Contacts of the helix formed by residues 260 - 273 (chain J) 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 ASP 260 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258J ASP 3.7 1.4 + - - -
259J ALA* 1.3 73.9 - - - +
261J MET* 1.3 61.6 + - - +
262J ASP* 3.2 22.3 + - - +
263J ASN* 3.4 26.7 + - + +
264J ALA* 3.3 21.1 + - - +
415J PHE* 5.6 0.5 - - - -
417J ARG* 4.9 8.6 - - + +
482K PRO* 5.8 3.3 - - + +
483K SER* 4.3 25.3 + - - +
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Residues in contact with MET 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255J VAL* 3.7 31.9 - - + -
256J MET 5.1 4.5 - - - +
257J PRO* 5.8 2.9 - - + +
259J ALA* 3.4 10.0 + - + +
260J ASP* 1.3 71.5 + - - +
262J ASP* 1.3 65.7 + - - +
264J ALA* 4.3 3.8 - - - -
265J VAL* 3.1 33.0 + - + +
293J ALA* 3.9 29.4 - - + +
296J ALA* 4.2 25.1 - - + +
297J LEU* 4.0 24.7 - - - -
300J LYS* 4.4 17.8 - - + +
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Residues in contact with ASP 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260J ASP* 3.2 13.8 + - - +
261J MET* 1.3 79.0 - - - +
263J ASN* 1.3 59.1 + - - +
265J VAL* 4.6 1.7 - - - +
266J ASN* 3.7 18.5 + - - +
300J LYS* 2.8 36.8 + - - +
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Residues in contact with ASN 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260J ASP* 3.4 28.5 + - + +
261J MET 3.2 0.2 - - - -
262J ASP* 1.3 77.7 - - - +
264J ALA* 1.3 67.1 + - - +
266J ASN* 3.4 7.5 + - - +
267J GLN* 2.9 51.3 + - - +
415J PHE* 4.8 4.2 - - - -
437J ASN* 5.0 0.7 - - - +
480K ARG* 3.9 17.4 - - - +
482K PRO* 3.6 28.5 - - + +
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Residues in contact with ALA 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255J VAL* 4.9 11.0 - - + -
259J ALA* 5.4 0.2 - - + -
260J ASP 3.3 15.4 + - - +
261J MET* 3.3 11.4 + - - +
263J ASN* 1.3 78.7 - - - +
265J VAL* 1.3 52.9 + - + +
267J GLN* 3.2 2.9 + - - +
268J LEU* 2.8 45.8 + - + +
297J LEU* 5.4 0.2 - - + -
415J PHE* 3.9 40.2 - - + -
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Residues in contact with VAL 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261J MET* 3.1 20.0 + - + +
262J ASP* 5.0 2.0 - - - +
264J ALA* 1.3 73.0 - - - +
266J ASN* 1.3 66.6 + - - +
267J GLN 3.2 0.2 + - - -
268J LEU* 3.2 8.1 + - - +
269J LEU* 3.0 23.0 + - - +
297J LEU* 3.7 37.5 - - + +
300J LYS* 3.8 22.0 - - + +
301J MET* 3.8 34.4 - - + +
304J ALA* 4.2 10.5 - - + -
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Residues in contact with ASN 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262J ASP 3.7 18.3 + - - +
263J ASN* 3.4 8.7 + - - +
264J ALA 3.4 0.2 - - - -
265J VAL* 1.3 80.6 - - - +
267J GLN* 1.3 62.2 + - - +
269J LEU* 3.4 32.6 - - - +
270J GLY* 4.0 2.4 + - - -
304J ALA* 6.1 0.2 - - - -
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Residues in contact with GLN 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263J ASN* 2.9 44.8 + - - +
264J ALA 3.7 3.1 - - - +
266J ASN* 1.3 79.3 - - + +
268J LEU* 1.3 61.5 + - - +
269J LEU 3.2 0.4 + - - -
270J GLY* 3.5 2.6 + - - -
271J ALA* 3.2 26.3 + - - +
415J PHE* 3.6 16.7 - - + -
437J ASN 3.5 19.3 + - - +
438J ILE* 5.1 2.1 - - - +
439J PRO* 3.7 27.7 - - + +
480K ARG* 3.5 20.0 + - - +
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Residues in contact with LEU 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253J ALA* 4.5 1.8 - - + -
255J VAL* 4.7 5.2 - - + -
264J ALA 2.8 26.0 + - - +
265J VAL* 3.2 6.3 + - + +
267J GLN* 1.3 71.6 - - - +
269J LEU* 1.3 64.3 + - - +
271J ALA* 4.1 2.5 - - - -
272J ALA* 2.8 27.9 + - - +
273J PHE* 4.4 0.5 - - - -
283J LEU* 3.7 44.0 - - + +
286J ALA* 4.4 15.7 - - + -
297J LEU* 4.0 26.5 - - + -
301J MET* 4.6 5.6 - - - -
388J LEU* 4.5 19.5 - - + +
415J PHE* 4.3 19.1 - - + -
439J PRO* 4.9 0.2 - - + -
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Residues in contact with LEU 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265J VAL 3.0 10.5 + - - +
266J ASN* 3.4 30.3 - - - +
267J GLN 3.2 0.2 - - - -
268J LEU* 1.3 75.9 - - - +
270J GLY* 1.3 58.4 + - - +
273J PHE* 3.0 47.4 + - + +
301J MET* 3.4 28.6 - - + +
304J ALA* 4.0 31.2 - - + +
305J MET* 4.4 0.2 - - - -
308J LEU* 4.0 30.5 - - + -
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Residues in contact with GLY 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266J ASN 4.0 3.0 + - - -
267J GLN 3.5 5.6 + - - -
269J LEU* 1.3 80.2 - - - +
271J ALA* 1.3 50.1 + - - +
274J GLY* 3.2 13.3 + - - -
279J ARG* 2.7 31.4 + - - -
440J LEU* 4.4 5.3 - - - +
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Residues in contact with ALA 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267J GLN 3.2 18.1 + - - +
268J LEU* 4.0 4.0 - - - +
270J GLY* 1.3 76.5 - - - +
272J ALA* 1.3 63.6 + - - +
279J ARG* 3.3 15.4 + - - +
282J ALA* 3.5 6.6 - - - +
283J LEU* 3.1 31.6 + - + -
439J PRO* 3.6 26.5 - - + -
440J LEU* 4.0 15.8 - - + +
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Residues in contact with ALA 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J LEU* 2.8 21.6 + - + +
271J ALA* 1.3 76.1 - - - +
273J PHE* 1.3 68.3 + - + +
277J GLY* 3.5 20.8 - - - -
282J ALA* 4.6 2.8 - - - +
283J LEU 3.3 24.8 + - - +
284J SER* 5.4 1.1 - - - +
385J GLY 4.4 5.2 - - - +
386J PRO* 4.4 0.3 - - - +
387J VAL 4.6 3.4 + - - +
388J LEU* 4.0 31.0 - - + +
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Residues in contact with PHE 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J LEU* 3.0 27.2 + - + +
272J ALA* 1.3 81.7 - - + +
274J GLY* 1.3 67.4 + - - +
276J SER* 3.0 19.1 + - - -
277J GLY 3.8 3.4 - - - +
301J MET* 4.1 17.0 - - + -
305J MET* 3.5 37.2 - - + -
308J LEU* 4.1 15.9 - - + -
320J PHE* 3.4 29.8 - - + -
366J GLY* 4.0 7.9 - - - -
367J THR 3.9 10.5 - - - -
386J PRO* 3.5 35.4 - - + -
388J LEU* 3.8 27.8 - - + -
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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