Contacts of the helix formed by residues 404 - 408 (chain A) in PDB entry 5KZX
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 404 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A CYS* 4.1 0.4 - - - -
375A ARG 3.6 22.2 + - - +
376A TRP* 3.3 18.3 - - + +
403A ASN* 1.3 76.9 + - - +
405A LEU* 1.3 73.3 + - - +
406A ASP* 2.9 15.6 + - - +
407A TYR* 3.2 18.0 + - - -
441A ILE* 3.4 14.4 - - - +
516A TRP* 3.5 13.4 - - + -
674A HIS* 3.3 14.2 - - - -
1014A GLC 2.7 49.8 + - - -
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A TRP* 4.1 18.8 - - + +
404A ASP* 1.3 80.8 + - - +
406A ASP* 1.3 64.1 + - - +
407A TYR 3.0 2.2 + - - -
408A MET* 3.1 45.7 + - + +
411A ARG* 4.3 23.4 + - + +
441A ILE* 3.5 10.0 - - + +
443A ASP* 3.5 24.7 - - - +
481A TRP* 3.7 35.7 - - + -
1014A GLC 3.5 30.7 - - - +
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Residues in contact with ASP 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ARG 4.0 1.0 - - - +
376A TRP* 3.7 13.2 - - - +
377A GLY* 3.0 40.0 + - - -
378A TYR* 3.2 27.2 + - - +
379A SER* 3.5 15.7 - - - +
403A ASN* 4.9 2.0 - - - +
404A ASP* 2.9 13.1 + - - +
405A LEU* 1.3 77.7 - - - +
407A TYR* 1.3 58.1 + - - +
408A MET 3.4 1.6 + - - +
417A ASN* 3.0 22.2 + - - -
421A PHE* 3.7 6.7 - - + -
677A LEU* 5.1 1.9 - - - +
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Residues in contact with TYR 407 (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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403A ASN* 4.3 5.6 - - + -
404A ASP 3.2 26.2 + - - +
405A LEU 3.0 2.0 + - - -
406A ASP* 1.3 79.9 - - - +
408A MET* 1.3 81.0 + - + +
413A ASP* 4.9 0.5 + - - -
414A PHE 4.7 4.9 + - - -
415A THR 3.3 24.0 - - - -
416A PHE* 3.1 9.5 - - - +
417A ASN* 3.0 24.3 + - - -
421A PHE* 3.6 34.8 - - + +
424A PHE* 3.7 22.7 - + + -
440A MET* 3.4 33.3 - - + +
441A ILE* 2.6 32.3 + - + -
442A VAL* 4.4 5.2 - - - +
506A PHE* 3.9 17.0 - + - -
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Residues in contact with MET 408 (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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405A LEU* 3.1 28.8 + - + +
406A ASP 3.8 2.1 - - - +
407A TYR* 1.3 113.3 - - + +
409A ASP* 1.3 61.2 + - - +
410A SER 3.6 3.3 + - - -
411A ARG* 3.4 31.0 + - - +
412A ARG 3.2 23.1 - - - +
413A ASP* 3.5 24.7 - - - +
415A THR 3.7 6.5 - - - -
417A ASN* 3.2 20.4 + - - +
441A ILE* 3.5 23.6 - - + +
442A VAL* 4.6 1.1 - - - -
443A ASP* 4.6 4.0 - - - +
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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