Contacts of the strand formed by residues 457 - 471 (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 LEU 457 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312G LYS* 3.2 5.2 - - - +
313G ARG* 3.1 69.2 + - + +
396G CYS* 4.4 13.9 - - + +
397G ARG* 3.7 15.7 - - + +
399G GLU* 3.5 33.0 - - + -
401G LEU* 6.4 0.4 - - + -
434G ILE* 5.0 3.6 - - + -
452G PRO* 5.3 0.2 - - + -
453G ARG* 3.8 34.3 - - + +
455G GLY* 4.5 3.8 - - - +
456G GLN* 1.3 77.9 - - - +
458G THR* 1.3 66.2 + - - +
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Residues in contact with THR 458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C NAG 4.8 2.4 - - - +
310G HIS* 4.3 14.4 + - - -
311G CYS 3.2 13.3 + - - -
312G LYS* 4.1 9.3 - - - +
396G CYS* 4.0 2.3 - - - -
397G ARG* 3.1 49.7 + - - +
456G GLN* 4.3 19.1 - - - +
457G LEU* 1.3 79.2 - - - +
459G CYS* 1.3 65.1 + - - +
460G ASN* 4.1 6.5 + - - +
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Residues in contact with CYS 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C NAG 4.1 14.4 - - + +
2C NAG 3.8 17.5 - - - -
309G VAL 3.9 0.6 - - - +
310G HIS* 3.0 17.7 + - - -
311G CYS* 2.9 26.3 + - + +
395G ASN 4.8 1.3 - - - +
396G CYS* 2.1 55.2 - - + -
397G ARG* 3.6 8.5 - - - -
458G THR* 1.3 76.0 + - - +
460G ASN* 1.3 67.5 + - - +
461G SER* 5.2 3.8 - - - +
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Residues in contact with ASN 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C NAG 3.3 24.3 - - - +
2C NAG 2.6 38.4 + - + +
278G ASN* 4.5 0.2 - - - +
310G HIS* 3.0 36.0 + - + +
397G ARG* 5.7 1.0 - - - +
458G THR* 4.1 7.3 + - - +
459G CYS* 1.3 84.0 - - - +
461G SER* 1.3 59.8 + - - +
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Residues in contact with SER 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C NAG 2.5 43.0 + - - +
277G PHE* 4.1 19.2 - - - +
278G ASN* 3.4 4.4 + - - -
308G THR* 3.1 8.7 - - - +
309G VAL* 2.6 52.1 + - - -
310G HIS* 4.9 0.8 - - - -
459G CYS* 5.2 4.1 - - - +
460G ASN* 1.3 71.4 + - - +
462G THR* 1.3 59.2 + - - +
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Residues in contact with THR 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G PHE* 3.3 3.1 - - - -
278G ASN* 2.7 54.0 + - - +
279G GLY 5.8 0.4 - - - +
307G LEU 3.8 10.2 + - - -
308G THR* 4.1 7.6 - - - +
461G SER* 1.3 71.0 - - - +
463G VAL* 1.3 61.4 + - - +
464G THR* 3.1 20.4 + - - +
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Residues in contact with VAL 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G PHE* 3.4 35.9 - - + -
276G GLY 3.6 11.7 - - - +
277G PHE* 4.0 6.5 - - + -
301G LEU* 4.1 13.6 - - + +
307G LEU* 3.2 23.2 + - + +
308G THR 3.7 8.1 - - - -
309G VAL* 3.3 36.1 - - + +
350G TRP* 3.6 25.8 - - + -
462G THR* 1.3 71.7 + - - +
464G THR* 1.3 63.5 + - - +
465G SER 4.4 0.9 - - - +
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Residues in contact with THR 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G GLY 3.0 16.0 + - - -
277G PHE 3.8 0.2 - - - -
279G GLY* 3.1 45.8 + - - +
280G THR 5.1 2.0 - - - -
281G ARG 6.1 0.6 - - - -
282G ALA* 4.2 20.7 - - + +
300G SER* 3.7 6.1 + - - -
301G LEU* 3.2 26.9 + - - +
462G THR* 3.1 26.7 - - - +
463G VAL* 1.3 74.0 - - - +
465G SER* 1.3 65.5 + - - +
492G LEU* 4.6 4.1 - - - +
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Residues in contact with SER 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G PHE* 3.2 8.3 - - - +
276G GLY* 2.8 45.8 + - - +
298G ILE* 3.7 21.8 - - - +
299G ILE 3.0 13.2 - - - -
301G LEU* 4.0 4.5 - - - +
463G VAL 3.9 0.4 - - - -
464G THR* 1.3 83.1 + - - +
466G ILE* 1.3 67.8 + - - +
489G LEU* 3.7 11.3 - - - +
492G LEU* 3.8 8.8 - - - +
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Residues in contact with ILE 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G TRP 3.5 2.2 - - - -
275G PHE* 3.1 39.0 - - + -
298G ILE* 3.5 4.2 - - - +
299G ILE* 2.8 48.5 + - + +
301G LEU* 3.7 28.5 - - + -
354G MET* 4.2 10.8 - - + -
357G VAL* 5.2 0.7 - - + -
378G PHE* 4.5 13.7 - - + -
465G SER* 1.3 74.3 - - - +
467G ILE* 1.3 72.1 + - - +
468G ALA* 3.9 10.9 + - + -
482G PHE* 3.4 31.9 - - + -
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Residues in contact with ILE 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G SER 3.9 20.6 - - - +
273G THR* 4.5 1.1 - - - -
274G TRP 2.8 23.6 + - - +
275G PHE 4.7 2.5 - - - +
297G THR 4.0 3.1 - - - +
298G ILE* 4.4 7.2 - - + -
466G ILE* 1.3 73.4 - - - +
468G ALA* 1.3 64.6 + - - +
482G PHE* 3.5 4.9 - - - -
483G SER* 3.0 51.5 + - - +
485G GLU* 4.2 7.9 - - + +
486G VAL 3.9 14.8 - - - +
488G GLU* 4.0 23.3 - - + +
489G LEU* 3.7 33.2 - - + +
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Residues in contact with ALA 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G ARG* 4.2 0.2 - - - -
297G THR* 2.7 43.8 + - + +
299G ILE* 4.6 13.0 - - + -
466G ILE* 3.9 14.7 + - + -
467G ILE* 1.3 78.5 - - - +
469G ASN* 1.3 71.6 + - - +
470G ILE* 4.9 0.2 - - + -
480G ILE* 4.7 11.7 - - + -
481G THR 3.3 18.4 - - - +
482G PHE* 4.4 0.2 - - - -
483G SER* 4.0 5.0 - - - -
488G GLU* 4.9 1.4 - - - +
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Residues in contact with ASN 469 (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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25B GLN* 3.4 29.2 + - - +
27B HIS* 5.0 8.1 + - - -
35B LYS* 6.3 0.4 - - - -
40B GLN* 4.2 8.7 + - - -
294G ASP* 4.9 3.6 + - - -
295G ASN* 3.2 19.5 + - - +
296G ARG* 3.5 12.0 - - - +
468G ALA* 1.3 77.6 - - - +
470G ILE* 1.3 63.9 + - - +
471G ASP* 3.8 11.8 + - - +
479G ASN 3.8 0.3 - - - +
480G ILE* 3.6 2.9 - - - -
481G THR* 3.1 38.7 + - - +
483G SER* 4.1 14.6 + - - -
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Residues in contact with ILE 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ILE* 6.2 1.3 - - + -
290G TRP* 3.8 35.2 - - + -
295G ASN* 3.2 34.6 + - - +
297G THR* 3.4 26.7 - - + -
299G ILE* 4.9 11.0 - - + -
361G LEU* 4.1 22.9 - - + -
367G TYR 5.3 3.1 - - - +
368G LYS 5.7 1.3 - - - +
468G ALA* 4.9 1.1 - - + -
469G ASN* 1.3 71.1 - - - +
471G ASP* 1.3 64.6 + - - +
472G GLY* 3.7 6.9 + - - +
478G THR* 3.9 16.2 - - - +
479G ASN 3.9 1.3 - - - -
480G ILE* 3.3 29.6 - - + -
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Residues in contact with ASP 471 (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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1A NAG 4.8 2.0 - - - -
295G ASN* 5.3 2.3 + - - +
469G ASN* 3.8 10.5 + - - +
470G ILE* 1.3 75.8 + - - +
472G GLY* 1.3 60.8 + - - +
473G GLY* 4.5 0.2 - - - -
477G GLN 4.4 1.7 - - - +
478G THR* 2.8 17.8 + - - -
479G ASN* 3.1 29.8 + - + +
481G THR* 4.9 13.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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