Contacts of the helix formed by residues 559 - 568 (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 GLN 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A PRO* 2.8 22.7 + - + +
552A LYS 3.2 30.2 + - - +
553A THR* 3.8 27.9 - - + +
558A ILE* 1.3 71.8 - - - +
560A ARG* 1.3 64.7 + - - +
561A ALA* 3.3 2.9 - - + +
562A LYS* 3.4 41.4 + - + +
563A LEU* 3.4 15.9 + - - +
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Residues in contact with ARG 560 (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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464A ASP* 3.5 39.9 + - + +
475A PRO* 4.3 7.6 - - - +
476A SER* 5.6 1.9 + - - -
479A GLU* 2.8 40.9 + - - -
491A THR 4.8 0.6 + - - -
492A ALA* 4.6 3.7 - - + +
493A VAL 3.7 15.0 - - - +
494A ILE* 4.0 18.8 - - + +
558A ILE* 3.5 49.8 + - + +
559A GLN* 1.3 69.7 - - - +
561A ALA* 1.3 56.8 + - - +
563A LEU* 3.0 7.1 + - - +
564A ARG* 2.8 38.2 + - - +
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Residues in contact with ALA 561 (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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464A ASP* 4.3 2.9 + - - +
559A GLN* 3.3 1.7 - - + -
560A ARG* 1.3 77.3 - - - +
562A LYS* 1.3 62.7 + - - +
564A ARG* 3.6 27.2 - - - +
565A ASP* 2.9 36.7 + - - +
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Residues in contact with LYS 562 (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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551A PRO* 4.2 23.9 - - + +
559A GLN* 3.4 37.8 + - + +
560A ARG 3.2 0.6 - - - -
561A ALA* 1.3 79.9 - - - +
563A LEU* 1.3 63.1 + - + +
565A ASP* 3.5 6.6 + - - +
566A LYS* 3.2 21.0 + - + +
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Residues in contact with LEU 563 (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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492A ALA* 3.9 15.3 - - + -
494A ILE* 3.8 10.9 - - + +
508A PHE* 3.8 45.8 - - + -
550A LEU* 3.8 22.0 - - + -
551A PRO* 3.7 27.1 - - + -
558A ILE* 4.8 3.1 - - + -
559A GLN 3.4 11.4 + - - +
560A ARG* 3.0 7.4 + - - +
562A LYS* 1.3 77.5 - - + +
564A ARG* 1.3 67.6 + - - +
566A LYS* 3.1 10.5 + - + +
567A GLU* 3.0 20.8 + - - +
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Residues in contact with ARG 564 (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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461A ARG* 4.6 10.1 + - - -
462A ALA 4.7 4.8 + - - -
463A ASP* 3.4 29.5 + - - +
464A ASP* 3.2 31.1 + - - +
465A ILE 6.0 1.3 - - - -
494A ILE* 3.6 22.3 - - + +
495A SER* 3.9 20.1 - - - +
560A ARG* 2.8 23.2 + - - +
561A ALA* 3.6 22.8 - - - +
563A LEU* 1.3 70.5 - - - +
565A ASP* 1.3 73.6 + - - +
567A GLU* 2.9 19.6 + - - +
568A TRP* 3.2 26.2 + - + +
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Residues in contact with ASP 565 (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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561A ALA* 2.9 26.2 + - - +
562A LYS* 3.8 6.4 - - - +
564A ARG* 1.3 84.9 + - - +
566A LYS* 1.3 58.1 + - - +
568A TRP* 2.9 29.7 + - - +
569A LYS 3.9 4.3 - - - +
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Residues in contact with LYS 566 (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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508A PHE* 6.4 1.6 - - + -
562A LYS 3.2 10.2 + - - +
563A LEU* 3.1 15.0 + - + +
565A ASP* 1.3 78.8 - - - +
567A GLU* 1.3 61.0 + - - +
568A TRP 2.9 12.1 + - - -
569A LYS* 3.8 5.9 + - - +
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Residues in contact with GLU 567 (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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494A ILE* 3.9 9.2 - - + -
495A SER 3.7 6.5 - - - +
496A SER* 3.2 36.1 + - - +
497A PRO* 3.4 15.5 - - + +
506A LYS* 3.2 38.3 + - - +
508A PHE* 3.5 15.6 - - - -
543A LYS* 4.3 4.5 + - - +
563A LEU 3.0 10.2 + - - +
564A ARG 2.9 11.4 + - - +
566A LYS* 1.3 77.1 - - - +
568A TRP* 1.3 59.3 + - + +
569A LYS* 3.8 3.0 + - - +
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Residues in contact with TRP 568 (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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495A SER* 3.2 38.6 + - - -
496A SER 4.0 4.3 - - - -
497A PRO* 3.5 43.5 - - + +
502A GLY 4.4 7.9 - - - -
503A GLU* 4.1 21.8 - - + -
564A ARG* 3.2 27.9 + - + +
565A ASP* 2.9 13.3 - - - +
566A LYS 2.9 1.4 + - - -
567A GLU* 1.3 79.7 - - - +
569A LYS* 1.3 70.5 + - - +
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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