Contacts of the helix formed by residues 486 - 495 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438C ARG* 3.2 33.1 + - - +
484C GLU* 3.1 8.1 + - - +
485C LYS* 1.3 77.9 - - - +
487C MET* 1.3 53.4 + - - +
489C ALA* 3.7 2.5 - - - +
490C GLU* 2.8 35.4 + - + +
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Residues in contact with MET 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C VAL* 3.4 32.1 - - + +
436C GLY 3.4 23.1 - - - +
437C GLY* 4.1 18.2 - - - -
438C ARG* 3.7 30.5 - - - +
482C THR* 4.3 14.6 - - + +
484C GLU* 2.9 35.9 + - + +
486C GLU* 1.3 73.1 - - - +
488C ALA* 1.3 56.6 + - - +
490C GLU* 2.7 10.4 + - - +
491C LEU* 2.5 40.0 + - - +
509C VAL* 4.6 4.9 - - + -
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Residues in contact with ALA 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C PHE* 3.4 17.3 - - - +
479C GLU* 3.3 32.1 - - + -
482C THR* 3.0 28.6 - - - +
484C GLU* 2.7 20.3 + - - +
485C LYS* 3.9 4.0 - - - -
487C MET* 1.3 73.2 - - - +
489C ALA* 1.3 58.8 + - - +
491C LEU* 3.1 2.4 + - - +
492C LYS* 2.9 25.6 + - - +
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Residues in contact with ALA 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLU* 4.0 6.7 + - - +
485C LYS* 3.1 23.2 + - + +
486C GLU* 3.9 2.5 - - - +
488C ALA* 1.3 79.4 - - - +
490C GLU* 1.3 61.7 + - - +
492C LYS* 3.5 12.5 - - + +
493C ALA* 3.1 21.0 + - - +
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Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C LYS* 3.0 59.8 + - + +
181C VAL* 4.5 7.9 - - + -
438C ARG* 4.9 7.7 + - - +
486C GLU* 2.8 20.5 + - + +
487C MET* 2.7 13.5 + - - +
489C ALA* 1.3 77.6 - - - +
491C LEU* 1.3 54.2 + - - +
493C ALA* 3.0 14.5 - - - +
494C LEU* 2.9 14.3 - - + +
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Residues in contact with LEU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C VAL* 4.8 1.3 - - + -
181C VAL* 3.6 34.8 - - + -
478C PHE* 3.4 18.2 - - + -
481C LEU* 4.2 15.7 - - + -
482C THR* 3.7 17.3 - - + -
487C MET 2.5 17.3 + - - +
488C ALA* 3.4 6.5 - - - +
490C GLU* 1.3 70.0 - - - +
492C LYS* 1.3 53.7 + - - +
493C ALA 2.8 3.8 - - - -
494C LEU* 2.5 36.5 + - + +
495C TYR* 2.9 20.2 + - + -
501C MET* 3.8 25.1 - - + -
509C VAL* 3.5 22.7 - - + -
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Residues in contact with LYS 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C SER* 5.0 2.6 - - - +
478C PHE* 3.4 28.8 - - + +
479C GLU* 3.1 42.0 + - - +
488C ALA 2.9 16.2 + - - +
489C ALA* 3.5 9.4 - - + +
491C LEU* 1.3 75.4 - - - +
493C ALA* 1.3 62.2 + - - +
496C SER* 3.0 43.2 + - - +
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Residues in contact with ALA 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C LYS* 5.0 3.6 - - - +
489C ALA 3.1 12.7 + - - +
490C GLU* 3.0 27.4 - - - +
491C LEU 2.7 0.2 + - - -
492C LYS* 1.3 80.3 - - - +
494C LEU* 1.3 59.3 + - + +
496C SER* 4.4 4.7 + - - -
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PRO* 3.7 36.0 - - + +
173C ASP 4.8 1.3 - - - +
176C GLU* 3.7 42.2 - - + +
177C VAL* 4.5 9.6 - - + +
180C LYS* 4.1 15.0 - - + +
181C VAL* 6.5 0.4 - - + -
490C GLU* 2.9 33.4 - - + +
491C LEU* 2.5 24.8 + - + +
493C ALA* 1.3 75.5 - - + +
495C TYR* 1.3 68.6 + - + +
496C SER* 3.4 6.3 + - - -
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Residues in contact with TYR 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C GLY* 6.0 0.5 - - - -
172C PRO* 3.2 37.8 - - + +
177C VAL* 3.6 34.2 - - + +
452C ILE* 5.6 0.2 - - - +
456C ARG* 4.1 1.0 + - - -
478C PHE* 3.1 23.3 - + + -
491C LEU* 2.9 23.7 + - + -
494C LEU* 1.3 73.9 - - + +
496C SER* 1.3 57.3 + - - +
497C ASP* 2.6 25.2 + - - +
500C VAL* 3.1 32.0 - - + +
501C MET* 3.5 30.1 - - + -
502C GLU* 3.6 38.4 + - + +
505C 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