Contacts of the helix formed by residues 275 - 296 (chain N) in PDB entry 6CNB
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 275 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B TYR* 4.3 14.6 + - - -
568B PRO* 5.5 3.8 - - - +
569B THR* 4.2 13.5 + - + +
274N LYS* 1.3 80.4 - - - +
276N ALA* 1.3 69.4 + - - +
277N ALA 3.2 2.7 + - - +
278N ALA* 3.4 8.3 + - - +
279N GLU* 3.0 35.3 + - - +
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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
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569B THR* 5.6 7.0 - - + -
275N GLU* 1.3 79.6 - - - +
277N ALA* 1.3 56.7 + - - +
279N GLU* 3.0 13.8 + - - +
280N LEU* 2.5 49.0 + - + +
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Residues in contact with ALA 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274N LYS* 5.2 16.6 - - + -
275N GLU 3.2 2.5 + - - +
276N ALA* 1.3 75.5 - - - +
278N ALA* 1.3 53.6 + - - +
280N LEU* 3.2 16.2 - - - +
281N GLU* 2.8 36.6 + - - +
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Residues in contact with ALA 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274N LYS* 5.8 6.6 - - + +
275N GLU* 3.4 8.3 + - - +
277N ALA* 1.3 76.6 - - - +
279N GLU* 1.3 64.2 + - - +
281N GLU* 3.1 7.7 + - - +
282N LEU* 2.9 35.3 + - + +
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Residues in contact with GLU 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B PHE* 3.7 32.6 - - + +
568B PRO* 3.8 5.8 - - + -
569B THR* 3.1 49.7 + - - +
570B LYS* 3.2 14.1 + - + +
275N GLU* 3.0 22.8 + - + +
276N ALA* 3.0 17.7 + - - +
278N ALA* 1.3 74.7 - - - +
280N LEU* 1.3 59.1 + - - +
282N LEU* 2.8 31.2 + - - +
283N LEU* 3.5 3.7 + - - +
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Residues in contact with LEU 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276N ALA* 2.5 41.5 + - + +
277N ALA* 3.2 13.7 - - - +
279N GLU* 1.3 74.7 - - - +
281N GLU* 1.3 70.6 + - + +
283N LEU* 3.1 36.9 - - + +
284N ASN* 3.9 2.6 + - - +
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Residues in contact with GLU 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277N ALA 2.8 19.0 + - - +
278N ALA* 3.3 11.0 - - - +
279N GLU 3.1 0.4 - - - -
280N LEU* 1.3 79.7 - - + +
282N LEU* 1.3 62.6 + - + +
283N LEU 3.0 5.8 + - - -
284N ASN* 3.1 22.3 + - - +
285N ALA* 2.9 27.4 + - + +
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Residues in contact with LEU 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ARG* 3.3 26.5 + - - +
567B PHE* 3.7 15.3 - - + -
278N ALA* 2.9 31.7 + - + +
279N GLU* 2.8 15.0 + - - +
281N GLU* 1.3 77.0 - - + +
283N LEU* 1.3 59.8 + - - +
285N ALA* 3.4 15.8 - - + +
286N ASP* 2.9 26.2 + - - +
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Residues in contact with LEU 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B PHE* 3.8 31.4 - - + -
570B LYS* 4.9 21.8 - - + -
279N GLU 3.5 3.4 + - - +
280N LEU* 3.1 31.0 - - + +
281N GLU 3.0 0.2 - - - -
282N LEU* 1.3 77.0 - - - +
284N ASN* 1.3 54.4 + - - +
286N ASP* 2.7 26.4 + - - +
287N HIS* 2.9 26.3 + - + +
384N LYS* 4.6 15.9 - - + +
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Residues in contact with ASN 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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280N LEU 3.9 2.6 + - - +
281N GLU* 3.1 24.9 + - - +
283N LEU* 1.3 77.5 - - - +
285N ALA* 1.3 64.0 + - - +
287N HIS* 3.0 15.4 + - + +
288N GLN* 2.9 24.3 + - - +
368N SER 4.9 6.1 + - - -
369N GLY* 3.5 27.8 - - - +
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Residues in contact with ALA 285 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281N GLU* 2.9 12.3 + - + +
282N LEU* 3.4 29.2 - - + +
284N ASN* 1.3 75.5 - - - +
286N ASP* 1.3 56.7 + - - +
288N GLN* 3.4 8.4 - - - +
289N HIS* 2.9 24.0 + - - +
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Residues in contact with ASP 286 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B PHE* 5.4 0.4 - - + -
282N LEU 2.9 11.9 + - - +
283N LEU* 2.7 19.1 + - - +
285N ALA* 1.3 68.3 - - - +
287N HIS* 1.3 56.4 + - - -
288N GLN 3.0 1.8 - - - -
289N HIS* 2.4 42.6 + - - +
290N ILE* 2.8 23.1 + - - +
384N LYS* 3.1 29.1 - - + +
385N GLY* 2.8 44.9 + - - +
416N ILE* 3.9 2.1 - - - +
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Residues in contact with HIS 287 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283N LEU* 2.9 29.1 + - + +
284N ASN* 3.0 20.3 + - + +
286N ASP* 1.3 70.4 - - - +
288N GLN* 1.3 50.5 + - - +
290N ILE* 3.7 6.9 - - - +
291N LEU* 2.5 41.1 + - - +
365N VAL* 4.9 9.4 - - + +
369N GLY* 2.3 36.5 + - - +
370N LYS* 3.3 28.0 - - + +
371N LEU* 3.7 6.8 - - + +
384N LYS* 3.2 43.4 - - + +
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Residues in contact with GLN 288 (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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284N ASN* 2.9 12.6 + - - +
285N ALA* 3.4 12.8 - - - +
287N HIS* 1.3 74.4 - - - +
289N HIS* 1.3 66.6 + - - +
291N LEU* 3.0 13.9 + - - +
292N ARG* 2.9 69.7 + - - +
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Residues in contact with HIS 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285N ALA 2.9 15.7 + - - +
286N ASP* 2.4 32.1 + - - +
288N GLN* 1.3 70.9 - - - +
290N ILE* 1.3 63.4 + - + +
291N LEU 3.1 0.2 + - - -
292N ARG* 3.4 28.3 + - - +
293N LYS* 2.8 60.5 + - + +
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Residues in contact with ILE 290 (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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286N ASP* 2.8 35.3 + - - +
287N HIS* 3.7 6.1 - - - +
289N HIS* 1.3 77.4 - - - +
291N LEU* 1.3 53.5 + - - +
293N LYS* 4.3 11.9 - - - +
294N LEU* 2.3 63.5 + - + +
305N MET* 4.7 10.1 - - + -
307N PHE* 5.5 4.3 - - + -
384N LYS* 3.3 35.0 - - - +
416N ILE* 3.4 31.0 - - + -
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Residues in contact with LEU 291 (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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74M PHE* 6.2 3.6 - - + -
287N HIS 2.5 26.1 + - - +
288N GLN* 3.0 20.1 + - - +
290N ILE* 1.3 78.0 - - - +
292N ARG* 1.3 68.6 + - + +
294N LEU* 3.3 12.1 - - + +
295N LYS* 3.0 53.7 + - + +
365N VAL* 4.8 24.2 - - + -
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Residues in contact with ARG 292 (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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288N GLN* 2.9 46.8 + - - +
289N HIS* 4.1 28.9 + - - +
291N LEU* 1.3 81.4 - - + +
293N LYS* 1.3 69.7 + - - +
295N LYS* 3.0 13.3 + - + +
296N LYS* 2.9 41.9 + - - +
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Residues in contact with LYS 293 (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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289N HIS* 2.8 57.4 + - + +
290N ILE* 4.3 7.2 - - - +
292N ARG* 1.3 82.2 - - - +
294N LEU* 1.3 66.8 + - - +
296N LYS* 3.4 18.0 + - + +
297N MET* 3.3 21.5 + - + +
305N MET* 4.4 20.6 - - + -
413N ASP* 4.7 20.9 + - - +
414N GLY* 4.1 17.9 - - - -
415N LYS 4.7 6.5 + - - +
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Residues in contact with LEU 294 (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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163M VAL* 4.3 18.1 - - + +
168M VAL* 5.3 6.5 - - + -
290N ILE* 2.3 56.9 + - + +
291N LEU* 3.3 14.4 - - + +
292N ARG 3.0 0.2 + - - -
293N LYS* 1.3 77.4 - - - +
295N LYS* 1.3 60.0 + - + +
297N MET* 2.8 28.6 + - - +
298N ASN 3.9 1.0 + - - -
305N MET* 4.2 21.3 - - + -
307N PHE* 5.7 8.3 - - + -
363N ILE* 5.8 12.6 - - + -
384N LYS* 6.1 0.2 - - - +
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Residues in contact with LYS 295 (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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163M VAL* 6.1 0.4 - - - -
291N LEU* 3.0 43.5 + - + +
292N ARG* 3.0 22.9 + - + +
294N LEU* 1.3 78.8 - - + +
296N LYS* 1.3 63.9 + - + +
297N MET 3.1 0.7 - - - -
298N ASN* 3.1 28.9 - - + +
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Residues in contact with LYS 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292N ARG* 2.9 40.0 + - - +
293N LYS* 3.4 17.9 - - + +
294N LEU 3.0 0.4 - - - -
295N LYS* 1.3 80.8 - - + +
297N MET* 1.3 61.7 + - + +
298N ASN* 3.1 3.0 + - - -
299N ASN* 3.1 18.7 + - - +
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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
------------------------------------------------------------
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