Contacts of the helix formed by residues 274 - 286 (chain N) in PDB entry 6CET
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 LYS 274 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408M THR* 4.9 5.4 - - - +
475M ASP* 5.9 1.2 + - - -
273N HIS* 1.3 104.4 - - + +
275N ARG* 1.3 105.9 + - - +
276N ALA 3.4 2.2 - - - +
277N SER* 3.5 7.5 + - - +
278N LEU* 3.0 37.9 + - + +
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Residues in contact with ARG 275 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311M GLN* 6.1 0.4 - - - +
407M HIS* 5.5 0.5 - - - -
408M THR* 3.8 19.4 + - - -
267N TYR* 3.9 20.6 - - + -
268N VAL* 3.8 22.5 - - + +
270N LYS 3.9 11.6 + - - +
271N GLN* 3.3 24.8 + - + +
272N GLY* 5.2 1.1 - - - -
274N LYS* 1.3 120.6 - - + +
276N ALA* 1.3 58.4 + - - +
278N LEU* 3.4 9.1 + - - +
279N ARG* 3.0 29.6 + - - +
371N ASN* 3.2 44.0 + - - +
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Residues in contact with ALA 276 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242N SER* 6.2 2.7 - - - -
245N TYR* 4.8 19.7 - - + -
258N LYS* 3.6 35.3 + - + +
267N TYR* 4.5 2.0 - - - -
271N GLN* 4.3 9.0 + - + +
273N HIS 6.4 0.4 - - - -
274N LYS 3.4 1.0 - - - +
275N ARG* 1.3 78.5 - - - +
277N SER* 1.3 58.0 + - - +
279N ARG* 3.3 2.8 + - - +
280N ASP* 2.8 29.7 + - - +
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Residues in contact with SER 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N VAL 4.6 1.6 + - - -
245N TYR* 3.6 32.4 + - - +
273N HIS 5.3 3.5 + - - -
274N LYS* 3.5 11.2 + - - +
275N ARG 3.3 0.4 - - - -
276N ALA* 1.3 75.1 - - - +
278N LEU* 1.3 65.8 + - - +
280N ASP* 3.9 7.8 + - - -
281N VAL* 3.0 38.6 + - - +
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Residues in contact with LEU 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405M GLN* 3.5 23.2 + - - +
406M LEU* 3.5 29.4 - - + +
407M HIS* 3.5 46.1 + - + +
408M THR* 4.5 11.2 - - - +
274N LYS* 3.0 36.8 + - + +
275N ARG* 3.7 7.6 - - - +
277N SER* 1.3 82.1 - - - +
279N ARG* 1.3 59.3 + - - +
281N VAL* 5.4 0.4 - - - -
282N PHE* 3.7 4.7 - - - +
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Residues in contact with ARG 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407M HIS* 5.2 2.9 - - + -
257N ASP* 2.7 37.0 + - - -
258N LYS* 3.0 24.7 - - - +
261N GLN* 3.2 34.1 + - - +
266N SER* 5.7 1.3 - - - +
267N TYR* 2.4 36.7 + - + +
275N ARG 3.0 14.9 + - - +
276N ALA 3.9 1.9 + - - +
278N LEU* 1.3 76.2 - - - +
280N ASP* 1.3 65.7 + - - +
282N PHE* 3.4 11.6 + - + +
283N GLN* 2.9 55.8 + - - +
354N ILE* 5.8 1.2 - - - +
367N GLU* 5.4 13.9 - - + -
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Residues in contact with ASP 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245N TYR 4.8 6.6 - - - +
248N THR* 4.7 13.8 - - - +
249N PRO 6.2 0.2 - - - -
250N LYS* 3.3 36.0 - - - +
253N ASP* 5.6 3.0 - - - +
276N ALA 2.8 18.5 + - - +
277N SER* 3.2 10.2 + - - +
279N ARG* 1.3 82.0 + - - +
281N VAL* 1.3 63.9 + - + +
283N GLN* 3.2 7.6 + - - +
284N LEU* 2.8 32.6 + - - +
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Residues in contact with VAL 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405M GLN* 3.4 29.0 - - + +
248N THR* 5.1 18.2 - - + +
277N SER* 3.0 18.4 + - - +
278N LEU* 5.4 0.2 - - - -
280N ASP* 1.3 77.7 - - + +
282N PHE* 1.3 63.0 + - - +
284N LEU* 3.6 9.5 - - + +
285N TYR* 3.0 41.5 + - + +
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Residues in contact with PHE 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316M LEU* 3.6 39.5 - - + -
318M TYR* 5.7 0.7 - + - -
405M GLN* 3.0 17.2 - - - +
278N LEU 3.7 11.4 + - - +
279N ARG* 3.4 15.9 + - + +
280N ASP 3.2 0.2 - - - -
281N VAL* 1.3 75.9 - - - +
283N GLN* 1.3 80.8 + - + +
286N CYS* 2.8 51.7 + - + +
357N LYS* 6.5 0.9 - - - -
362N TYR* 6.1 2.0 - + - -
363N HIS* 4.5 11.0 - - + -
366N ASP* 4.5 15.5 - - + -
367N GLU* 3.2 42.0 - - + -
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Residues in contact with GLN 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261N GLN* 5.1 3.1 - - - -
279N ARG* 2.9 49.9 + - - +
280N ASP* 3.2 6.7 + - - +
282N PHE* 1.3 103.8 - - - +
284N LEU* 1.3 62.3 + - - +
286N CYS 3.6 9.0 + - - +
287N SER* 3.4 23.9 + - - -
353N GLU* 5.1 11.2 + - - +
354N ILE* 4.5 19.2 - - - +
357N LYS* 5.0 15.4 - - - +
367N GLU* 4.1 5.7 - - - +
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Residues in contact with LEU 284 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321M LYS* 4.0 7.4 - - - +
248N THR* 3.7 29.6 - - + -
249N PRO 3.9 16.2 - - - +
250N LYS* 5.2 6.1 - - + -
280N ASP* 2.8 22.5 + - - +
281N VAL* 3.2 13.2 + - + +
283N GLN* 1.3 78.7 - - - +
285N TYR* 1.3 84.3 + - + +
287N SER* 3.8 11.8 - - - -
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Residues in contact with TYR 285 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318M TYR 4.6 3.1 - - - +
319M TRP* 3.4 19.7 - + + -
320M GLY 3.1 26.2 + - - +
321M LYS* 3.2 31.6 + - - +
403M LEU* 5.2 20.6 - - + +
405M GLN* 4.8 8.7 - - + +
281N VAL* 3.0 30.7 + - + +
282N PHE 4.8 0.2 - - - +
284N LEU* 1.3 101.9 - - + +
286N CYS* 1.3 59.7 + - - +
287N SER 3.2 7.2 + - - -
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Residues in contact with CYS 286 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316M LEU* 4.0 1.6 - - - -
318M TYR* 3.7 36.6 - - - -
319M TRP* 5.1 0.2 - - - -
320M GLY 5.2 1.3 - - - +
405M GLN* 5.5 0.7 - - - -
282N PHE* 2.8 54.3 + - + +
283N GLN* 3.6 10.6 + - - +
285N TYR* 1.3 76.0 - - - +
287N SER* 1.3 59.5 + - - +
357N LYS* 3.3 31.1 + - - +
362N TYR* 6.4 2.0 - - + -
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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