Contacts of the helix formed by residues 517 - 522 (chain A) in PDB entry 1ZRZ
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 517 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A ASN 3.4 9.1 + - - +
516A VAL* 1.3 73.3 - - - +
518A TRP* 1.3 66.0 + - - +
519A ASP* 3.5 8.3 - - - +
520A MET* 2.7 43.7 + - + +
521A MET* 3.0 21.0 + - - +
526A VAL* 4.3 10.7 - - - +
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Residues in contact with TRP 518 (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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351A ALA* 3.8 42.2 - - + -
354A SER* 4.2 8.7 - - - -
355A LEU* 3.8 25.9 - - + +
504A PHE* 4.4 7.4 - + - -
507A ILE* 4.4 5.6 - - + -
508A GLN* 3.1 62.5 + - + +
513A PHE* 3.7 37.1 + + + +
516A VAL* 3.3 30.3 + - + +
517A ASP* 1.3 69.8 - - - +
519A ASP* 1.3 57.2 + - - +
520A MET 2.8 0.7 + - - -
521A MET* 2.9 4.6 + - + +
522A GLU* 2.7 37.6 + - - +
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Residues in contact with ASP 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASP* 4.5 5.7 - - - +
518A TRP* 1.3 75.7 - - - +
520A MET* 1.3 80.3 + - - +
522A GLU* 4.0 9.9 - - - +
523A GLN* 3.8 18.2 + - - +
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Residues in contact with MET 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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517A ASP* 2.7 37.0 - - + +
518A TRP 2.9 0.2 - - - -
519A ASP* 1.3 85.8 + - - +
521A MET* 1.3 64.5 + - - +
523A GLN* 3.2 8.3 + - - +
525A GLN* 2.9 57.9 + - + +
526A VAL* 3.7 12.8 - - + -
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Residues in contact with MET 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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305A PHE* 3.4 11.3 - - + -
348A PHE* 3.7 25.8 - - + -
351A ALA* 4.1 22.7 - - + -
352A GLU* 3.8 20.4 - - + +
355A LEU* 4.4 6.3 - - + -
516A VAL* 3.9 26.7 - - + -
517A ASP* 3.0 11.1 + - - +
518A TRP* 2.9 9.4 + - + +
520A MET* 1.3 73.0 - - - +
522A GLU* 1.3 55.3 - - - +
523A GLN 2.8 5.4 - - - -
524A LYS* 2.7 23.8 + - - +
525A GLN 4.3 0.7 - - - +
526A VAL* 3.3 41.1 - - + +
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Residues in contact with GLU 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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303A HIS* 3.0 35.9 + - - -
304A PRO* 3.8 24.7 - - + +
305A PHE* 4.3 4.5 - - - -
355A LEU* 2.7 44.0 - - + +
358A ASN* 5.4 1.9 + - - -
504A PHE* 5.4 0.2 - - - -
518A TRP 2.7 22.7 + - - +
519A ASP* 4.0 10.1 - - - +
520A MET 3.3 0.2 - - - -
521A MET* 1.3 69.8 - - - +
523A GLN* 1.3 63.4 + - - +
524A LYS 3.5 0.2 - - - -
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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