Contacts of the helix formed by residues 528 - 535 (chain A) in PDB entry 4CQ8
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 TYR 528 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A HIS* 3.5 13.0 - - - -
224A ALA* 4.1 9.9 - - + -
225A ALA 3.5 16.2 - - - -
226A GLY 2.9 38.5 + - - -
227A PHE* 3.5 30.6 - + + -
272A ILE* 4.5 1.1 - - + -
527A LEU* 1.3 75.8 - - - +
529A SER* 1.3 69.2 + - - +
530A CYS 3.1 1.3 - - - +
531A LEU* 3.0 19.3 + - - +
532A VAL* 3.4 13.1 + - + +
800A FMN 3.3 77.4 + + + +
4000A JBW 3.9 13.9 - + - -
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Residues in contact with SER 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 3.3 29.1 - - - +
477A SER* 3.5 1.7 - - - -
478A GLY* 3.3 19.3 + - - -
509A PHE* 3.6 24.5 - - - -
528A TYR* 1.3 71.5 - - - +
530A CYS* 1.4 61.0 + - - +
532A VAL* 3.2 1.5 + - - -
533A PHE* 3.0 33.4 + - - -
800A FMN 2.7 31.8 + - - -
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Residues in contact with CYS 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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508A ILE 3.3 20.4 + - - +
509A PHE* 3.7 27.1 - - + -
527A LEU* 4.0 25.4 - - + -
528A TYR 3.1 1.2 + - - +
529A SER* 1.4 76.9 - - - +
531A LEU* 1.3 54.4 + - - +
534A ASN* 2.7 55.0 + - - +
538A SER* 2.9 28.3 + - - -
542A ILE* 4.9 0.9 - - - -
800A FMN 4.8 0.6 + - - -
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Residues in contact with LEU 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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188A PHE* 4.8 2.5 - - + -
223A VAL* 3.8 29.4 - - + -
227A PHE* 3.6 36.3 - - + -
237A ILE* 4.8 4.5 - - + -
240A LEU* 4.2 20.4 - - + -
242A PHE* 3.9 18.4 - - + -
527A LEU* 5.1 4.6 - - + +
528A TYR* 3.0 11.9 + - - +
530A CYS* 1.3 77.1 - - - +
532A VAL* 1.3 57.3 + - - +
535A GLY* 3.1 45.7 + - - +
536A MET* 4.9 0.7 - - - +
538A SER* 3.4 10.5 + - - +
4000A JBW 3.3 18.2 - - + +
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Residues in contact with VAL 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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172A LEU* 3.4 26.9 - - - +
176A LEU* 3.8 7.4 - - + +
227A PHE* 4.3 5.2 - - + -
265A ARG* 3.9 17.5 - - - -
272A ILE* 3.8 25.8 - - + -
528A TYR* 3.7 21.1 - - + +
529A SER 3.2 8.4 + - - +
531A LEU* 1.3 77.0 - - - +
533A PHE* 1.3 67.0 + - + +
4000A JBW 3.5 47.3 - - + +
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Residues in contact with PHE 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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172A LEU* 3.8 8.9 - - - +
176A LEU* 4.3 20.5 - - + +
265A ARG* 4.0 17.0 - - + -
266A ASP 4.0 0.4 - - - -
267A VAL* 3.8 40.2 - - + -
270A ARG* 3.5 35.2 - - + -
271A SER 3.3 24.7 - - - -
272A ILE* 3.7 22.4 - - + -
509A PHE* 4.0 15.0 - + + -
529A SER* 3.0 25.8 + - - +
532A VAL* 1.3 78.1 - - + +
534A ASN* 1.3 67.9 + - - +
535A GLY 3.5 0.4 - - - -
537A LYS* 5.3 0.7 + - - -
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Residues in contact with ASN 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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169A ASP* 3.5 4.3 - - - +
172A LEU* 4.1 2.5 - - - -
270A ARG* 4.9 7.0 + - - +
509A PHE* 3.5 34.6 + - - +
530A CYS* 2.7 32.3 + - - +
533A PHE* 1.3 78.1 - - - +
535A GLY* 1.3 60.1 + - - +
537A LYS* 2.8 41.1 + - + +
538A SER* 3.5 14.4 + - - +
541A GLN* 4.4 15.3 + - - +
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Residues in contact with GLY 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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168A TYR* 6.0 1.1 - - - -
169A ASP* 5.0 1.6 - - - -
172A LEU* 3.5 17.6 - - - +
530A CYS 3.6 0.2 + - - -
531A LEU* 3.1 26.3 + - - +
533A PHE 3.5 1.4 - - - -
534A ASN* 1.3 75.7 - - - +
536A MET* 1.4 64.9 + - - -
537A LYS 3.3 3.1 - - - -
538A SER* 2.7 26.0 + - - -
4000A JBW 3.7 9.4 - - - -
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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