Contacts of the helix formed by residues 518 - 533 (chain A) in PDB entry 5ZRV
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 SER 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A GLU 4.1 7.3 + - - -
516A LYS 3.3 6.4 + - - -
517A THR* 1.3 77.2 - - - +
519A LYS* 1.3 61.8 + - - +
520A ASP 3.2 3.1 - - - +
521A THR* 3.3 6.5 + - - +
522A SER* 3.0 25.1 + - - -
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Residues in contact with LYS 519 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A PHE* 5.4 2.3 - - - +
517A THR 3.9 0.2 + - - -
518A SER* 1.3 72.5 - - - +
520A ASP* 1.3 57.5 + - - +
522A SER* 3.8 1.0 - - - +
523A ALA* 2.9 26.0 + - - -
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Residues in contact with ASP 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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358A GLN 5.3 3.6 + - - +
518A SER* 3.2 1.0 - - - +
519A LYS* 1.3 73.0 - - - +
521A THR* 1.3 59.4 + - - +
523A ALA* 3.9 1.1 - - - +
524A SER* 2.9 26.7 + - - -
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Residues in contact with THR 521 (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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493A LYS* 6.2 4.3 - - - +
517A THR* 6.1 0.9 - - - +
518A SER* 3.3 12.6 + - - +
520A ASP* 1.3 77.6 - - - +
522A SER* 1.3 55.8 + - - +
524A SER* 3.4 1.8 + - - +
525A ALA* 2.9 25.1 + - - -
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Residues in contact with SER 522 (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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517A THR* 5.9 0.8 - - - +
518A SER 3.0 15.8 + - - -
519A LYS* 3.9 1.6 - - - +
521A THR* 1.3 75.5 - - - +
523A ALA* 1.3 57.6 + - - +
525A ALA* 3.2 2.1 + - - +
526A VAL* 2.9 24.9 + - - -
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Residues in contact with ALA 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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352A ASN 5.9 1.3 - - - -
354A PHE* 4.4 22.4 - - - +
356A ALA 5.5 3.4 - - - -
357A PRO* 5.2 10.8 - - - +
519A LYS 2.9 17.4 + - - -
520A ASP* 4.0 1.3 - - - +
522A SER* 1.3 75.5 - - - +
524A SER* 1.3 57.7 + - - +
526A VAL* 3.3 1.9 + - - +
527A ALA* 2.9 26.0 + - - -
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Residues in contact with SER 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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358A GLN 5.2 10.8 + - - +
359A LYS 6.1 0.7 - - - -
360A ASP* 6.5 0.7 - - - +
520A ASP 2.9 18.6 + - - -
521A THR* 3.7 1.8 - - - +
523A ALA* 1.3 75.7 - - - +
525A ALA* 1.3 62.3 + - - +
527A ALA* 3.7 2.3 + - - +
528A VAL 3.6 11.3 + - - -
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Residues in contact with ALA 525 (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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521A THR 2.9 15.2 + - - -
522A SER* 3.7 3.6 - - - +
523A ALA 3.2 0.4 - - - -
524A SER* 1.3 78.3 - - - +
526A VAL* 1.3 56.7 + - - +
528A VAL* 2.9 19.1 + - - -
529A GLY* 3.0 8.7 + - - -
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Residues in contact with VAL 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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352A ASN* 5.6 13.7 - - - -
522A SER 2.9 15.7 + - - -
523A ALA* 3.7 1.6 - - - +
525A ALA* 1.3 72.3 - - - +
527A ALA* 1.3 59.7 + - - +
528A VAL 3.3 0.2 - - - -
529A GLY* 3.4 5.7 - - - +
530A LEU* 2.9 24.9 + - - -
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Residues in contact with ALA 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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523A ALA 2.9 16.9 + - - -
524A SER* 3.7 3.8 + - - +
525A ALA 3.1 0.6 - - - -
526A VAL* 1.3 77.5 - - - +
528A VAL* 1.3 57.0 + - - +
531A LYS* 2.9 28.6 + - - -
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Residues in contact with VAL 528 (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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524A SER 3.6 7.5 + - - -
525A ALA 2.9 9.5 + - - -
527A ALA* 1.3 75.3 - - - +
529A GLY* 1.3 56.2 + - - +
531A LYS* 5.1 0.4 - - - +
532A GLN* 2.9 26.6 + - - +
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Residues in contact with GLY 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 ALA 3.0 11.7 + - - -
526A VAL* 3.2 7.6 + - - -
527A ALA 3.1 0.6 - - - -
528A VAL* 1.3 80.0 - - - +
530A LEU* 1.3 60.6 + - - +
532A GLN* 3.6 1.2 + - - -
533A GLY 3.3 10.4 + - - -
534A LYS 3.2 22.3 + - - +
536A ILE* 6.0 1.6 - - - -
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A LYS* 6.5 1.3 - - - +
526A VAL 2.9 14.6 + - - -
527A ALA 4.2 0.2 - - - -
529A GLY* 1.3 74.0 - - - +
531A LYS* 1.3 61.9 + - - +
532A GLN 3.1 0.9 - - - -
533A GLY* 2.9 21.5 + - - +
534A LYS 4.7 3.1 - - - -
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Residues in contact with LYS 531 (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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383A LYS 5.5 2.9 - - - +
527A ALA 2.9 17.7 + - - -
528A VAL* 4.2 0.7 - - - +
530A LEU* 1.3 72.1 - - - +
532A GLN* 1.3 63.9 + - - +
533A GLY* 4.4 0.2 - - - -
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Residues in contact with GLN 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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379A VAL 5.2 6.6 - - - +
380A SER* 6.2 4.3 - - - +
528A VAL 2.9 21.5 + - - -
529A GLY 3.8 2.7 - - - -
531A LYS* 1.3 77.9 - - - +
533A GLY* 1.3 57.0 + - - +
534A LYS 3.5 3.3 + - - -
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Residues in contact with GLY 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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529A GLY 3.3 2.6 + - - -
530A LEU* 2.9 19.5 + - - -
531A LYS 4.4 0.7 - - - -
532A GLN* 1.3 78.1 - - - +
534A LYS* 1.3 60.6 + - - +
535A VAL* 3.8 2.3 + - - -
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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