Contacts of the helix formed by residues 519 - 535 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A HIS* 1.3 69.0 - - - +
520A PRO* 1.3 68.3 - - - +
521A GLU* 2.9 37.0 + - - +
522A GLN* 3.7 26.1 + - + +
523A LEU* 2.8 30.8 + - - +
102C GLY 4.2 0.2 - - - -
104C GLN* 3.6 29.3 - - + +
107C ASP* 5.2 5.4 - - - +
155C LYS* 5.3 7.0 + - - -
178C ARG* 4.1 10.2 + - - -
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Residues in contact with PRO 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A HIS 3.0 11.8 - - - +
519A ASP* 1.3 88.6 - - - +
521A GLU* 1.3 51.2 + - - +
523A LEU* 4.5 2.5 - - + -
524A THR* 2.7 38.8 + - - -
546A PHE* 3.7 25.7 - - + -
101C CYS 4.6 4.3 - - - +
102C GLY* 3.9 8.7 - - - +
178C ARG* 3.3 36.1 - - + +
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Residues in contact with GLU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ASP* 2.9 23.6 + - - +
520A PRO* 1.3 72.7 - - - +
522A GLN* 1.3 63.3 + - - +
524A THR* 3.3 7.4 + - - -
525A LYS* 3.1 53.2 + - - +
155C LYS* 4.4 16.5 - - - -
178C ARG* 4.7 14.2 + - - +
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Residues in contact with GLN 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ASP* 3.1 26.1 + - + +
521A GLU* 1.3 80.8 - - - +
523A LEU* 1.3 57.9 + - - +
525A LYS* 3.4 12.2 + - + +
526A GLU* 3.0 28.7 + - + +
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A HIS* 4.8 0.7 - - + -
487A ALA* 4.4 7.6 - - + -
511A LEU* 3.6 36.8 - - + -
515A PHE* 3.7 40.8 - - + +
518A HIS* 4.2 13.9 + - + +
519A ASP 2.8 16.8 + - - +
520A PRO* 4.0 4.5 - - + +
522A GLN* 1.3 74.1 - - - +
524A THR* 1.3 67.1 + - - +
526A GLU* 3.3 22.7 + - - +
527A LEU* 2.9 32.6 + - + +
546A PHE* 3.9 14.6 - - + -
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Residues in contact with THR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A PRO 2.7 23.0 + - - -
521A GLU* 3.5 7.1 - - - -
523A LEU* 1.3 76.4 - - - +
525A LYS* 1.3 64.6 + - + +
527A LEU* 3.1 3.6 + - - +
528A GLN* 2.9 42.9 + - - +
543A LYS* 5.7 0.2 - - - -
544A ILE* 3.7 41.1 + - + +
546A PHE* 3.6 16.1 - - - -
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Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLU* 3.1 44.9 + - - +
522A GLN* 3.7 12.3 - - + +
523A LEU 3.4 0.2 - - - -
524A THR* 1.3 77.4 - - - +
526A GLU* 1.3 56.5 + - - +
528A GLN* 3.1 16.7 + - - +
529A GLN* 2.8 32.4 + - - +
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Residues in contact with GLU 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A HIS* 2.7 35.2 + - + +
515A PHE* 5.1 3.8 - - - -
518A HIS* 5.1 6.4 + - - -
522A GLN* 3.0 18.2 + - + +
523A LEU* 3.3 23.1 + - + +
525A LYS* 1.3 75.7 - - - +
527A LEU* 1.3 57.7 + - - +
529A GLN* 3.4 5.7 + - - +
530A HIS* 2.8 28.2 + - + +
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A LEU* 4.3 10.4 - - + +
485A HIS* 3.4 46.9 - - + +
487A ALA* 4.6 2.2 - - + -
488A VAL* 3.9 20.9 - - + -
509A VAL* 4.7 7.9 - - + -
511A LEU* 5.0 2.5 - - + -
523A LEU* 2.9 28.2 + - + +
524A THR 3.1 0.2 + - - -
526A GLU* 1.3 76.9 - - - +
528A GLN* 1.3 62.2 + - - +
530A HIS* 3.3 5.9 + - + +
531A VAL* 3.0 28.4 + - - +
544A ILE* 3.8 22.7 - - + -
546A PHE* 4.0 25.8 - - + -
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Residues in contact with GLN 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A THR* 2.9 35.3 + - + +
525A LYS* 3.5 23.3 + - - +
527A LEU* 1.3 76.3 - - - +
529A GLN* 1.3 63.1 + - - +
531A VAL* 3.2 5.7 + - - +
532A LYS* 3.1 29.4 + - - +
540A TYR* 3.9 20.7 - - + +
541A PRO* 2.9 34.1 + - - +
542A ARG* 3.4 23.4 + - - +
543A LYS* 4.0 0.4 - - - +
544A ILE* 4.3 5.1 - - + +
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Residues in contact with GLN 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A LYS 2.8 19.7 + - - +
526A GLU* 3.8 5.6 - - - +
528A GLN* 1.3 69.5 - - - +
530A HIS* 1.3 66.4 + - - +
532A LYS* 3.2 28.8 + - - +
533A SER* 3.0 33.5 + - - +
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Residues in contact with HIS 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A ALA 2.8 33.3 + - - -
482A LEU* 4.5 3.4 - - + -
484A GLU* 3.9 11.5 - - + +
485A HIS* 3.8 42.3 + + + -
526A GLU* 2.8 16.5 + - + +
527A LEU* 3.4 11.7 - - - +
528A GLN 3.3 0.2 - - - -
529A GLN* 1.3 75.9 - - - +
531A VAL* 1.3 68.9 + - + +
533A SER* 2.8 24.1 + - - -
534A VAL* 3.2 29.2 + - + +
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Residues in contact with VAL 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A VAL* 4.7 7.9 - - + -
481A ALA* 4.0 14.4 - - + -
482A LEU* 3.7 28.7 - - + -
527A LEU 3.0 15.5 + - - +
528A GLN 3.2 6.7 + - - +
530A HIS* 1.3 79.5 - - + +
532A LYS* 1.3 63.0 + - - +
534A VAL* 3.1 16.8 + - - +
535A THR* 3.1 32.5 + - + +
536A ALA 5.7 0.4 - - - +
539A LYS* 4.8 1.6 - - + +
540A TYR* 4.1 20.6 - - + +
541A PRO* 3.8 15.9 - - + -
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Residues in contact with LYS 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS* 3.1 25.1 + - - -
528A GLN* 3.1 16.0 + - - +
529A GLN* 3.6 30.6 + - - +
531A VAL* 1.3 75.8 - - - +
533A SER* 1.3 57.1 + - - +
535A THR 3.3 10.5 - - - +
537A PRO* 4.0 26.8 - - + +
540A TYR* 3.7 55.3 + - + -
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Residues in contact with SER 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS* 4.0 16.6 - - - +
529A GLN* 3.0 22.7 + - - +
530A HIS* 2.8 21.8 + - - -
532A LYS* 1.3 79.2 - - - +
534A VAL* 1.3 65.4 + - - +
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS* 3.9 11.3 - - - +
143A THR* 4.4 17.9 + - - +
144A ASP* 4.6 0.9 - - - +
481A ALA* 3.6 35.4 - - + -
484A GLU* 3.9 21.5 - - - +
530A HIS* 3.2 28.9 + - + +
531A VAL* 3.1 10.3 + - - +
533A SER* 1.3 84.7 - - - +
535A THR* 1.3 64.5 + - + +
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Residues in contact with THR 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS* 3.6 7.3 - - - +
144A ASP* 2.7 27.5 + - - -
477A GLU* 5.1 3.4 - - - +
481A ALA* 4.5 10.8 - - + -
531A VAL* 3.1 30.8 + - + +
532A LYS 3.3 15.1 - - - +
534A VAL* 1.3 79.5 - - - +
536A ALA* 1.3 71.1 + - - +
537A PRO* 3.2 3.8 - - - +
539A LYS* 3.2 37.2 + - + -
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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
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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