Contacts of the helix formed by residues 292 - 307 (chain K) in PDB entry 4ZZ7
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 ALA 292 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257K PRO* 6.3 4.7 - - + -
289K VAL 5.1 0.7 - - - +
290K GLY* 3.8 6.3 - - - -
291K ASP* 1.3 73.8 + - - +
293K ALA* 1.3 70.5 + - + +
295K ASP* 3.1 16.8 + - - +
296K ALA* 3.4 9.9 + - - +
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Residues in contact with ALA 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K VAL* 3.9 15.5 - - + +
256K MET 4.8 5.4 - - - +
257K PRO* 5.1 4.5 - - + +
261K MET* 3.9 23.3 - - + +
288K ALA* 4.3 6.7 - - + -
289K VAL 3.9 19.1 - - - +
290K GLY 3.7 0.6 + - - +
291K ASP* 3.5 1.2 - - - +
292K ALA* 1.3 77.2 - - - +
294K GLY* 1.3 55.5 + - - +
296K ALA* 2.9 5.9 + - - +
297K LEU* 2.7 34.9 + - - +
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Residues in contact with GLY 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288K ALA* 3.5 20.5 - - - +
290K GLY 3.1 8.5 + - - -
291K ASP* 3.5 3.1 - - - +
292K ALA 3.1 1.0 + - - -
293K ALA* 1.3 77.0 - - - +
295K ASP* 1.3 58.5 + - - +
297K LEU* 4.0 1.5 - - - +
298K VAL* 3.2 31.5 + - - +
390K VAL* 5.2 1.1 - - - -
392K ARG* 3.3 26.9 + - - -
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Residues in contact with ASP 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291K ASP* 3.4 24.3 - - - +
292K ALA 3.1 8.1 + - - +
294K GLY* 1.3 73.5 - - - +
296K ALA* 1.3 60.7 + - - +
298K VAL* 3.5 2.6 + - - +
299K SER* 2.9 33.1 + - - -
392K ARG* 3.7 16.8 + - - +
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Residues in contact with ALA 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261K MET* 4.3 21.0 - - + +
292K ALA 3.4 8.1 + - - +
293K ALA* 2.9 9.8 + - - +
295K ASP* 1.3 80.6 - - - +
297K LEU* 1.3 61.4 + - - +
299K SER* 3.8 4.0 - - - -
300K LYS* 3.1 36.0 + - - +
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Residues in contact with LEU 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K VAL* 4.3 14.6 - - + -
261K MET* 3.9 24.6 - - + -
264K ALA* 5.4 0.4 - - + -
265K VAL* 4.0 15.2 - - + +
268K LEU* 4.0 20.9 - - + -
286K ALA* 3.7 26.9 - - + -
288K ALA* 4.4 9.2 - - + -
293K ALA 2.7 21.4 + - - +
294K GLY 4.0 3.4 - - - +
296K ALA* 1.3 73.2 - - - +
298K VAL* 1.3 59.4 + - + +
300K LYS* 4.3 0.7 - - - +
301K MET* 2.9 39.5 + - + +
388K LEU* 6.4 0.4 - - + -
390K VAL* 4.2 23.6 - - + -
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Residues in contact with VAL 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294K GLY 3.2 19.3 + - - +
295K ASP* 4.0 3.1 - - - +
297K LEU* 1.3 75.8 - - - +
299K SER* 1.3 58.7 + - - +
301K MET* 4.0 4.6 - - - +
302K THR* 2.6 35.5 + - - +
347K VAL* 4.0 28.5 - - + -
368K LEU* 4.2 5.6 - - + +
370K ASP* 3.3 34.1 - - + +
390K VAL* 3.8 23.8 - - + -
392K ARG* 4.0 2.5 - - - +
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Residues in contact with SER 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295K ASP 2.9 20.1 + - - -
296K ALA* 3.8 5.4 - - - -
298K VAL* 1.3 81.9 - - - +
300K LYS* 1.3 65.5 + - - +
302K THR* 3.3 11.5 + - - -
303K GLN* 3.3 16.7 + - - +
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Residues in contact with LYS 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261K MET* 4.4 20.2 - - + +
262K ASP* 2.7 41.1 + - - +
265K VAL* 3.8 15.2 - - + +
296K ALA* 3.1 21.9 + - - +
299K SER* 1.3 78.4 - - - +
301K MET* 1.3 63.9 - - - +
303K GLN* 3.5 9.7 + - - +
304K ALA* 3.1 24.6 + - - +
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Residues in contact with MET 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265K VAL* 3.7 26.2 - - + +
268K LEU* 4.6 9.9 - - - -
269K LEU* 3.3 42.2 - - + -
273K PHE* 4.0 6.3 - - + -
297K LEU* 2.9 26.1 + - + +
298K VAL* 4.0 3.6 - - - +
300K LYS* 1.3 73.5 - - - +
302K THR* 1.3 60.9 + - - +
304K ALA* 3.5 0.8 + - + -
305K MET* 2.9 56.1 + - + +
368K LEU* 3.8 13.0 - - + -
388K LEU* 3.8 24.5 - - + -
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Residues in contact with THR 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298K VAL* 2.6 23.4 + - - +
299K SER* 3.3 5.8 + - - -
301K MET* 1.3 75.4 - - - +
303K GLN* 1.3 60.4 + - - +
305K MET* 3.2 14.8 + - - +
306K GLN* 2.6 35.3 + - - +
347K VAL* 3.4 24.4 - - + +
348K VAL* 3.8 19.7 - - + -
368K LEU* 3.8 4.1 - - - +
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Residues in contact with GLN 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299K SER* 3.3 11.9 + - - +
300K LYS* 3.5 12.6 - - - +
302K THR* 1.3 78.1 - - - +
304K ALA* 1.3 63.0 + - - +
306K GLN* 3.1 26.9 + - - +
307K LYS* 4.1 6.3 + - - +
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Residues in contact with ALA 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265K VAL* 4.3 11.9 - - + -
266K ASN* 6.1 0.2 - - - -
269K LEU* 4.0 32.5 - - + +
300K LYS 3.1 13.6 + - - +
301K MET 4.0 3.4 - - - +
303K GLN* 1.3 79.3 - - - +
305K MET* 1.3 60.5 + - - +
306K GLN 3.3 0.7 + - - -
307K LYS* 3.5 26.7 + - + +
308K LEU* 4.1 3.8 + - - +
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Residues in contact with MET 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269K LEU* 4.5 1.5 - - - +
273K PHE* 3.8 21.1 - - + -
301K MET* 2.9 56.2 + - + +
302K THR* 3.2 7.4 + - - +
304K ALA* 1.3 74.9 - - - +
306K GLN* 1.3 63.8 + - - +
308K LEU* 3.4 44.3 - - + +
348K VAL* 3.9 24.0 - - + +
366K GLY 3.8 22.4 - - - +
367K THR 4.2 0.2 - - - -
368K LEU* 3.6 26.5 - - + -
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Residues in contact with GLN 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K THR* 2.6 43.2 + - - +
303K GLN* 3.1 15.0 + - - +
305K MET* 1.3 75.2 + - - +
307K LYS* 1.3 63.6 + - + +
308K LEU 3.2 7.1 + - - +
348K VAL* 4.5 18.8 - - - +
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Residues in contact with LYS 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303K GLN 4.4 6.3 - - - +
304K ALA* 3.5 21.3 + - + +
305K MET 3.4 0.4 - - - -
306K GLN* 1.3 76.9 - - + +
308K LEU* 1.3 64.1 + - - +
309K LYS* 3.4 19.2 - - - +
319K ASP* 4.1 1.6 - - - +
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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