Contacts of the helix formed by residues 516 - 528 (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 ASN 516 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A TRP* 5.1 4.3 - - - -
463A TYR* 3.6 27.8 + - + +
478B THR* 3.8 30.6 + - + -
481B GLN* 6.1 0.2 - - - +
482B LEU* 5.4 5.7 - - - +
514B SER* 3.4 3.3 - - - +
515B ASP* 1.3 74.5 - - - +
517B PRO* 1.4 64.7 - - - +
518B ASP* 3.2 21.6 + - - +
519B LEU* 3.4 30.6 - - + +
520B ARG* 2.8 29.0 + - - +
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Residues in contact with PRO 517 (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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462A TRP* 5.0 8.3 - - + -
463A TYR* 3.7 26.5 - - + -
466A ILE* 4.4 27.8 - - + -
467A GLN 6.2 0.2 - - - +
502A TYR* 3.7 24.1 + - + +
602A MET* 5.5 0.2 - - - +
605A PHE* 5.4 9.0 - - + -
515B ASP 2.8 15.9 - - - +
516B ASN* 1.4 84.4 - - - +
518B ASP* 1.3 56.1 + - - +
519B LEU 3.5 0.2 - - - -
520B ARG* 3.9 13.0 - - + +
521B ASP* 3.4 29.3 + - - +
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Residues in contact with ASP 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A TRP* 6.2 2.5 - - + -
502A TYR* 5.3 0.2 - - - -
536A PRO 4.8 4.3 - - - +
539A ALA* 4.8 1.6 - - - -
540A LEU* 3.0 44.1 + - + +
543A SER* 4.7 2.5 + - - -
579A ARG* 2.9 43.7 + - - -
482B LEU* 4.3 8.5 - - - +
516B ASN* 3.2 14.3 + - - +
517B PRO* 1.3 76.8 - - - +
519B LEU* 1.3 64.2 + - - +
520B ARG 3.3 0.2 - - - -
521B ASP* 3.7 5.6 - - - +
522B ARG* 3.2 23.0 + - - +
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Residues in contact with LEU 519 (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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473B PHE* 4.9 4.9 - - + -
478B THR* 4.7 2.7 - - - +
481B GLN* 4.0 23.8 - - + +
482B LEU* 3.8 42.0 - - + +
485B LEU* 5.1 5.4 - - + -
510B ALA* 3.7 23.2 - - + +
514B SER* 3.2 33.4 - - - -
516B ASN* 3.0 27.7 + - + +
518B ASP* 1.3 76.4 + - - +
520B ARG* 1.3 57.2 + - - +
522B ARG* 3.3 4.1 + - + +
523B GLY* 2.7 32.9 + - - -
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Residues in contact with ARG 520 (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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470A ILE* 4.9 1.8 - - - +
602A MET* 3.7 13.2 + - + +
603A PRO 3.2 18.8 + - - -
604A PRO* 3.2 32.5 + - - +
605A PHE* 3.4 52.0 - - - +
606A PRO* 5.0 2.0 - - - +
510B ALA 3.0 13.4 + - - +
511B THR* 3.0 26.7 + - - +
512B GLN* 5.4 2.2 + - - +
514B SER 4.7 5.8 - - - +
516B ASN 2.8 15.6 + - - +
517B PRO* 3.9 9.6 - - + +
519B LEU* 1.3 77.1 - - - +
521B ASP* 1.3 51.9 + - - +
523B GLY* 3.7 0.5 - - - -
524B TYR* 2.8 58.9 + - + +
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Residues in contact with ASP 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A TYR* 3.0 23.9 + - - -
506A GLU* 4.5 1.0 - - - +
540A LEU* 5.5 1.1 - - + +
543A SER* 5.2 5.4 - - - +
547A LYS* 3.4 29.6 + - - -
602A MET* 2.8 46.7 - - - +
517B PRO 3.4 13.0 + - - +
518B ASP* 3.7 7.9 - - - +
520B ARG* 1.3 78.1 - - - +
522B ARG* 1.3 57.4 + - + +
524B TYR* 3.4 1.7 + - - +
525B ILE* 3.0 43.6 + - + +
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Residues in contact with ARG 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A SER* 4.4 3.6 - - - +
575A GLU* 4.0 6.3 + - - -
578A GLN* 3.7 9.3 - - - +
579A ARG* 3.3 48.6 - - - +
582A GLU* 3.2 29.7 + - - -
583A TYR* 3.0 34.6 + - - +
482B LEU* 3.4 27.6 - - + +
485B LEU* 5.5 0.9 - - - -
486B THR* 3.5 10.1 + - - -
518B ASP* 3.2 14.9 + - - +
519B LEU* 3.3 2.4 + - + +
521B ASP* 1.3 76.3 - - + +
523B GLY* 1.3 64.2 + - - +
525B ILE* 3.7 8.1 - - + +
526B TYR* 3.3 56.5 + - + -
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Residues in contact with GLY 523 (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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485B LEU* 4.1 11.6 - - - +
507B LEU* 3.7 7.9 - - - +
510B ALA* 3.7 22.0 - - - +
511B THR* 3.4 8.0 + - - -
519B LEU 2.7 21.5 + - - -
520B ARG 3.7 1.1 - - - -
522B ARG* 1.3 69.7 - - - +
524B TYR* 1.3 66.2 + - - +
526B TYR* 3.3 6.9 + - - +
527B TRP* 3.1 14.6 + - - +
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Residues in contact with TYR 524 (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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602A MET* 3.6 25.4 - - + -
603A PRO* 3.4 48.0 + - + +
604A PRO 4.3 2.4 + - - -
511B THR* 2.7 34.7 + - + +
512B GLN* 3.9 7.1 + - - -
520B ARG* 2.8 48.7 + - + +
521B ASP* 3.6 4.7 - - - +
523B GLY* 1.3 67.4 - - - +
525B ILE* 1.3 70.4 + - - +
526B TYR 2.7 2.8 + - - -
527B TRP* 2.7 31.8 + + + +
528B ARG* 2.9 28.9 + - + +
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Residues in contact with ILE 525 (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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543A SER* 4.9 4.0 - - - +
547A LYS* 6.2 0.4 - - - -
583A TYR* 3.2 42.6 - - + +
586A LEU* 5.1 4.5 - - + -
598A VAL* 3.9 35.3 - - + +
599A LEU* 4.4 14.1 - - + -
521B ASP* 3.0 36.1 + - + +
522B ARG* 3.7 9.4 - - + +
524B TYR* 1.3 74.3 - - - +
526B TYR* 1.3 79.9 + - + +
528B ARG* 3.5 12.6 - - - +
529B LEU* 3.3 21.8 - - + +
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Residues in contact with TYR 526 (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* 4.2 0.2 + - - -
582A GLU* 2.7 28.9 + - - -
485B LEU* 4.4 13.2 - - + -
486B THR* 2.6 40.2 + - - +
489B VAL* 3.7 39.5 - - + -
507B LEU* 4.0 10.8 - - + -
522B ARG* 3.3 28.5 + - + -
523B GLY 3.3 7.5 + - - +
524B TYR 2.7 4.4 + - - -
525B ILE* 1.3 85.5 - - + +
527B TRP* 1.3 55.3 + - - +
528B ARG 3.0 0.9 - - - -
529B LEU* 2.3 38.2 + - + +
530B LEU* 3.0 13.3 + - + -
541B VAL* 4.6 17.4 - - + +
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Residues in contact with TRP 527 (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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507B LEU* 3.6 26.9 - - + +
511B THR* 4.9 7.9 - - + +
512B GLN* 4.8 14.8 - - + -
523B GLY 3.1 11.6 + - - +
524B TYR* 2.7 33.3 + + + +
526B TYR* 1.3 70.0 - - - +
528B ARG* 1.3 55.6 + - + +
529B LEU 3.0 5.5 + - - -
530B LEU* 4.6 2.7 - - + +
531B SER* 3.3 49.2 + - - +
532B THR* 3.8 7.4 + - - -
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Residues in contact with ARG 528 (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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597A THR* 3.3 29.4 + - + +
598A VAL* 3.1 33.3 + - - +
599A LEU* 4.3 0.2 - - - +
600A GLU* 3.4 45.7 + - - +
602A MET* 4.1 10.9 - - - +
603A PRO* 2.9 40.3 - - - +
524B TYR* 2.9 30.4 + - + +
525B ILE* 3.5 12.7 - - - +
526B TYR 3.3 0.4 - - - -
527B TRP* 1.3 73.6 - - + +
529B LEU* 1.3 66.5 + - - +
532B THR* 3.7 16.3 + - - +
533B ASP* 5.4 0.7 - - - +
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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