Contacts of the helix formed by residues 477 - 493 (chain B) 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 SER 477 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PRO* 3.5 34.8 - - - +
475B ASP 4.2 1.4 + - - -
476B GLU* 1.3 72.4 - - - +
478B THR* 1.3 62.9 + - - +
479B GLN* 3.6 17.9 + - - +
480B VAL* 2.8 33.8 + - - +
481B GLN* 3.4 1.6 + - - +
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Residues in contact with THR 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLU* 5.3 1.1 - - - +
463A TYR* 4.2 19.1 - - - +
536A PRO* 5.8 3.5 - - - +
476B GLU 3.9 5.6 - - - +
477B SER* 1.3 72.9 + - - +
479B GLN* 1.3 64.9 + - - +
481B GLN* 3.1 19.1 + - - +
482B LEU* 3.0 33.5 + - - +
516B ASN* 3.8 23.4 + - + +
519B LEU* 4.7 2.6 - - - +
362M LYS* 5.3 11.0 - - - +
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Residues in contact with GLN 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A VAL* 4.0 27.3 - - - +
536A PRO* 4.3 21.6 - - + +
573A ASP* 4.7 7.8 - - - +
575A GLU* 5.0 10.2 - - + +
443B ASP* 5.9 4.2 + - - +
446B ALA* 4.2 5.9 - - + +
477B SER* 3.0 12.4 + - - +
478B THR* 1.3 82.9 + - - +
480B VAL* 1.3 58.9 + - - +
482B LEU* 4.0 14.7 - - + +
483B THR* 3.4 24.3 + - - -
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PRO* 4.1 7.4 + - + +
445B ARG* 3.8 28.9 - - + -
446B ALA* 4.0 15.0 - - - +
449B ILE* 4.1 13.6 - - + +
476B GLU* 3.1 46.0 - - + +
477B SER* 2.8 28.8 + - - +
479B GLN* 1.3 78.2 - - - +
481B GLN* 1.3 60.4 + - + +
483B THR* 3.5 3.0 + - - -
484B LEU* 2.9 24.0 + - + +
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Residues in contact with GLN 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 2.7 60.4 + - + +
474B HIS* 3.7 13.8 - - - +
476B GLU* 3.4 20.2 + - - +
477B SER 3.7 6.7 - - - +
478B THR* 3.1 18.5 + - - +
480B VAL* 1.3 81.5 - - + +
482B LEU* 1.3 57.3 + - - +
483B THR 3.0 0.9 - - - -
484B LEU* 3.0 8.3 + - - +
485B LEU* 2.7 38.3 + - - +
514B SER* 4.9 3.5 - - - -
516B ASN* 6.1 0.2 - - - +
519B LEU* 4.0 23.1 - - + +
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO* 6.1 4.9 - - + -
539A ALA* 5.5 0.7 - - + -
575A GLU* 3.1 35.3 - - + +
579A ARG* 3.5 19.7 - - - +
478B THR* 3.0 20.6 + - - +
479B GLN* 4.0 15.3 - - + +
481B GLN* 1.3 76.2 - - - +
483B THR* 1.3 59.3 + - - +
485B LEU* 3.6 4.3 + - + +
486B THR* 3.3 27.8 + - - +
516B ASN* 5.4 5.8 - - - +
518B ASP* 4.3 7.6 - - - +
519B LEU* 3.8 20.4 - - + +
522B ARG* 3.4 36.8 - - + +
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Residues in contact with THR 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 4.4 18.8 - - - +
575A GLU* 4.5 4.8 + - - -
415B ARG* 5.9 0.2 + - - -
446B ALA* 3.4 35.5 + - - +
449B ILE* 3.2 23.3 - - + -
450B TRP* 3.8 9.0 - - + +
479B GLN 3.4 17.5 + - - -
480B VAL 3.7 4.0 - - - +
481B GLN 3.0 0.8 - - - -
482B LEU* 1.3 75.9 - - - +
484B LEU* 1.3 65.2 + - - +
486B THR* 4.2 3.5 - - - +
487B ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 3.7 27.3 - - + +
466B LEU* 4.6 10.5 - - + +
469B PHE* 4.3 20.9 - - + -
470B LEU* 4.1 18.8 - - + -
473B PHE* 3.3 37.2 - - + -
480B VAL* 2.9 16.8 + - + +
481B GLN* 3.4 8.7 - - - +
483B THR* 1.3 77.0 - - - +
485B LEU* 1.3 64.1 + - + +
487B ALA* 3.4 1.7 + - - +
488B ILE* 2.9 49.8 + - + +
506B VAL* 4.8 2.9 - - + -
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 4.9 8.7 - - + -
481B GLN 2.7 22.1 + - - +
482B LEU* 4.0 6.1 - - + +
484B LEU* 1.3 76.8 - - + +
486B THR* 1.3 68.4 + - - +
488B ILE* 2.9 15.2 + - - +
489B VAL* 3.1 15.6 + - + +
506B VAL* 3.0 34.3 - - + -
507B LEU* 4.6 19.1 - - + +
510B ALA* 3.3 33.9 - - + -
519B LEU* 5.1 5.4 - - + -
522B ARG 6.4 0.2 - - - -
523B GLY* 4.1 14.4 - - - +
526B TYR* 4.4 12.8 - - + -
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Residues in contact with THR 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 6.3 2.2 - - + -
575A GLU* 4.7 3.6 + - - +
578A GLN* 3.0 33.3 - - + +
450B TRP* 5.7 6.3 - - + -
482B LEU* 3.3 15.4 + - - +
483B THR* 4.5 4.0 - - - +
485B LEU* 1.3 76.6 - - - +
487B ALA* 1.3 57.8 + - + +
489B VAL* 3.2 5.2 - - + +
490B LYS* 3.1 37.6 + - + +
522B ARG* 3.5 13.7 + - - -
526B TYR* 2.6 32.1 + - - +
541B VAL* 6.0 0.9 - - + -
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Residues in contact with ALA 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 3.6 32.8 - - + +
450B TRP* 4.7 3.8 - - + -
452B VAL 4.9 0.9 - - - +
453B GLY* 3.9 14.6 - - - -
456B ALA* 6.0 0.2 - - - +
466B LEU* 4.0 9.3 - - + +
483B THR 3.0 21.3 + - - +
484B LEU 3.6 1.1 - - - +
485B LEU 3.0 1.2 - - - -
486B THR* 1.3 78.6 - - + +
488B ILE* 1.3 58.9 + - - +
489B VAL 3.4 0.9 - - - -
490B LYS* 3.9 11.4 - - + +
491B LEU* 3.5 19.2 + - - +
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Residues in contact with ILE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B LEU* 3.4 37.0 - - + -
470B LEU* 4.9 4.7 - - + -
484B LEU* 2.9 28.3 + - + +
485B LEU 2.9 9.0 + - - +
487B ALA* 1.3 72.3 - - - +
489B VAL* 1.3 60.9 + - + +
490B LYS 3.5 0.4 - - - -
491B LEU* 3.8 11.3 - - + +
492B PHE 3.5 12.8 + - - -
499B THR* 5.2 2.0 - - + -
502B LEU* 5.3 7.6 - - + -
503B VAL* 3.5 32.4 - - + +
506B VAL* 3.3 42.4 - - + -
507B LEU* 5.7 0.9 - - + -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LEU* 3.1 12.8 + - + +
486B THR* 3.2 16.4 - - + +
488B ILE* 1.3 77.8 - - + +
490B LYS* 1.3 62.9 + - - +
491B LEU 3.2 0.4 - - - -
492B PHE* 3.9 3.5 - - - +
493B LEU* 3.4 30.6 + - + +
506B VAL* 6.5 0.2 - - + -
507B LEU* 4.1 26.9 - - + -
526B TYR* 3.7 44.6 - - + -
530B LEU* 4.3 18.6 - - + +
541B VAL* 4.9 12.0 - - + +
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Residues in contact with LYS 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A GLN* 4.3 13.3 + - - +
450B TRP* 3.5 24.3 - - + +
453B GLY* 3.7 28.6 - - - +
454B GLU* 2.6 40.3 + - - +
456B ALA* 4.7 3.7 - - - +
486B THR* 3.1 35.7 + - + +
487B ALA* 3.8 6.9 + - + +
489B VAL* 1.3 78.5 - - - +
491B LEU* 1.3 59.4 + - - +
493B LEU* 4.2 4.1 + - - +
494B LYS* 4.1 19.2 + - - +
541B VAL* 4.5 10.3 - - + -
542B LEU* 3.9 30.1 - - + +
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B VAL 5.9 0.9 - - - +
453B GLY 5.1 0.2 + - - -
456B ALA* 4.7 15.3 - - + -
462B ALA* 4.0 29.6 - - + +
463B ASP* 4.1 15.7 - - - +
466B LEU* 4.1 13.9 - - + -
487B ALA 3.5 14.7 + - - +
488B ILE* 3.9 10.5 - - + +
489B VAL 3.2 0.2 - - - -
490B LYS* 1.3 79.2 - - - +
492B PHE* 1.3 58.3 + - - +
494B LYS* 3.5 4.1 + - - +
495B LYS* 3.0 33.0 + - + +
499B THR* 2.9 49.8 - - + +
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Residues in contact with PHE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ILE 3.5 12.3 + - - +
489B VAL 3.9 0.6 - - - -
490B LYS 3.5 0.4 - - - -
491B LEU* 1.3 76.4 - - - +
493B LEU* 1.3 54.0 + - - +
494B LYS 2.6 24.8 + - - +
495B LYS 3.7 5.8 + - - +
496B PRO* 4.1 22.6 - - + +
499B THR* 3.3 30.3 - - + -
500B GLN* 3.0 36.3 - - + -
503B VAL* 3.7 12.8 - - + -
530B LEU* 3.3 46.7 - - + -
534B PRO* 6.5 0.9 - - + -
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B VAL* 3.4 20.5 + - + +
490B LYS 4.6 2.0 - - - +
491B LEU 3.5 0.6 - - - -
492B PHE* 1.3 76.2 - - - +
494B LYS* 1.3 62.0 + - - +
530B LEU* 4.5 12.8 - - + +
534B PRO 3.6 19.1 - - - +
537B ALA* 3.6 22.9 - - + +
538B LYS* 3.2 66.5 + - + +
541B VAL* 4.0 20.4 - - + -
542B LEU* 4.2 17.6 - - + +
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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
------------------------------------------------------------
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