Contacts of the helix formed by residues 260 - 274 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G ASP 3.7 2.8 + - - -
259G ALA* 1.3 69.0 - - - +
261G MET* 1.3 61.1 + - - +
262G ASP* 3.5 14.7 + - - +
263G ASN* 3.6 25.0 + - + +
264G ALA* 3.2 24.8 + - - +
415G PHE* 5.6 0.9 - - - -
417G ARG* 4.9 5.5 - - - +
482H PRO* 5.4 5.0 - - + +
483H SER* 4.3 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 261 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G VAL* 3.7 32.8 - - + -
256G MET 4.3 7.9 - - - +
257G PRO 5.0 4.5 - - - +
259G ALA* 3.1 18.5 + - + +
260G ASP* 1.3 72.3 + - - +
262G ASP* 1.3 62.3 + - - +
264G ALA* 3.7 7.9 - - - -
265G VAL* 3.1 36.8 + - + +
293G ALA* 4.4 15.7 - - + +
296G ALA* 4.2 25.8 - - + +
297G LEU* 4.7 17.0 - - - -
300G LYS* 4.1 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 262 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G ASP* 3.4 9.9 + - - +
261G MET* 1.3 73.9 - - - +
263G ASN* 1.3 60.8 + - - +
265G VAL* 4.3 2.6 - - - +
266G ASN* 3.1 31.9 + - - +
300G LYS* 2.7 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G ASP* 3.6 29.1 + - + +
261G MET 3.4 0.2 - - - -
262G ASP* 1.3 77.7 - - - +
264G ALA* 1.3 65.4 + - - +
266G ASN* 4.1 3.9 - - - +
267G GLN* 3.1 50.0 + - - +
415G PHE* 5.0 3.6 - - + -
437G ASN* 5.2 1.2 + - - +
480H ARG* 3.8 11.3 + - - +
482H PRO* 3.1 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G VAL* 5.1 3.8 - - + -
259G ALA* 5.4 0.9 - - + -
260G ASP 3.2 14.8 + - - +
261G MET* 3.8 17.5 - - - +
262G ASP 3.3 0.4 - - - -
263G ASN* 1.3 78.3 - - - +
265G VAL* 1.3 54.9 + - + +
267G GLN* 3.2 3.8 + - - +
268G LEU* 2.8 43.9 + - + +
297G LEU* 5.6 0.4 - - + -
415G PHE* 3.8 38.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G MET* 3.1 23.3 + - + +
262G ASP* 4.3 3.1 - - - +
264G ALA* 1.3 76.4 - - + +
266G ASN* 1.3 67.2 + - - +
268G LEU* 3.3 8.2 + - - +
269G LEU* 3.1 23.4 + - - +
297G LEU* 3.8 26.7 - - + +
300G LYS* 3.7 40.2 - - + +
301G MET* 3.8 24.0 - - + +
304G ALA* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 266 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G ASP 3.1 20.2 + - - +
263G ASN* 4.1 5.5 - - - +
265G VAL* 1.3 79.1 - - - +
267G GLN* 1.3 67.5 + - - +
269G LEU* 3.4 27.8 - - - +
270G GLY 4.1 2.3 + - - -
304G ALA* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G ASN* 3.1 38.9 + - - +
264G ALA 3.6 2.5 - - - +
265G VAL 3.2 0.2 - - - -
266G ASN* 1.3 78.6 - - + +
268G LEU* 1.3 64.3 + - - +
269G LEU 3.1 3.2 + - - -
270G GLY* 3.3 4.0 + - - -
271G ALA* 3.3 19.8 + - - +
415G PHE* 4.1 6.0 - - + -
437G ASN 3.3 25.4 + - - +
438G ILE* 5.0 4.3 - - - +
439G PRO* 3.7 30.3 - - + +
480H ARG* 3.7 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253G ALA* 4.4 2.5 - - + -
255G VAL* 4.8 3.8 - - + -
264G ALA* 2.8 28.1 + - + +
265G VAL* 3.3 7.2 + - - +
267G GLN* 1.3 70.1 - - - +
269G LEU* 1.3 64.3 + - - +
271G ALA* 3.9 3.6 - - - -
272G ALA* 3.1 27.9 + - - +
273G PHE* 4.5 1.2 - - - -
283G LEU* 3.8 41.5 - - + +
286G ALA* 4.6 12.1 - - + -
297G LEU* 4.1 26.0 - - + -
301G MET* 4.5 9.4 - - - -
388G LEU* 4.7 14.5 - - + +
415G PHE* 3.9 24.2 - - + -
439G PRO* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G VAL 3.1 15.6 + - - +
266G ASN* 3.4 26.5 - - - +
267G GLN 3.1 0.4 - - - -
268G LEU* 1.3 75.7 - - - +
270G GLY* 1.3 57.3 + - - +
273G PHE* 2.9 45.9 + - + +
274G GLY 3.7 0.3 + - - -
301G MET* 3.3 24.0 - - + +
304G ALA* 3.8 32.8 - - + +
308G LEU* 3.9 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 270 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G ASN 4.1 2.2 + - - -
267G GLN 3.3 6.8 + - - -
269G LEU* 1.3 79.3 - - - +
271G ALA* 1.3 51.9 + - - +
274G GLY* 2.8 20.0 + - - -
279G ARG* 2.6 28.5 + - - -
440G LEU* 5.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267G GLN 3.3 10.3 + - - +
268G LEU* 4.0 4.5 - - - +
269G LEU 3.3 0.4 - - - -
270G GLY* 1.3 79.3 - - - +
272G ALA* 1.3 62.2 + - - +
274G GLY 4.3 0.7 + - - +
279G ARG* 3.5 13.4 + - - +
282G ALA* 3.6 8.5 - - - +
283G LEU* 3.5 29.1 + - + -
439G PRO* 3.7 32.3 - - + -
440G LEU* 4.0 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G LEU 3.1 17.0 + - - +
271G ALA* 1.3 81.9 - - - +
273G PHE* 1.3 71.8 + - + +
277G GLY* 3.3 22.3 - - - -
282G ALA* 4.6 2.4 - - - +
283G LEU 3.4 24.2 + - - +
284G SER* 5.4 0.2 - - - +
385G GLY 4.3 1.6 - - - +
386G PRO* 4.3 3.1 - - - +
387G VAL 4.5 4.8 + - - +
388G LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 273 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G LEU 4.6 0.4 - - - -
269G LEU* 2.9 29.0 + - + +
272G ALA* 1.3 82.5 - - + +
274G GLY* 1.3 68.6 + - - +
276G SER* 3.0 14.6 + - - -
277G GLY 3.9 2.9 - - - +
301G MET* 4.1 13.7 - - + -
305G MET* 3.8 26.5 - - + -
308G LEU* 4.2 16.2 - - + -
320G PHE* 3.3 34.3 - - + -
366G GLY* 3.9 7.9 - - - -
367G THR 3.3 31.6 - - - -
386G PRO* 3.3 32.5 - - + -
387G VAL 4.1 0.2 - - - -
388G LEU* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 274 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ASP* 4.6 5.2 - - - -
269G LEU 3.7 1.0 + - - -
270G GLY* 2.8 26.7 + - - -
271G ALA 4.5 0.3 - - - +
272G ALA 3.6 0.5 - - - +
273G PHE* 1.3 77.3 - - - +
275G SER* 1.3 70.4 + - - -
277G GLY* 2.9 14.7 + - - -
278G GLU 4.4 0.2 + - - -
279G ARG* 3.5 16.7 + - - -
319G ASP 5.3 3.1 - - - -
320G PHE* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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