Contacts of the helix formed by residues 305 - 320 (chain O) 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 GLY 305 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304O VAL* 1.3 77.7 - - - +
306O SER* 1.3 56.3 + - - -
307O VAL* 3.2 6.1 - - - -
308O THR* 3.0 10.2 + - - -
309O ALA* 2.4 38.3 + - - +
202P PRO* 5.5 3.4 - - - -
203P LYS* 3.8 28.2 - - - +
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Residues in contact with SER 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301O LYS* 5.5 6.4 + - - +
304O VAL 4.1 0.6 + - - -
305O GLY* 1.3 69.9 - - - -
307O VAL* 1.3 57.5 - - - +
309O ALA* 3.4 8.6 - - - +
310O GLN* 2.8 31.9 + - - +
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Residues in contact with VAL 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305O GLY* 4.5 6.7 - - - -
306O SER* 1.3 79.5 - - - +
308O THR* 1.3 79.1 + - - +
310O GLN* 3.7 4.2 - - - +
311O VAL* 2.9 29.7 + - + +
449O SER* 4.2 7.0 - - - +
456O HIS* 3.6 33.2 - - + +
459O ILE* 5.9 2.9 - - + -
203P LYS* 5.4 6.3 - - - +
205P ASN* 4.3 16.4 - - - +
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Residues in contact with THR 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304O VAL* 4.1 20.0 - - + -
305O GLY* 3.0 14.8 + - - -
307O VAL* 1.3 83.9 - - - +
309O ALA* 1.3 66.3 + - - +
311O VAL* 3.3 10.6 - - + +
312O TYR* 2.9 21.1 + - + +
459O ILE* 3.2 30.4 - - + +
460O LEU* 6.3 0.4 - - - -
462O SER* 3.3 22.2 + - - +
463O SER* 5.0 6.7 - - - +
203P LYS* 5.2 6.2 - - - -
205P ASN* 5.1 0.2 + - - -
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Residues in contact with ALA 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297O ILE* 5.7 3.8 - - + +
300O ALA* 5.7 1.3 - - + -
301O LYS* 4.5 27.1 - - + +
304O VAL* 3.9 15.6 - - + +
305O GLY 2.4 32.8 + - - +
306O SER* 3.4 11.9 - - - +
308O THR* 1.3 65.7 - - - +
310O GLN* 1.3 56.3 + - - +
312O TYR* 2.7 32.6 + - - +
313O LYS* 2.8 11.9 + - - +
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Residues in contact with GLN 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306O SER 2.8 19.9 + - - +
307O VAL* 3.7 4.5 - - - +
309O ALA* 1.3 70.6 - - - +
311O VAL* 1.3 64.1 + - - +
313O LYS* 2.9 59.4 + - - +
314O ILE* 3.0 28.1 + - + +
369O HIS* 4.5 14.6 + - + -
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Residues in contact with VAL 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307O VAL* 2.9 29.5 + - + +
308O THR* 3.3 12.3 - - + +
310O GLN* 1.3 79.3 - - + +
312O TYR* 1.3 59.4 + - - +
314O ILE* 3.0 16.8 + - + +
315O ALA* 2.8 27.4 + - + +
370O LEU* 6.3 2.0 - - + -
456O HIS* 4.9 11.7 - - + +
457O LEU* 5.8 7.9 - - + -
459O ILE* 4.2 24.7 - - + -
460O LEU* 6.3 0.9 - - - -
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Residues in contact with TYR 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296O LEU* 3.7 37.8 - - + +
297O ILE* 4.4 10.3 - - + -
300O ALA* 4.0 27.6 - - + -
304O VAL* 6.1 1.1 - - + -
308O THR* 2.9 13.8 + - + +
309O ALA* 2.7 16.7 + - - +
311O VAL* 1.3 75.4 - - - +
313O LYS* 1.3 61.1 + - - +
315O ALA* 3.0 20.2 + - + +
316O LEU* 3.3 41.3 + - + +
467O PHE* 4.5 9.8 - + - -
468O LEU* 3.4 47.2 - - + +
480O TYR* 4.6 6.2 + - - -
483O LEU* 5.8 0.2 - - - +
487O LEU* 5.1 3.1 - - - +
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Residues in contact with LYS 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294O LYS* 6.3 1.3 - - - +
297O ILE* 3.6 44.6 - - + +
309O ALA 2.8 7.0 + - - +
310O GLN* 2.9 50.3 + - - +
312O TYR* 1.3 78.9 - - - +
314O ILE* 1.3 58.9 + - + +
316O LEU* 4.1 1.6 + - - +
317O ARG* 3.3 39.8 + - - +
369O HIS* 6.0 0.2 + - - -
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Residues in contact with ILE 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310O GLN* 3.0 22.6 + - + +
311O VAL* 3.1 20.6 - - + +
313O LYS* 1.3 76.8 - - + +
315O ALA* 1.3 63.7 + - - +
316O LEU 3.4 1.1 - - - -
317O ARG* 3.4 25.2 + - + +
318O LEU* 3.8 10.2 + - - +
365O ASP* 5.7 0.2 - - - +
368O ARG* 3.9 27.8 - - + +
369O HIS* 3.2 33.2 - - + +
370O LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 315 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311O VAL* 2.8 16.5 + - + +
312O TYR* 3.0 25.2 + - + +
314O ILE* 1.3 77.9 - - - +
316O LEU* 1.3 66.3 + - + +
317O ARG 3.6 0.2 + - - -
318O LEU* 3.7 9.9 + - - +
319O THR* 3.6 13.0 + - - +
362O ASN* 5.5 15.7 - - + +
365O ASP* 5.3 9.2 - - - +
478O VAL* 6.4 1.1 - - + -
480O TYR* 5.5 3.3 + - - +
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Residues in contact with LEU 316 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O LYS* 5.5 1.6 - - - +
293O SER* 3.4 45.3 - - - +
296O LEU* 4.6 10.3 - - + -
297O ILE* 5.3 2.2 - - + -
312O TYR* 3.3 55.3 + - + +
313O LYS* 4.5 5.4 - - - +
314O ILE 3.4 0.2 - - - -
315O ALA* 1.3 74.0 - - + +
317O ARG* 1.3 58.3 + - - +
318O LEU 3.0 2.7 - - - -
319O THR* 2.6 20.0 + - + -
320O GLU* 2.3 39.5 + - + -
325O LYS* 5.5 0.7 - - - +
480O TYR* 4.2 13.5 - - + +
484O MET* 5.3 7.9 - - + -
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Residues in contact with ARG 317 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142O THR* 5.3 14.1 + - - +
290O GLY 5.2 1.4 + - - -
293O SER* 4.1 18.2 - - - -
294O LYS* 4.9 12.9 - - - +
297O ILE* 3.8 20.6 - - - +
313O LYS* 3.3 39.2 + - - +
314O ILE* 3.5 20.6 - - + +
315O ALA 3.3 1.0 - - - -
316O LEU* 1.3 77.8 - - - +
318O LEU* 1.3 61.6 + - + +
320O GLU* 2.9 50.9 + - - +
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Residues in contact with LEU 318 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314O ILE 3.8 6.8 + - - +
315O ALA 3.7 7.9 + - - +
316O LEU 2.9 1.6 + - - -
317O ARG* 1.3 82.5 - - + +
319O THR* 1.3 58.8 + - - +
321O GLN* 4.4 9.4 + - - +
360O THR* 4.9 11.5 - - - +
361O PHE 6.5 0.4 - - - -
362O ASN* 6.2 6.7 - - + +
365O ASP* 3.9 29.6 - - + +
368O ARG* 3.4 56.3 - - + +
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Residues in contact with THR 319 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O LYS* 3.8 5.7 + - - +
315O ALA 3.6 6.5 + - - +
316O LEU* 2.6 34.7 + - + +
318O LEU* 1.3 72.7 - - - +
320O GLU* 1.3 60.2 + - - -
321O GLN* 3.0 8.1 + - - -
322O LYS* 3.3 11.9 + - - -
323O SER* 4.1 5.5 + - - -
360O THR* 5.2 2.5 - - - -
361O PHE* 3.0 46.3 - - - -
362O ASN* 5.2 5.2 - - + -
480O TYR* 4.3 25.1 - - + +
484O MET* 6.1 2.5 - - + -
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Residues in contact with GLU 320 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142O THR* 4.3 7.7 + - - +
197O MET* 3.4 36.6 - - + +
289O LYS* 2.9 45.4 + - + +
290O GLY* 5.0 5.9 - - - -
293O SER* 4.2 12.3 + - - +
316O LEU* 2.3 26.5 + - + +
317O ARG* 2.9 70.0 + - - +
319O THR* 1.3 68.2 - - - +
321O GLN* 1.3 59.1 + - + +
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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
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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