Contacts of the helix formed by residues 417 - 436 (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 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A VAL* 5.6 2.6 - - - +
386A ARG* 3.4 41.1 + - - +
412A TYR* 5.2 0.4 + - - -
415A THR 3.4 5.0 + - - +
416A ALA* 1.4 83.6 - - - +
418A TYR* 1.3 66.8 + - - +
419A SER* 3.6 10.3 + - - +
420A ILE* 3.9 5.4 + - + +
421A ARG* 3.5 10.9 + - - +
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Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA 5.1 1.1 - - - -
417A ASP* 1.3 72.7 - - - +
419A SER* 1.3 70.6 + - - +
420A ILE 3.0 4.0 + - - -
421A ARG* 3.2 40.9 + - - +
422A GLU* 4.3 1.7 + - - +
456A TYR* 4.1 16.9 + + - +
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Residues in contact with SER 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.6 22.9 - - - +
386A ARG* 4.1 3.6 + - - -
417A ASP* 3.6 14.9 + - - +
418A TYR* 1.3 74.4 - - - +
420A ILE* 1.3 74.7 + - - +
422A GLU* 4.6 7.8 + - - +
423A GLU* 3.7 9.6 - - - +
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 5.1 0.7 - - + -
383A VAL* 5.1 4.7 - - + +
386A ARG* 3.0 55.6 - - + +
387A GLN* 4.9 4.5 - - + +
390A VAL* 4.5 7.2 - - + -
412A TYR* 4.1 13.0 - - + +
416A ALA* 5.1 1.6 - - + -
417A ASP* 3.9 7.4 + - + +
418A TYR 3.1 1.0 - - - -
419A SER* 1.3 87.4 - - - +
421A ARG* 1.3 68.1 + - - +
422A GLU 3.2 2.5 - - - -
423A GLU* 3.1 31.1 + - + +
424A ILE* 3.2 34.2 + - + +
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Residues in contact with ARG 421 (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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413A LEU* 2.8 42.0 + - + +
414A GLU 3.9 10.1 + - - -
416A ALA* 3.6 15.1 + - + +
417A ASP 3.5 12.3 - - - +
418A TYR* 3.2 35.8 + - - +
420A ILE* 1.3 78.1 - - - +
422A GLU* 1.3 65.7 + - - +
424A ILE* 3.1 3.1 + - - +
425A VAL* 2.9 29.3 + - + +
452A ILE* 3.2 37.0 + - - +
453A ALA* 3.2 21.2 - - - +
456A TYR* 3.9 24.7 - - + -
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A TYR 4.3 1.9 + - - +
419A SER 5.0 7.1 - - - +
420A ILE 3.1 0.8 + - - -
421A ARG* 1.3 81.2 - - - +
423A GLU* 1.3 62.7 + - - +
425A VAL* 4.0 2.1 - - - +
426A LEU* 3.3 20.7 + - + +
456A TYR* 3.6 31.0 - - + +
288M ARG* 5.3 7.9 + - - +
290M ILE* 4.7 13.4 - - + +
308M LYS* 2.7 46.9 + - - +
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Residues in contact with GLU 423 (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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383A VAL* 5.9 0.7 - - - +
387A GLN* 2.6 48.9 + - - +
390A VAL* 5.2 6.3 - - + -
391A ASP* 5.3 2.9 - - - +
419A SER 3.7 7.9 + - - +
420A ILE* 3.1 38.6 + - + +
422A GLU* 1.3 80.6 - - - +
424A ILE* 1.3 59.2 + - + +
426A LEU* 3.3 10.3 + - - +
427A LYS* 3.1 45.6 + - - +
188M GLN* 4.5 5.4 - - - +
288M ARG* 5.2 8.4 + - - +
290M ILE* 5.9 7.0 - - + -
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Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 5.7 0.7 - - + -
390A VAL* 4.2 23.6 - - + -
409A MET* 3.9 33.7 - - + +
412A TYR* 3.5 30.5 - - + -
413A LEU* 4.1 23.3 - - + -
416A ALA* 5.0 0.9 - - + -
420A ILE* 3.2 36.3 + - + +
421A ARG 3.1 5.4 + - - +
423A GLU* 1.3 73.2 - - + +
425A VAL* 1.3 59.7 + - - +
426A LEU 3.0 1.6 - - - -
427A LYS* 2.8 25.7 + - - +
428A VAL* 2.9 19.9 + - + +
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Residues in contact with VAL 425 (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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413A LEU* 3.9 10.3 - - + -
421A ARG 2.9 22.8 + - - +
422A GLU 4.0 3.6 - - - +
424A ILE* 1.3 75.5 - - - +
426A LEU* 1.3 62.0 + - - +
428A VAL* 3.9 2.5 - - - +
429A ALA* 3.4 22.5 + - + +
449A LEU* 4.0 19.1 - - + +
453A ALA* 3.2 40.8 - - + +
456A TYR* 3.8 34.3 - - + +
457A VAL* 4.1 8.1 - - + -
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Residues in contact with LEU 426 (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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422A GLU 3.3 12.1 + - - +
423A GLU* 3.4 12.1 - - - +
424A ILE 3.0 0.6 - - - -
425A VAL* 1.3 80.8 - - - +
427A LYS* 1.3 67.2 + - + +
429A ALA* 3.9 4.6 - - + +
430A ILE* 3.1 47.5 + - + +
290M ILE* 3.8 45.3 - - + -
292M LEU* 5.0 6.1 - - + -
306M VAL* 4.1 19.7 - - + -
308M LYS* 5.3 7.0 - - - -
363M GLU* 3.9 22.2 - - - +
365M GLN* 5.2 1.1 - - - +
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Residues in contact with LYS 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A VAL* 3.8 23.0 - - + +
391A ASP* 2.6 41.8 + - - +
394A TYR* 3.4 37.0 - - + +
409A MET* 4.4 12.6 - - + -
423A GLU* 3.1 28.5 + - - +
424A ILE* 2.8 11.8 + - - +
426A LEU* 1.3 76.7 - - + +
428A VAL* 1.3 58.4 + - - +
430A ILE* 3.2 6.3 + - - +
431A LEU* 2.8 35.2 + - - +
290M ILE* 6.1 2.7 - - - -
292M LEU* 3.9 26.8 - - + +
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A VAL* 4.4 9.6 - - + -
409A MET* 3.8 33.7 - - + -
410A LEU* 4.3 15.0 - - + -
413A LEU* 5.0 0.7 - - + -
424A ILE* 2.9 25.6 + - + +
425A VAL* 3.9 6.1 - - - +
427A LYS* 1.3 73.1 - - - +
429A ALA* 1.3 70.4 + - - +
430A ILE 2.8 1.7 + - - -
431A LEU* 2.9 4.6 + - - +
432A ALA* 2.7 27.2 + - + +
445A THR* 3.9 24.9 - - + -
449A LEU* 3.7 19.1 - - + -
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 3.4 15.9 + - + +
426A LEU* 3.9 7.6 - - + +
428A VAL* 1.3 80.0 - - - +
430A ILE* 1.3 65.4 + - + +
432A ALA* 3.7 5.7 - - - +
433A GLU* 3.0 37.4 + - - +
446A ILE* 6.0 3.6 - - - -
449A LEU* 3.9 10.6 - - + +
457A VAL* 5.9 1.1 - - + -
461A VAL* 4.1 21.1 - - + -
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Residues in contact with ILE 430 (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 TYR* 4.4 13.2 - - + +
426A LEU* 3.1 32.0 + - + +
427A LYS* 3.2 8.6 + - - +
428A VAL 2.8 5.1 + - - -
429A ALA* 1.3 76.1 - - + +
431A LEU* 1.3 64.7 + - + +
433A GLU* 3.0 18.8 + - - +
434A LYS* 3.1 13.2 + - + +
292M LEU* 3.4 31.6 - - + -
302M GLU* 6.0 0.4 - - - +
304M LYS* 3.5 36.1 - - + +
306M VAL* 5.0 2.9 - - + -
365M GLN* 4.1 21.1 - - - +
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Residues in contact with LEU 431 (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 TYR* 4.2 28.3 - - + +
397A CYS* 3.3 40.2 - - + +
402A ALA* 5.7 0.7 - - + -
405A ILE* 4.2 7.4 - - + -
406A VAL* 4.2 17.0 - - + -
409A MET* 3.8 33.9 - - + -
427A LYS 2.8 24.0 + - - +
428A VAL* 2.9 2.4 + - - +
430A ILE* 1.3 69.1 - - + +
432A ALA* 1.3 70.5 + - - +
433A GLU 3.1 0.7 + - - -
434A LYS* 3.1 10.6 + - + +
435A TYR* 3.3 30.4 + - + +
294M ARG* 5.6 3.4 - - - +
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Residues in contact with ALA 432 (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* 4.7 8.0 - - + +
428A VAL* 2.7 22.4 + - + +
429A ALA* 3.7 7.4 - - - +
431A LEU* 1.3 76.8 - - - +
433A GLU* 1.3 57.3 + - + +
436A ALA* 3.0 35.4 + - + +
441A TRP* 5.3 5.2 - - - +
442A TYR* 4.6 20.2 - - + -
445A THR* 4.7 22.4 - - + +
446A ILE* 5.5 4.0 - - + -
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Residues in contact with GLU 433 (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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429A ALA* 3.0 22.0 + - - +
430A ILE* 3.0 11.6 + - + +
432A ALA* 1.3 79.4 - - - +
434A LYS* 1.3 60.5 + - - +
435A TYR 3.5 0.2 + - - -
436A ALA 5.1 0.5 + - - +
442A TYR* 2.8 42.9 + - + +
446A ILE* 5.0 0.9 - - - +
461A VAL* 3.7 26.3 - - - +
464A ARG* 5.0 12.5 + - - -
304M LYS* 6.6 0.2 - - - -
365M GLN* 4.3 15.8 + - - -
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Residues in contact with LYS 434 (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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430A ILE* 3.1 15.0 + - + +
431A LEU* 3.1 2.6 + - + +
433A GLU* 1.3 77.2 - - - +
435A TYR* 1.3 106.9 + - + +
294M ARG* 4.2 1.7 - - - +
302M GLU* 3.3 31.4 + - - +
304M LYS* 4.3 20.4 - - - +
369M GLU* 5.5 8.7 - - - -
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Residues in contact with TYR 435 (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* 2.9 48.9 + - - -
398A ASP* 3.6 8.1 - - + +
399A ARG* 3.7 40.0 - - + +
402A ALA* 3.8 19.6 - - + +
431A LEU* 3.3 26.6 + - + +
433A GLU 3.3 1.6 + - - -
434A LYS* 1.3 118.3 + - + +
436A ALA* 1.3 73.3 + - - +
437A VAL* 3.0 11.3 + - - +
294M ARG* 3.4 19.8 + - - -
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Residues in contact with ALA 436 (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* 5.5 1.5 - - - +
432A ALA* 3.0 22.2 + - - +
433A GLU 5.1 0.2 + - - -
435A TYR* 1.3 76.9 + - - +
437A VAL* 1.3 63.8 + - - +
438A ASP 3.3 4.6 + - - +
441A TRP* 3.4 35.4 - - + +
442A TYR* 4.3 19.7 - - + +
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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
------------------------------------------------------------
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