Contacts of the helix formed by residues 524 - 543 (chain B) in PDB entry 2VGB
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 ILE 524 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B GLU* 3.9 5.3 - - - +
523B ALA* 1.3 78.0 - - + +
525B TRP* 1.3 67.7 + - - +
526B ALA* 3.9 15.9 - - + +
527B ASP* 3.0 41.6 + - - +
528B ASP 3.2 8.3 + - - -
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Residues in contact with TRP 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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522B GLU 5.1 1.8 - - - -
523B ALA 3.4 6.0 + - - -
524B ILE* 1.3 71.0 - - - +
526B ALA* 1.3 67.1 + - + +
528B ASP* 2.8 32.6 + - + +
529B VAL* 2.9 32.0 + - + +
532B ARG* 3.9 10.5 - - - +
557B GLY 3.3 23.6 - - - -
558B TRP 3.5 17.3 - - - -
559B ARG* 3.4 17.3 - - - -
560B PRO* 3.4 38.2 - - + +
580B FBP 2.9 33.7 + - - -
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Residues in contact with ALA 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B ILE* 3.3 12.4 - - + +
525B TRP* 1.3 86.1 - - + +
527B ASP* 1.3 62.8 + - - +
529B VAL* 3.3 11.2 + - - +
530B ASP* 3.0 28.3 + - - +
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Residues in contact with ASP 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B GLU* 4.3 13.4 - - + +
524B ILE* 3.0 41.9 + - - +
526B ALA* 1.3 74.4 - - - +
528B ASP* 1.3 66.9 + - - +
530B ASP* 3.1 11.5 + - - +
531B ARG* 2.9 42.2 + - - +
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Residues in contact with ASP 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ARG* 2.9 42.2 + - - -
517B TYR* 4.8 3.8 + - - -
520B PRO 4.1 1.2 - - - +
521B PRO* 3.1 6.2 - - - +
522B GLU* 2.9 41.4 + - - +
524B ILE 3.2 4.0 + - - +
525B TRP* 2.8 22.4 + - + +
527B ASP* 1.3 73.3 - - - +
529B VAL* 1.3 65.9 + - - +
531B ARG* 3.5 3.5 + - - +
532B ARG* 3.1 42.8 + - - +
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Residues in contact with VAL 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B LEU* 3.8 20.6 - - + +
525B TRP* 2.9 51.6 + - + +
526B ALA* 3.4 10.5 - - - +
528B ASP* 1.3 74.9 - - - +
530B ASP* 1.3 72.3 + - - +
532B ARG* 3.1 21.5 + - - +
533B VAL* 3.1 23.3 + - + +
556B THR* 4.1 18.6 - - + +
557B GLY 5.6 1.3 - - - +
569B ARG* 5.1 3.1 - - - +
580B FBP 5.0 1.1 - - - +
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Residues in contact with ASP 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B ALA* 3.0 20.2 + - - +
527B ASP* 3.1 12.9 + - - +
529B VAL* 1.3 83.3 - - - +
531B ARG* 1.3 53.0 + - + +
533B VAL* 3.2 7.2 + - - +
534B GLN* 2.7 47.8 + - - +
569B ARG* 4.6 12.3 + - - -
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Residues in contact with ARG 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B TYR* 3.6 18.5 - - + +
522B GLU* 3.2 41.9 + - + +
527B ASP* 2.9 37.8 + - - +
528B ASP* 3.8 3.4 - - - +
530B ASP* 1.3 70.9 - - + +
532B ARG* 1.3 53.5 + - - +
534B GLN* 3.6 7.2 - - - +
535B PHE* 2.7 35.1 + - - +
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Residues in contact with ARG 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B LEU* 4.2 25.2 - - + +
475B THR 6.0 0.2 - - - +
496B VAL* 4.0 23.7 + - + +
497B THR* 6.0 2.8 - - - +
498B ARG* 3.6 21.9 - - - +
517B TYR* 3.7 31.2 - - + -
525B TRP* 3.9 11.5 - - - +
528B ASP* 3.1 34.5 + - - +
529B VAL* 3.1 21.3 + - - +
531B ARG* 1.3 78.1 - - - +
533B VAL* 1.3 64.5 + - - +
535B PHE* 3.1 9.9 + - - +
536B GLY* 2.9 19.9 + - - -
580B FBP 2.6 47.2 + - - -
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 4.4 10.0 - - + +
474B LEU* 3.8 19.7 - - + +
529B VAL* 3.1 15.9 + - + +
530B ASP* 3.6 8.7 - - - +
532B ARG* 1.3 75.4 - - - +
534B GLN* 1.3 69.5 + - - +
536B GLY* 3.1 11.6 + - - -
537B ILE* 3.1 25.2 + - + +
554B VAL* 3.7 42.8 - - + -
556B THR* 4.2 5.8 - - + -
569B ARG* 4.1 11.9 - - - +
571B LEU* 4.6 8.1 - - + -
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Residues in contact with GLN 534 (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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530B ASP* 2.7 34.2 + - - +
531B ARG* 3.6 8.7 - - - +
533B VAL* 1.3 77.7 - - - +
535B PHE* 1.3 62.1 + - - +
537B ILE* 3.0 40.2 + - + +
538B GLU* 2.9 29.7 + - - +
571B LEU* 5.6 3.3 - - - +
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Residues in contact with PHE 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 4.3 26.2 - - + -
146B LEU* 3.9 23.8 - - + -
496B VAL* 4.2 11.2 - - + -
515B LEU* 3.9 22.0 - - + -
516B LEU 3.6 25.8 - - - -
517B TYR* 3.5 33.7 - + + -
518B ARG 5.7 0.4 - - - -
531B ARG 2.7 18.4 + - - +
532B ARG 3.2 8.1 - - - +
534B GLN* 1.3 73.0 - - - +
536B GLY* 1.3 55.6 + - - +
538B GLU* 3.4 7.1 + - + +
539B SER* 2.5 45.1 + - - -
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Residues in contact with GLY 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 4.3 10.3 - - - -
494B ILE* 4.4 9.3 - - - +
496B VAL* 4.0 18.4 - - - -
515B LEU* 4.1 8.8 - - - +
532B ARG 2.9 12.9 + - - -
533B VAL 3.1 4.6 + - - -
535B PHE* 1.3 74.3 - - - +
537B ILE* 1.3 52.0 + - - +
539B SER* 3.7 5.3 - - - -
540B GLY* 2.7 32.6 + - - -
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Residues in contact with ILE 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 3.7 18.6 - - + +
533B VAL* 3.1 19.3 + - + +
534B GLN* 3.0 36.7 + - + +
536B GLY* 1.3 71.6 - - - +
538B GLU* 1.3 55.7 + - - +
540B GLY* 2.9 3.1 + - - -
541B LYS* 2.6 56.5 + - + +
546B LEU* 3.8 9.4 - - + +
552B VAL* 5.1 1.3 - - + -
571B LEU* 4.9 11.0 - - + -
573B ILE* 3.8 33.9 - - + -
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Residues in contact with GLU 538 (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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146B LEU* 4.2 28.2 - - + +
534B GLN* 2.9 19.4 + - - +
535B PHE* 3.7 11.1 - - - +
537B ILE* 1.3 75.4 - - - +
539B SER* 1.3 64.4 + - - +
541B LYS* 2.9 13.6 + - + +
542B LEU* 2.9 23.3 + - - +
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Residues in contact with SER 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO 5.7 0.2 - - - -
146B LEU* 3.9 29.5 - - - +
515B LEU* 3.1 30.9 - - - +
535B PHE* 2.5 41.2 + - - -
536B GLY 3.7 0.2 - - - -
538B GLU* 1.3 72.3 - - - +
540B GLY* 1.3 64.2 + - - +
542B LEU* 3.3 2.4 + - - +
543B ARG* 2.9 35.1 + - - +
545B PHE* 5.5 0.2 - - - -
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Residues in contact with GLY 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ILE* 4.5 3.4 - - - -
515B LEU* 4.9 0.4 - - - +
536B GLY 2.7 16.1 + - - -
537B ILE 2.9 6.2 + - - -
539B SER* 1.3 79.3 - - - +
541B LYS* 1.3 65.1 + - - +
543B ARG* 3.1 7.1 + - - -
545B PHE* 3.1 31.2 + - - +
546B LEU* 3.9 20.6 - - - -
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Residues in contact with LYS 541 (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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537B ILE* 2.6 37.0 + - + +
538B GLU* 2.9 13.2 + - + +
540B GLY* 1.3 68.9 - - - +
542B LEU* 1.3 58.7 + - - +
544B GLY* 2.9 22.2 + - - -
546B LEU* 3.5 23.5 + - + +
547B ARG* 5.3 4.5 - - - -
548B VAL* 5.2 14.5 - - + +
573B ILE* 4.3 22.9 + - + +
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Residues in contact with LEU 542 (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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144B SER* 6.1 0.9 - - - +
146B LEU* 3.4 48.5 - - + +
147B SER* 4.2 13.5 - - - -
538B GLU 2.9 11.9 + - - +
539B SER 3.6 8.1 - - - +
541B LYS* 1.3 78.9 - - - +
543B ARG* 1.3 59.4 + - + +
544B GLY 3.3 2.8 + - - -
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Residues in contact with ARG 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO 4.0 5.3 + - - -
146B LEU 2.8 30.5 + - - +
147B SER* 3.6 16.5 + - - +
148B TYR 3.1 25.3 + - - +
149B ARG* 4.8 9.3 - - - +
150B PRO* 5.7 1.0 - - - +
513B PHE* 5.8 2.2 - - - +
514B PRO 4.8 2.2 + - - -
515B LEU* 3.4 32.9 - - - +
539B SER* 2.9 20.4 + - - +
540B GLY 3.1 2.0 + - - +
542B LEU* 1.3 76.3 - - + +
544B GLY* 1.3 62.8 + - - +
545B PHE* 3.4 41.0 + - + -
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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