Contacts of the helix formed by residues 528 - 535 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B HIS* 3.5 12.8 - - - -
224B ALA* 4.1 9.6 - - + -
225B ALA 3.5 16.2 - - - -
226B GLY 2.9 38.7 + - - -
227B PHE* 3.5 32.0 - + + -
272B ILE* 4.6 1.6 - - + -
527B LEU* 1.3 75.2 - - - +
529B SER* 1.4 69.6 + - - +
530B CYS 3.1 1.7 - - - +
531B LEU* 3.0 19.0 + - - +
532B VAL* 3.4 12.4 + - + +
800B FMN 3.3 78.5 + + + +
4000B JBW 3.9 15.4 - + - -
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Residues in contact with SER 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ILE* 3.4 28.8 - - - +
477B SER* 3.6 2.6 - - - -
478B GLY* 3.3 20.1 + - - -
509B PHE* 3.6 24.3 - - - -
528B TYR* 1.4 71.3 - - - +
530B CYS* 1.4 61.0 + - - +
532B VAL* 3.2 1.3 + - - -
533B PHE* 3.0 33.2 + - - -
800B FMN 2.7 32.0 + - - -
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Residues in contact with CYS 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ILE 3.3 20.7 + - - +
509B PHE* 3.7 25.4 - - + -
527B LEU* 4.0 25.4 - - + -
528B TYR 3.1 1.4 + - - +
529B SER* 1.4 77.3 - - - +
531B LEU* 1.3 54.2 + - - +
534B ASN* 2.7 55.3 + - - +
538B SER* 2.9 28.2 + - - -
542B ILE* 4.9 1.1 - - - -
800B FMN 4.8 0.2 + - - -
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Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PHE* 5.0 2.0 - - + -
223B VAL* 3.8 31.6 - - + -
227B PHE* 3.7 34.5 - - + -
237B ILE* 5.0 3.6 - - + -
240B LEU* 4.2 17.5 - - + -
242B PHE* 3.8 21.3 - - + -
527B LEU* 5.1 6.5 - - + +
528B TYR* 3.0 11.0 + - - +
530B CYS* 1.3 76.5 - - - +
532B VAL* 1.3 57.7 + - - +
535B GLY* 3.0 45.4 + - - +
536B MET* 4.9 0.9 - - - +
538B SER* 3.4 11.9 - - - +
4000B JBW 3.3 16.3 - - + +
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Residues in contact with VAL 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B LEU* 3.4 27.0 - - - +
176B LEU* 3.8 6.1 - - + +
227B PHE* 4.3 4.9 - - + -
265B ARG* 4.0 12.8 - - - +
272B ILE* 3.7 29.8 - - + -
528B TYR* 3.7 21.5 - - + +
529B SER 3.2 8.0 + - - +
531B LEU* 1.3 76.8 - - - +
533B PHE* 1.3 67.5 + - + +
4000B JBW 3.7 50.0 - - + +
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Residues in contact with PHE 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ASP* 5.6 0.2 - - - +
172B LEU* 3.8 8.5 - - - +
176B LEU* 4.3 17.4 - - + +
265B ARG* 3.7 23.3 - - + -
266B ASP 3.9 1.1 - - - -
267B VAL* 3.8 41.3 - - + -
270B ARG* 3.5 38.4 - - + -
271B SER 3.6 22.9 - - - -
272B ILE* 3.6 22.2 - - + -
509B PHE* 4.0 12.3 - + + -
529B SER* 3.0 25.3 + - - +
532B VAL* 1.3 78.4 - - + +
534B ASN* 1.3 67.3 + - - +
535B GLY 3.5 0.4 - - - -
537B LYS* 5.3 0.3 + - - -
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Residues in contact with ASN 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ASP* 3.5 4.8 - - - +
172B LEU* 4.1 2.7 - - - -
270B ARG* 4.7 9.0 + - - +
509B PHE* 3.5 34.6 + - - +
530B CYS* 2.7 32.4 + - - +
533B PHE* 1.3 78.6 - - - +
535B GLY* 1.3 59.2 + - - +
537B LYS* 2.8 40.5 + - + +
538B SER* 3.5 13.5 + - - +
541B GLN* 4.3 14.8 + - - +
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Residues in contact with GLY 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B TYR 5.9 1.1 - - - -
169B ASP* 5.0 1.6 - - - -
172B LEU* 3.5 17.0 - - - +
531B LEU* 3.0 26.4 + - - +
533B PHE 3.5 1.8 - - - -
534B ASN* 1.3 75.5 - - - +
536B MET* 1.4 64.9 + - - -
537B LYS 3.2 3.4 - - - -
538B SER* 2.7 27.2 + - - -
4000B JBW 3.7 9.9 - - - -
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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