 - - - +
409A MET* 1.3 73.4 - - - +
411A SER* 1.3 65.5 + - - +
413A LEU* 3.3 25.0 + - + +
414A GLU* 3.5 12.6 + - - +
428A VAL* 4.3 10.3 - - + -
441A TRP* 5.4 4.3 - - + -
445A THR* 3.4 35.7 - - + +
448A ASN* 4.9 11.4 - - + -
449A LEU* 4.0 41.3 - - + +
452A ILE* 5.3 2.6 - - + +
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Residues in contact with SER 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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378A LYS* 5.7 5.9 - - - +
407A ALA 2.9 18.5 + - - -
408A GLU* 3.2 17.6 + - - -
410A LEU* 1.3 77.6 - - - +
412A TYR* 1.3 65.7 + - - +
414A GLU* 3.3 18.7 + - - +
415A THR* 4.3 3.6 + - - +
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Residues in contact with TYR 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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377A LEU* 3.5 48.8 + - + -
378A LYS* 4.2 22.7 - - + -
380A GLU 4.8 0.7 + - - -
386A ARG* 3.4 33.8 + - - -
408A GLU 2.7 21.9 + - - +
409A MET* 3.4 5.8 - - - +
411A SER* 1.3 74.5 - - - +
413A LEU* 1.3 61.7 + - - +
414A GLU 3.1 1.2 + - - -
415A THR* 3.2 10.7 + - - -
416A ALA* 3.0 44.0 + - + +
417A ASP 5.2 0.3 + - - -
420A ILE* 4.3 7.6 - - + -
424A ILE* 3.5 28.9 - - + -
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Residues in contact with LEU 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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409A MET 2.9 12.2 + - - +
410A LEU* 3.4 22.9 - - + +
411A SER 3.3 0.2 - - - -
412A TYR* 1.3 76.5 - - - +
414A GLU* 1.3 59.7 + - - +
415A THR 3.2 0.9 + - - -
416A ALA* 3.3 11.0 + - + -
421A ARG* 2.8 76.8 + - + +
424A ILE* 4.1 21.8 - - + -
425A VAL* 3.9 11.4 - - + +
428A VAL* 5.0 0.7 - - + -
449A LEU* 3.9 28.7 - - + -
452A ILE* 3.9 10.1 - - + -
453A ALA* 4.1 7.0 - - + -
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Residues in contact with GLU 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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410A LEU 3.7 13.6 - - - +
411A SER* 3.3 11.0 + - - +
412A TYR 3.1 2.0 + - - -
413A LEU* 1.3 76.7 - - - +
415A THR* 1.3 66.1 + - + +
421A ARG* 3.9 8.0 + - - -
451A ARG* 3.6 19.0 + - - -
452A ILE* 3.0 43.1 - - + +
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Residues in contact with THR 415 (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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411A SER 4.3 3.1 + - - +
412A TYR* 3.2 11.7 + - - -
414A GLU* 1.3 85.2 - - + +
416A ALA* 1.3 66.0 + - - +
417A ASP* 3.4 5.4 + - - +
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Residues in contact with ALA 416 (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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412A TYR* 3.0 49.0 + - + +
413A LEU* 3.3 21.5 + - + +
415A THR* 1.3 77.7 - - - +
417A ASP* 1.4 72.2 + - - +
418A TYR* 5.1 1.9 - - - -
420A ILE* 5.1 3.1 - - + -
421A ARG* 3.6 16.5 + - + -
424A ILE* 5.0 2.7 - - + -
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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