Contacts of the helix formed by residues 486 - 495 (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 GLU 486 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438D ARG* 3.6 30.8 + - - +
484D GLU* 3.1 7.9 + - - +
485D LYS* 1.3 80.0 - - - +
487D MET* 1.3 53.8 + - + +
489D ALA* 3.7 2.2 - - - +
490D GLU* 2.7 36.0 + - + +
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Residues in contact with MET 487 (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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181D VAL* 3.4 32.8 - - + +
436D GLY 3.4 23.8 - - - +
437D GLY* 4.1 17.5 - - - -
438D ARG* 3.4 29.2 - - - +
482D THR* 4.3 13.0 - - + +
484D GLU* 2.9 43.9 + - + +
486D GLU* 1.3 70.6 - - - +
488D ALA* 1.3 56.1 + - - +
490D GLU* 2.7 12.7 + - - +
491D LEU* 2.5 39.3 + - - +
509D VAL* 4.6 5.6 - - + -
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Residues in contact with ALA 488 (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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478D PHE* 3.4 9.0 - - - +
479D GLU* 3.3 34.1 - - + -
482D THR* 3.0 28.2 - - - +
484D GLU* 2.7 19.2 + - - +
485D LYS 3.8 3.8 - - - +
487D MET* 1.3 73.6 - - - +
489D ALA* 1.3 58.7 + - - +
491D LEU* 2.9 5.1 + - - +
492D LYS* 2.8 27.5 + - - +
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Residues in contact with ALA 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D GLU* 3.9 6.7 + - - +
485D LYS* 3.1 21.9 + - + +
486D GLU 3.8 2.2 - - - +
488D ALA* 1.3 80.0 - - - +
490D GLU* 1.3 62.1 + - - +
492D LYS* 3.4 13.4 - - + +
493D ALA* 3.0 21.3 + - - +
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Residues in contact with GLU 490 (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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180D LYS* 3.1 59.0 + - + +
181D VAL* 4.5 7.9 - - + -
438D ARG* 4.7 9.3 + - - +
486D GLU* 2.7 17.8 + - + +
487D MET* 2.7 21.6 + - - +
489D ALA* 1.3 72.7 - - - +
491D LEU* 1.3 53.0 + - - -
493D ALA* 3.0 14.4 - - - +
494D LEU* 2.9 15.2 - - + +
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Residues in contact with LEU 491 (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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177D VAL* 4.8 2.2 - - + -
181D VAL* 3.6 33.2 - - + -
478D PHE* 3.3 18.4 - - + -
481D LEU* 4.1 15.9 - - + -
482D THR* 3.6 18.4 - - + -
487D MET 2.5 20.9 + - - +
488D ALA* 3.3 6.7 - - - +
490D GLU* 1.3 68.5 - - - +
492D LYS* 1.3 52.7 + - - +
493D ALA 2.8 4.6 + - - -
494D LEU* 2.6 34.7 + - + +
495D TYR* 2.9 21.4 + - + -
501D MET* 3.8 24.7 - - + -
509D VAL* 3.5 22.9 - - + -
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Residues in contact with LYS 492 (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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477D SER* 5.0 2.8 - - - +
478D PHE* 3.2 40.1 - - + +
479D GLU* 3.2 31.4 + - - +
488D ALA 2.8 15.8 + - - +
489D ALA* 3.4 9.4 - - + +
491D LEU* 1.3 74.5 - - - +
493D ALA* 1.3 61.0 + - - +
496D SER* 3.1 39.0 + - - +
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Residues in contact with ALA 493 (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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180D LYS* 4.9 4.0 - - - +
489D ALA 3.0 11.3 + - - +
490D GLU* 3.0 27.8 - - - +
491D LEU 2.8 0.8 + - - -
492D LYS* 1.3 80.2 - - - +
494D LEU* 1.3 61.1 + - + +
496D SER* 4.4 4.9 + - - -
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Residues in contact with LEU 494 (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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172D PRO* 3.7 34.1 - - + +
173D ASP 5.0 0.7 - - - +
176D GLU* 3.7 42.6 - - + +
177D VAL* 4.5 9.0 - - + +
180D LYS* 4.0 17.9 - - + +
181D VAL* 6.5 0.4 - - + -
490D GLU* 2.9 32.1 - - + +
491D LEU* 2.6 24.6 + - + +
493D ALA* 1.3 74.7 - - - +
495D TYR* 1.3 68.4 + - + +
496D SER* 3.4 6.5 + - - -
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Residues in contact with TYR 495 (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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167D GLY* 6.0 0.5 - - - -
171D LEU* 4.8 0.2 - - + -
172D PRO* 3.3 38.7 - - + +
177D VAL* 3.5 35.0 - - + +
456D ARG* 4.1 0.5 + - - -
478D PHE* 3.1 22.4 - + + -
491D LEU* 2.9 23.8 + - + -
494D LEU* 1.3 74.9 - - + +
496D SER* 1.3 56.6 + - - +
497D ASP 2.6 26.1 + - - +
500D VAL* 3.3 30.3 - - + +
501D MET* 3.6 28.3 - - + -
502D GLU* 3.6 40.6 + - + +
505D PRO* 4.1 6.2 - - - +
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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