Contacts of the helix formed by residues 349 - 363 (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 GLU 349 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304G PHE* 4.2 14.9 - - - +
305G TYR* 3.4 19.9 - - + -
306G ASN* 3.5 24.6 + - - +
307G LEU* 3.8 7.4 - - - +
348G GLY* 1.3 71.7 - - - -
350G TRP* 1.3 58.6 + - - +
351G LYS* 3.3 4.9 + - + +
352G GLU* 3.6 5.1 + - + +
353G ALA* 3.0 27.9 + - - +
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Residues in contact with TRP 350 (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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275G PHE* 3.6 24.7 - + - -
301G LEU* 4.5 0.7 - - + -
307G LEU* 3.4 28.9 - - + +
308G THR 4.0 2.2 - - - -
346G PHE* 3.5 45.6 + + + -
347G LYS 2.9 19.8 + - - -
348G GLY 3.0 21.2 + - - +
349G GLU* 1.3 70.5 - - - +
351G LYS* 1.3 66.6 + - - +
353G ALA* 4.2 0.9 - - - -
354G MET* 2.8 60.0 + - + +
408G PHE* 3.7 18.4 - + + -
411G TRP* 4.8 7.2 - - - +
412G VAL* 4.4 15.0 - - + -
463G VAL* 3.6 41.3 - - + -
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Residues in contact with LYS 351 (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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349G GLU* 5.0 2.5 - - + -
350G TRP* 1.3 81.0 - - - +
352G GLU* 1.3 68.8 + - + +
354G MET* 4.3 2.1 - - - +
355G LYS* 3.4 36.7 + - + +
411G TRP* 5.3 10.6 - - + +
412G VAL* 4.7 15.6 - - - +
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Residues in contact with GLU 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G TYR* 3.4 26.4 + - + -
349G GLU* 3.6 5.9 + - + +
350G TRP 3.2 0.2 - - - -
351G LYS* 1.3 87.2 - - + +
353G ALA* 1.3 61.7 + - - +
354G MET 3.3 1.1 - - - -
355G LYS* 3.5 39.0 + - + +
356G GLU* 3.0 27.7 + - - +
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Residues in contact with ALA 353 (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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286G THR* 4.7 3.6 - - - +
301G LEU* 5.5 2.0 - - + +
302G ASN 5.2 2.5 - - - +
305G TYR* 3.5 33.2 - - + -
307G LEU* 3.9 24.5 - - + -
349G GLU 3.0 19.3 + - - +
350G TRP* 4.0 2.7 - - - +
352G GLU* 1.3 75.7 - - - +
354G MET* 1.3 62.2 + - + +
356G GLU* 3.2 4.3 + - - +
357G VAL* 3.1 27.9 + - - +
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Residues in contact with MET 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G PHE* 5.3 2.5 - - - -
301G LEU* 4.1 20.0 - - + -
350G TRP* 2.8 58.3 + - + +
351G LYS 4.3 2.5 - - - +
353G ALA* 1.3 78.8 - - + +
355G LYS* 1.3 61.5 + - - +
357G VAL* 3.1 30.4 - - + +
358G LYS* 3.2 18.6 + - - +
378G PHE* 3.5 34.9 - - + -
408G PHE* 5.4 3.8 - - + -
412G VAL* 4.4 27.4 - - + +
466G ILE* 4.2 8.5 - - + -
482G PHE* 5.5 1.8 - - - -
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Residues in contact with LYS 355 (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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351G LYS* 3.4 36.2 + - + +
352G GLU* 3.5 46.2 + - + +
354G MET* 1.3 75.4 - - - +
356G GLU* 1.3 61.6 + - - +
358G LYS* 3.5 13.0 + - + +
359G LEU* 2.9 31.9 + - + +
373G THR* 5.5 13.5 + - + +
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Residues in contact with GLU 356 (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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285G ARG* 4.6 0.3 - - - -
286G THR* 3.3 26.6 + - + +
302G ASN* 2.9 25.8 + - - +
305G TYR* 2.5 30.5 + - + +
352G GLU 3.0 19.7 + - - +
353G ALA 3.4 6.7 - - - +
354G MET 3.2 0.2 - - - -
355G LYS* 1.3 74.9 - - - +
357G VAL* 1.3 59.6 + - - +
359G LEU* 3.1 8.9 + - + +
360G THR* 2.8 42.2 + - + +
610G NAG 2.7 17.0 + - - -
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Residues in contact with VAL 357 (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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286G THR* 4.2 8.0 - - + +
288G ILE* 5.1 2.0 - - + -
299G ILE* 3.6 47.1 - - + -
301G LEU* 4.7 6.7 - - + -
353G ALA 3.1 14.1 + - - +
354G MET* 3.1 34.8 - - + +
356G GLU* 1.3 74.4 - - - +
358G LYS* 1.3 61.7 + - - +
360G THR* 3.3 8.7 + - - +
361G LEU* 3.0 24.4 + - + +
378G PHE* 3.9 21.1 - - + -
466G ILE* 5.2 0.7 - - + -
480G ILE* 5.0 3.6 - - + -
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Residues in contact with LYS 358 (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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354G MET* 3.2 19.5 + - - +
355G LYS* 3.6 12.1 - - + +
356G GLU 3.3 0.2 - - - -
357G VAL* 1.3 76.9 - - - +
359G LEU* 1.3 61.1 + - - +
361G LEU* 3.5 10.1 + - - +
362G ALA* 3.2 20.8 + - - +
373G THR* 5.3 9.6 - - + +
374G GLU* 5.5 4.2 + - - +
376G ILE* 2.8 59.1 + - + +
377G ARG* 4.5 0.7 - - - +
378G PHE* 3.8 31.2 - - + -
412G VAL 4.7 5.6 + - - -
413G GLU* 3.4 26.1 + - - -
480G ILE* 4.9 4.7 - - + -
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Residues in contact with LEU 359 (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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355G LYS* 2.9 20.9 + - + +
356G GLU* 3.1 9.2 + - + +
358G LYS* 1.3 78.1 - - - +
360G THR* 1.3 59.9 + - + +
362G ALA* 3.1 25.6 + - + +
363G LYS* 3.3 22.8 + - + +
372G ASP* 5.5 6.1 - - + +
373G THR* 4.8 15.2 + - - +
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Residues in contact with THR 360 (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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286G THR* 2.9 39.3 + - - +
287G TYR* 6.0 0.2 - - - -
288G ILE* 4.1 12.0 - - - +
356G GLU* 2.8 29.0 + - + +
357G VAL* 3.3 9.9 + - - -
359G LEU* 1.3 73.4 - - + +
361G LEU* 1.3 65.7 + - - +
362G ALA 3.3 0.2 - - - -
363G LYS* 3.6 17.3 + - - +
364G HIS* 3.2 26.0 + - - +
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Residues in contact with LEU 361 (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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288G ILE* 4.0 15.2 - - + +
290G TRP* 3.5 37.2 - - + -
299G ILE* 6.3 1.3 - - + -
357G VAL* 3.0 19.9 + - + +
358G LYS* 3.5 5.2 - - - +
360G THR* 1.3 77.8 + - - +
362G ALA* 1.3 62.1 + - - +
364G HIS* 3.3 13.0 + - - +
367G TYR* 3.3 27.6 - - - +
370G THR* 5.5 0.9 - - + +
376G ILE* 4.2 18.8 - - + -
470G ILE* 4.1 16.6 - - + -
478G THR* 4.9 2.7 - - + -
480G ILE* 3.5 35.9 - - + -
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Residues in contact with ALA 362 (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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358G LYS 3.2 10.1 + - - +
359G LEU* 3.1 18.2 + - + +
361G LEU* 1.3 81.4 - - - +
363G LYS* 1.3 57.4 + - - +
364G HIS 3.5 0.2 - - - -
367G TYR* 3.1 28.1 - - - +
370G THR* 4.5 10.7 - - + +
372G ASP* 3.9 44.3 - - + +
373G THR 5.0 1.1 - - - +
376G ILE* 6.4 0.2 - - + -
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Residues in contact with LYS 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359G LEU* 3.3 24.4 + - + +
360G THR* 3.7 17.5 - - - +
361G LEU 3.3 0.4 - - - -
362G ALA* 1.3 77.8 - - + +
364G HIS* 1.3 61.8 + - - +
365G PRO* 4.1 3.3 - - - +
367G TYR* 4.0 10.2 - - + -
372G ASP* 5.8 1.3 - - - +
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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