Contacts of the helix formed by residues 519 - 535 (chain B) in PDB entry 2VZE
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 519 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517B SER 3.8 2.2 + - - -
518B HIS* 1.3 71.5 - - - +
520B PRO* 1.4 72.2 - - - +
521B GLU* 3.2 31.4 + - - +
522B GLN* 3.8 26.9 + - + +
523B LEU* 3.0 28.3 + - - +
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Residues in contact with PRO 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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518B HIS 3.1 9.8 - - - +
519B ASP* 1.4 90.6 - - - +
521B GLU* 1.3 54.9 + - + +
523B LEU* 4.6 2.2 - - + -
524B THR* 2.5 37.9 + - - +
546B PHE* 3.7 25.5 - - + -
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Residues in contact with GLU 521 (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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519B ASP* 3.2 22.2 + - - +
520B PRO* 1.3 76.4 - - + +
522B GLN* 1.3 66.7 + - + +
524B THR* 3.1 6.7 + - - -
525B LYS* 2.9 29.8 + - + +
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Residues in contact with GLN 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ASP* 3.4 27.0 + - + +
521B GLU* 1.3 79.3 - - + +
523B LEU* 1.3 57.9 + - - +
525B LYS* 3.5 7.7 + - - +
526B GLU* 3.1 28.3 + - - +
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Residues in contact with LEU 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 HIS* 5.0 0.2 - - + -
487B ALA* 4.4 5.6 - - + -
511B LEU* 3.6 37.2 - - + -
515B PHE* 4.1 26.0 - - + +
518B HIS* 3.9 26.2 - - + +
519B ASP 3.0 17.7 + - - +
520B PRO* 4.3 2.7 - - + +
522B GLN* 1.3 74.5 - - - +
524B THR* 1.3 65.2 + - - +
526B GLU* 4.1 19.5 - - - +
527B LEU* 3.0 45.2 + - + +
546B PHE* 4.0 13.7 - - + -
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Residues in contact with THR 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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520B PRO* 2.5 26.5 + - - +
521B GLU* 3.1 8.3 + - - +
523B LEU* 1.3 77.0 - - - +
525B LYS* 1.3 64.2 + - + +
526B GLU 3.3 0.2 + - - -
527B LEU* 3.3 2.1 + - - +
528B GLN* 3.0 50.1 + - - +
542B ARG 5.8 0.2 - - - +
544B ILE* 3.8 31.1 + - + +
546B PHE* 3.7 15.6 - - - -
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Residues in contact with LYS 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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521B GLU* 2.9 20.7 + - + +
522B GLN* 3.8 7.0 - - - +
524B THR* 1.3 77.7 - - + +
526B GLU* 1.3 56.9 + - - +
528B GLN* 3.4 15.6 + - - +
529B GLN* 2.8 30.3 + - - +
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Residues in contact with GLU 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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485B HIS* 3.1 31.3 + - - +
515B PHE* 5.3 3.0 - - - -
518B HIS* 4.9 8.5 + - - -
522B GLN 3.1 17.7 + - - +
523B LEU* 3.8 18.4 - - - +
524B THR 3.2 0.2 - - - -
525B LYS* 1.3 74.3 - - - +
527B LEU* 1.3 64.0 + - - +
529B GLN* 3.4 6.6 + - - +
530B HIS* 3.1 23.4 + - - +
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Residues in contact with LEU 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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482B LEU* 4.2 7.8 - - + +
485B HIS* 3.6 44.4 - - + +
487B ALA* 4.6 1.1 - - + -
488B VAL* 4.1 21.3 - - + -
509B VAL* 4.3 7.0 - - + -
511B LEU* 4.7 2.2 - - + -
523B LEU* 3.0 29.9 + - + +
526B GLU* 1.3 74.9 - - - +
528B GLN* 1.3 61.9 + - - +
530B HIS* 3.4 7.0 + - + +
531B VAL* 3.2 28.6 + - - +
541B PRO* 5.5 0.2 - - - -
544B ILE* 3.6 20.9 - - + -
546B PHE* 3.7 30.7 - - + -
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Residues in contact with GLN 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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524B THR* 3.0 39.4 + - - +
525B LYS* 3.6 15.6 - - - +
527B LEU* 1.3 73.9 - - - +
529B GLN* 1.3 63.7 + - - +
531B VAL* 3.3 4.0 + - - +
532B LYS* 3.1 30.8 + - - +
540B TYR* 3.7 24.3 + - + -
541B PRO* 2.9 33.5 + - + +
542B ARG* 3.3 19.8 + - - +
543B LYS* 4.8 1.0 - - - +
544B ILE* 4.0 9.5 - - + +
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Residues in contact with GLN 529 (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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525B LYS 2.8 20.5 + - - +
526B GLU* 3.4 7.2 + - - +
528B GLN* 1.3 72.0 - - - +
530B HIS* 1.3 56.8 + - - +
532B LYS* 3.4 14.7 + - + +
533B SER* 3.0 28.8 + - - -
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Residues in contact with HIS 530 (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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481B ALA 2.8 30.7 + - - -
482B LEU* 4.6 3.1 - - + -
484B GLU* 4.1 17.9 - - + -
485B HIS* 3.8 40.3 + + + -
526B GLU* 3.1 17.6 + - + +
527B LEU* 3.6 7.6 - - - +
528B GLN 3.1 0.2 - - - -
529B GLN* 1.3 76.0 - - - +
531B VAL* 1.3 69.4 + - + +
533B SER* 2.9 21.5 + - - -
534B VAL* 3.2 30.0 - - + +
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Residues in contact with VAL 531 (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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478B VAL* 4.6 8.7 - - + +
481B ALA* 4.3 11.0 - - + -
482B LEU* 3.8 29.8 - - + -
527B LEU 3.2 15.8 + - - +
528B GLN 3.3 5.1 + - - +
530B HIS* 1.3 81.1 - - + +
532B LYS* 1.3 63.4 + - - +
534B VAL* 3.2 6.6 + - - +
535B THR* 3.1 42.8 + - + +
536B ALA 5.6 0.2 - - - +
539B LYS* 4.6 0.9 - - + +
540B TYR* 3.8 24.7 - - + +
541B PRO* 3.9 15.7 - - + -
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Residues in contact with LYS 532 (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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141B LYS* 3.1 15.2 + - - -
528B GLN* 3.1 19.5 + - - +
529B GLN* 3.6 14.7 - - - +
530B HIS 3.3 0.2 - - - -
531B VAL* 1.3 78.3 - - - +
533B SER* 1.3 55.8 + - - +
535B THR 3.1 17.2 - - - +
537B PRO* 4.0 27.4 - - + +
540B TYR* 3.8 50.8 + - + -
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Residues in contact with SER 533 (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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141B LYS* 3.6 21.3 - - - +
529B GLN 3.0 13.5 + - - -
530B HIS* 2.9 22.6 + - - -
532B LYS* 1.3 78.8 - - - +
534B VAL* 1.3 66.3 + - - +
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Residues in contact with VAL 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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141B LYS* 3.8 12.1 - - - +
143B THR* 4.2 19.8 + - - +
144B ASP* 4.4 1.0 - - - +
481B ALA* 3.7 28.9 - - + -
484B GLU* 3.8 22.9 - - - +
530B HIS* 3.2 32.5 - - + +
531B VAL* 3.6 4.9 - - - +
533B SER* 1.3 86.0 - - - +
535B THR* 1.3 63.1 + - + +
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Residues in contact with THR 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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141B LYS* 3.7 6.6 - - - +
144B ASP* 2.9 27.2 + - - -
477B GLU* 5.0 4.5 + - - +
478B VAL* 5.8 0.2 - - - -
481B ALA* 4.3 12.3 - - + -
531B VAL* 3.1 34.0 + - + +
532B LYS 3.1 17.7 - - - +
533B SER 3.7 0.4 - - - -
534B VAL* 1.3 80.0 - - - +
536B ALA* 1.3 66.8 + - - +
537B PRO* 3.2 1.2 - - - +
539B LYS* 3.0 37.0 + - + +
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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
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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