Contacts of the helix formed by residues 521 - 539 (chain B) in PDB entry 5VND
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 THR 521 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B PHE* 5.0 7.6 - - + -
516B LEU* 4.9 1.0 - - - +
519B ASP 4.2 7.4 - - - +
520B ALA* 1.3 78.2 - - - +
522B GLU* 1.3 65.3 + - - +
523B LYS* 3.1 17.8 + - - +
524B ASP* 2.8 29.6 + - - +
525B LEU* 3.2 12.1 + - - +
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Residues in contact with GLU 522 (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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460B VAL* 3.4 27.9 + - + +
461B SER* 5.4 1.1 - - - +
462B GLU* 3.1 43.3 - - + +
521B THR* 1.3 71.9 - - - +
523B LYS* 1.3 66.7 + - - +
525B LEU* 3.5 12.7 + - + +
526B SER* 3.1 24.8 + - - -
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Residues in contact with LYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B THR* 3.1 9.4 + - - +
522B GLU* 1.3 81.3 + - - +
524B ASP* 1.3 65.5 + - - +
526B SER* 2.8 27.2 + - - +
527B ASP* 3.0 45.4 + - - +
647B ASP* 5.3 10.6 + - - -
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Residues in contact with ASP 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B PHE* 3.2 46.4 - - + +
516B LEU* 3.8 8.7 - - + +
520B ALA* 3.3 13.5 - - + -
521B THR* 2.8 34.9 + - - +
523B LYS* 1.3 79.8 - - - +
525B LEU* 1.3 56.9 + - - +
527B ASP* 3.2 13.8 + - - +
528B LEU* 2.9 29.3 + - - +
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Residues in contact with LEU 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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461B SER* 3.4 38.6 - - - +
462B GLU* 4.8 2.7 - - - +
465B LEU* 4.3 7.6 - - + -
516B LEU* 3.9 27.4 - - + +
521B THR 3.2 7.8 + - - +
522B GLU* 3.6 15.5 - - + +
524B ASP* 1.3 78.5 - - - +
526B SER* 1.3 61.7 + - - +
528B LEU* 3.2 1.7 + - + +
529B ILE* 3.0 38.3 + - + +
557B LEU* 3.9 30.1 - - + -
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Residues in contact with SER 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B VAL* 6.4 2.0 - - - -
461B SER* 5.5 3.3 + - - -
522B GLU* 3.1 15.3 + - - -
523B LYS* 2.8 32.2 + - - +
525B LEU* 1.3 78.6 - - - +
527B ASP* 1.3 58.2 + - - +
529B ILE* 3.8 11.8 - - - +
530B SER* 2.9 32.2 + - - -
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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
----------------------------------------------------------
523B LYS* 3.0 53.1 + - - +
524B ASP* 3.5 14.1 - - - +
526B SER* 1.3 75.6 + - - +
528B LEU* 1.3 65.5 + - - +
530B SER* 3.5 7.6 + - - -
531B GLU* 3.0 23.3 + - - +
645B ALA* 5.4 11.1 - - + +
647B ASP* 5.3 3.6 - - - +
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LYS* 3.7 35.9 - - + +
515B MET* 4.0 33.0 - - - -
516B LEU* 4.1 17.3 - - + +
524B ASP 2.9 16.4 + - - +
525B LEU* 3.2 4.2 + - - +
527B ASP* 1.3 73.5 - - - +
529B ILE* 1.3 65.3 + - - +
531B GLU* 3.3 8.0 + - - +
532B MET* 3.1 21.0 + - - +
557B LEU* 3.7 28.3 - - + +
559B VAL* 3.8 14.6 - - + -
801B 9ES 4.7 2.7 - - - -
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Residues in contact with ILE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B SER* 3.7 31.9 - - - +
465B LEU* 3.9 16.8 - - + -
466B PRO* 5.7 4.3 - - + -
525B LEU* 3.0 28.3 + - + +
526B SER* 3.8 7.6 - - - +
528B LEU* 1.3 76.0 - - - +
530B SER* 1.3 59.0 - - - +
532B MET* 3.3 14.5 + - + +
533B GLU* 2.9 42.4 + - + +
557B LEU* 3.8 18.8 - - + -
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Residues in contact with SER 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B SER 2.9 19.4 + - - -
527B ASP* 3.5 10.1 + - - -
529B ILE* 1.3 78.7 - - - +
531B GLU* 1.3 56.9 + - - +
533B GLU* 3.8 6.1 - - - +
534B MET* 2.9 33.0 + - - +
643B GLY 5.0 1.3 - - - -
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Residues in contact with GLU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LYS* 3.1 40.9 + - - -
527B ASP 3.0 13.5 + - - +
528B LEU* 3.6 10.5 - - + +
529B ILE 3.3 0.2 - - - -
530B SER* 1.3 78.5 - - - +
532B MET* 1.3 63.7 + - - +
534B MET* 3.4 2.3 + - - +
535B MET* 3.0 31.1 + - - +
643B GLY* 3.8 27.3 - - - +
644B LEU* 3.2 25.3 - - + +
801B 9ES 3.3 27.7 - - - +
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Residues in contact with MET 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B LEU* 5.6 2.0 - - + -
528B LEU 3.1 12.0 + - - +
529B ILE* 3.5 21.8 - - + +
531B GLU* 1.3 77.2 - - - +
533B GLU* 1.3 72.7 + - + +
535B MET* 3.2 8.1 + - - +
536B LYS* 3.0 46.1 + - - +
547B LEU* 4.0 11.9 - - + +
550B ALA* 3.6 30.7 - - - -
552B THR* 4.3 9.9 - - + -
557B LEU* 4.3 16.4 - - + -
559B VAL* 4.1 30.9 - - + +
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Residues in contact with GLU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ASP* 5.4 0.3 - - - +
529B ILE* 2.9 34.7 + - + +
530B SER* 3.8 6.3 - - - +
532B MET* 1.3 83.6 - - + +
534B MET* 1.3 66.1 + - - +
536B LYS* 2.7 44.4 + - - +
537B MET* 3.0 30.9 + - + +
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Residues in contact with MET 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 SER 2.9 17.7 + - - +
531B GLU 3.6 4.9 - - - +
533B GLU* 1.3 76.4 - - - +
535B MET* 1.3 61.8 + - - +
537B MET* 3.1 12.8 + - + +
538B ILE* 2.9 42.3 + - + +
618B LYS 5.8 0.2 - - - +
619B CYS* 4.2 21.3 - - + -
620B ILE 5.4 3.4 - - - +
622B ARG* 5.9 3.6 - - - +
642B PHE 4.0 19.7 - - - +
643B GLY* 4.0 22.0 - - - +
644B LEU 4.9 5.4 - - - +
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Residues in contact with MET 535 (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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531B GLU* 3.0 23.0 + - + +
532B MET* 3.2 7.6 + - - +
534B MET* 1.3 75.0 - - - +
536B LYS* 1.3 63.2 + - - +
538B ILE* 3.3 7.6 + - - +
539B GLY* 3.2 21.1 + - - +
545B ILE 3.5 25.1 - - - +
546B ASN* 4.5 0.2 - - - -
547B LEU* 3.6 39.1 - - + +
561B VAL* 3.9 17.3 - - + -
642B PHE* 4.0 17.9 - - + -
643B GLY* 4.9 3.6 - - - -
801B 9ES 3.9 43.3 - - - +
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Residues in contact with LYS 536 (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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468B ASP* 2.9 33.2 + - - +
470B ARG* 4.9 4.3 - - - +
471B TRP* 3.5 45.7 - - + +
532B MET* 3.0 37.7 + - - +
533B GLU* 2.7 42.4 + - - +
535B MET* 1.3 78.9 - - - +
537B MET* 1.3 60.8 + - - +
538B ILE 3.4 0.2 + - - -
539B GLY* 3.5 9.7 + - - -
547B LEU* 3.6 14.6 - - + +
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Residues in contact with MET 537 (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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533B GLU* 3.0 21.3 + - + +
534B MET* 3.4 12.3 - - - +
536B LYS* 1.3 77.5 - - - +
538B ILE* 1.3 63.4 + - + +
539B GLY* 4.5 0.3 - - - -
617B LYS* 4.9 6.5 + - - +
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Residues in contact with ILE 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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534B MET* 2.9 40.4 + - + +
535B MET* 3.9 4.9 - - - +
536B LYS 3.3 0.4 - - - -
537B MET* 1.3 78.3 - - + +
539B GLY* 1.3 60.8 + - - +
544B ILE* 4.2 4.9 - - + -
613B TYR* 2.6 37.7 + - + -
614B LEU* 3.8 21.8 - - + -
617B LYS* 3.5 33.3 - - + +
619B CYS* 3.9 20.2 - - + -
642B PHE* 3.9 25.8 - - + -
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Residues in contact with GLY 539 (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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535B MET 3.2 13.3 + - - +
536B LYS 3.5 8.2 + - - -
537B MET 3.4 3.0 - - - -
538B ILE* 1.3 83.9 - - - +
540B LYS* 1.3 65.8 + - - -
544B ILE* 3.6 18.4 - - - +
546B ASN* 4.1 1.7 - - - +
613B TYR* 3.5 4.2 + - - -
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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