Contacts of the helix formed by residues 486 - 495 (chain G) in PDB entry 5CAY
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 VAL 486 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.4 0.2 - - + -
271G THR* 4.4 8.1 - - + -
272G SER 3.2 28.7 - - - +
273G THR* 4.0 10.3 - - + -
393G TRP* 5.0 2.7 - - + -
441G TRP* 3.7 46.7 - - + -
467G ILE* 3.9 12.8 - - - +
484G ALA 3.3 19.3 - - - +
485G GLU* 1.3 71.7 - - - +
487G ALA* 1.3 66.0 + - - +
488G GLU 3.0 2.5 - - - +
489G LEU* 2.9 26.8 + - + +
490G TYR* 3.3 21.6 - - - +
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Residues in contact with ALA 487 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G VAL* 3.5 31.7 - - + +
441G TRP* 4.5 5.5 - - + -
442G HIS* 5.5 1.3 - - - +
485G GLU* 2.5 19.4 + - - +
486G VAL* 1.3 75.1 - - - +
488G GLU* 1.3 56.5 + - - +
490G TYR* 3.0 34.5 + - - +
491G ARG* 3.5 28.3 + - - +
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Residues in contact with GLU 488 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 4.6 1.2 + - - -
78G TRP* 3.0 22.7 + - + +
296G ARG* 2.5 44.2 + - - +
297G THR 3.9 15.8 + - - +
298G ILE* 3.6 23.7 - - + +
467G ILE* 4.0 12.6 - - + +
468G ALA 4.9 1.0 - - - +
483G SER* 5.0 0.3 + - - -
485G GLU* 3.4 25.1 + - + +
486G VAL 3.0 1.4 - - - -
487G ALA* 1.3 74.2 - - - +
489G LEU* 1.3 64.4 + - - +
490G TYR 3.1 0.2 - - - -
491G ARG* 3.2 24.3 + - + +
492G LEU 3.2 16.6 + - - -
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Residues in contact with LEU 489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268G GLU 5.7 0.4 - - - +
270G GLN* 3.7 25.8 - - - +
271G THR* 4.5 0.2 - - - -
272G SER* 3.7 30.1 - - - +
276G GLY* 3.5 26.2 - - - -
298G ILE* 4.0 6.3 - - + +
465G SER* 3.7 12.3 - - - +
467G ILE* 3.7 23.2 - - + +
486G VAL* 2.9 18.3 + - - +
488G GLU* 1.3 75.6 - - - +
490G TYR* 1.3 75.6 + - + +
492G LEU* 3.2 7.6 + - - +
493G GLU* 3.2 26.0 + - + +
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Residues in contact with TYR 490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G THR* 4.0 4.1 - - - +
86G ALA* 4.2 21.4 - - + +
87G VAL* 4.2 12.1 - - + -
90G VAL* 3.3 36.8 - - + +
267G MET* 4.6 6.1 - - - -
268G GLU 3.4 25.8 - - - -
269G THR 3.9 0.4 - - - -
270G GLN 2.6 27.0 + - - -
271G THR* 3.2 22.7 - - - +
441G TRP* 4.4 4.7 - + - -
486G VAL* 3.3 23.5 - - + +
487G ALA* 3.0 22.5 + - - +
489G LEU* 1.3 86.6 - - + +
491G ARG* 1.3 58.0 + - - +
493G GLU* 3.2 8.6 + - + +
494G LEU* 3.0 31.2 + - - +
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Residues in contact with ARG 491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER* 3.7 21.6 + - - -
77G ALA* 3.6 22.6 + - + +
78G TRP* 3.3 46.2 + - + +
83G THR* 3.9 19.4 + - - -
84G GLU* 5.5 7.5 - - - +
87G VAL* 4.1 13.2 - - + +
289G TYR* 3.4 10.7 - - - -
296G ARG* 3.4 12.5 - - - +
298G ILE* 5.0 1.6 - - + -
485G GLU* 4.7 0.8 + - - -
487G ALA* 3.5 35.1 - - - +
488G GLU* 3.4 34.1 - - + +
490G TYR* 1.3 76.2 - - - +
492G LEU* 1.3 58.9 + - - +
495G GLY* 2.9 27.2 + - - -
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Residues in contact with LEU 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G THR 5.0 1.8 - - - +
281G ARG* 3.0 35.1 + - + -
287G TYR* 4.0 32.3 - - + +
289G TYR* 4.0 22.0 - - + -
298G ILE* 3.3 40.3 - - + +
300G SER* 4.3 18.8 - - - +
464G THR* 4.6 4.0 - - - +
465G SER* 3.8 16.6 - - - +
488G GLU 3.2 5.5 + - - -
489G LEU 3.2 4.7 + - - +
491G ARG* 1.3 75.1 - - - +
493G GLU* 1.3 72.6 + - - +
494G LEU 3.3 0.9 + - - -
495G GLY 4.1 2.1 + - - -
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Residues in contact with GLU 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G ARG* 2.8 28.7 + - - -
267G MET* 3.8 23.9 - - + -
268G GLU* 3.2 30.1 + - - +
279G GLY* 3.5 7.8 - - - -
280G THR* 2.5 50.9 + - - +
281G ARG* 3.8 5.1 - - - +
489G LEU* 3.2 17.8 + - + +
490G TYR* 3.2 11.8 + - - +
492G LEU* 1.3 84.2 - - - +
494G LEU* 1.3 65.2 + - + +
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Residues in contact with LEU 494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ASN* 4.0 2.4 + - - -
82G VAL* 3.9 12.9 - - + +
83G THR* 3.7 14.3 - - + +
86G ALA* 4.1 7.0 - - + -
232G TYR* 3.7 27.4 - - + -
264G THR* 3.8 16.6 - - - +
265G ARG* 4.1 11.4 - - + +
267G MET* 3.6 34.8 - - + -
490G TYR 3.0 10.1 + - - +
493G GLU* 1.3 88.1 - - + +
495G GLY* 1.3 56.8 + - - +
496G ASP* 3.2 4.7 - - - -
497G TYR* 3.0 52.1 + - + +
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Residues in contact with GLY 495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G ASP 3.7 1.4 + - - +
77G ALA* 3.4 23.2 + - - -
80G ASN* 3.7 7.0 + - - -
83G THR* 3.7 7.2 - - - +
248G TYR* 2.7 28.6 + - - -
289G TYR* 4.0 1.1 - - - -
491G ARG 2.9 24.3 + - - -
492G LEU 4.1 2.2 + - - -
493G GLU 3.9 0.4 - - - -
494G LEU* 1.3 76.3 - - - +
496G ASP* 1.3 56.0 + - - +
497G TYR 3.3 1.6 + - - +
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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