Contacts of the helix formed by residues 348 - 353 (chain D) in PDB entry 5COX
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 348 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PHE* 4.4 15.8 - + - -
201D PHE* 3.4 28.3 - + + -
202D ALA* 3.0 44.4 - - + +
205D PHE* 4.8 8.1 - + - -
206D THR* 4.7 0.7 - - - +
343D ILE 3.5 1.0 + - - -
344D VAL* 3.8 25.6 - - + +
347D ASP* 1.3 78.5 - - - +
349D VAL* 1.3 78.8 + - + +
351D HIS* 3.7 1.9 - - - +
352D LEU* 3.0 44.3 + - + +
385D TYR* 2.8 33.6 + - - -
387D TRP* 3.8 4.6 - + - -
580D PHE* 3.5 19.2 - + + -
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Residues in contact with VAL 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D VAL* 3.0 32.0 + - + +
345D ILE* 3.7 9.4 - - + +
347D ASP 3.4 0.2 - - - -
348D TYR* 1.3 89.1 - - + +
350D GLN* 1.3 66.7 + - - +
352D LEU* 3.7 5.9 - - + +
353D SER* 2.9 26.1 + - - -
359D LEU* 3.5 21.3 - - + -
530D SER* 4.9 10.8 - - - +
531D LEU* 5.5 11.9 - - + -
534D LEU* 4.9 7.9 - - + -
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Residues in contact with GLN 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ARG* 5.2 0.2 - - - +
345D ILE 3.3 6.3 + - - +
346D GLU* 3.0 32.9 + - - +
347D ASP* 3.0 3.1 + - - +
349D VAL* 1.3 78.5 - - - +
351D HIS* 1.3 61.3 + - - +
353D SER* 2.8 19.9 + - - -
354D GLY* 3.3 3.8 + - - -
355D TYR* 4.2 8.1 + - - +
356D HIS 5.3 0.7 + - - -
357D PHE 2.9 21.4 - - - +
358D LYS* 3.2 22.6 - - - +
359D LEU* 3.1 43.9 + - - +
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Residues in contact with HIS 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D GLN* 3.7 24.4 + - + -
194D SER* 2.9 37.9 + - - -
198D PHE* 3.7 11.4 - + - -
347D ASP 2.6 21.7 + - - +
348D TYR 3.7 2.9 - - - +
350D GLN* 1.3 69.3 - - - +
352D LEU* 1.3 71.6 + - + +
353D SER 2.5 16.8 + - - -
354D GLY* 2.8 15.6 + - - -
579D SER* 5.6 0.7 - - - -
580D PHE* 2.8 43.1 + - + -
581D ASN* 4.0 12.3 + - + -
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Residues in contact with LEU 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D GLN* 4.0 12.8 - - - +
194D SER* 4.8 1.8 - - - +
198D PHE* 3.4 31.9 - - + -
348D TYR* 3.0 32.8 + - + +
349D VAL* 3.7 6.7 - - + +
351D HIS* 1.3 85.4 + - - +
353D SER* 1.3 59.2 + - - +
385D TYR* 5.2 0.2 - - - +
387D TRP* 3.4 26.7 - - + -
517D ILE* 3.9 12.1 - - + -
518D PHE* 3.2 39.1 - - + -
523D VAL* 5.7 3.1 - - - +
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Residues in contact with SER 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D HIS* 4.8 7.8 + - - -
192D GLN* 4.4 4.9 + - - +
349D VAL* 2.9 18.1 + - - -
350D GLN* 2.8 13.2 + - - -
351D HIS 2.5 7.3 + - - -
352D LEU* 1.3 77.4 - - - +
354D GLY* 1.3 65.0 + - - +
355D TYR* 2.9 52.4 - - - +
359D LEU* 4.7 5.8 - - - +
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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