Contacts of the helix formed by residues 260 - 274 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482E PRO* 5.5 4.4 - - + +
483E SER* 4.6 22.5 + - - +
258F ASP 3.6 1.8 + - - -
259F ALA* 1.3 71.4 - - - +
261F MET* 1.3 61.6 + - - +
262F ASP* 3.9 13.4 + - - +
263F ASN* 3.3 29.4 + - + +
264F ALA* 3.0 28.1 + - - +
415F PHE* 5.5 0.7 - - - -
417F ARG* 4.9 4.8 - - - +
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Residues in contact with MET 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F VAL* 3.7 31.6 - - + -
256F MET 4.7 5.6 - - - +
257F PRO* 6.1 0.7 - - + -
259F ALA* 3.3 10.1 + - + +
260F ASP* 1.3 71.8 + - - +
262F ASP* 1.3 55.3 + - - +
264F ALA* 3.2 4.0 + - - +
265F VAL* 2.7 43.8 + - + +
293F ALA* 3.8 29.4 - - + +
296F ALA* 3.9 26.7 - - + +
297F LEU* 4.0 23.8 - - - -
300F LYS* 4.2 18.6 - - + +
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Residues in contact with ASP 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F ASP* 3.3 13.1 + - - +
261F MET* 1.3 77.4 - - - +
263F ASN* 1.3 61.8 + - - +
265F VAL* 3.9 4.1 - - - +
266F ASN* 3.0 28.0 + - - +
300F LYS* 2.9 36.5 + - - +
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Residues in contact with ASN 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480E ARG* 3.7 20.7 + - - +
482E PRO* 3.7 25.8 - - + +
260F ASP* 3.3 28.3 + - + +
261F MET 3.4 0.2 - - - -
262F ASP* 1.3 78.4 - - - +
264F ALA* 1.3 62.7 + - - +
266F ASN* 3.9 8.0 - - - +
267F GLN* 3.1 51.0 + - - +
415F PHE* 4.8 4.9 - - - -
437F ASN* 4.8 0.7 - - - +
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Residues in contact with ALA 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F VAL* 4.8 11.2 - - + -
259F ALA* 5.2 0.4 - - + -
260F ASP 3.0 19.0 + - - +
261F MET* 3.2 12.3 + - - +
263F ASN* 1.3 77.2 + - - +
265F VAL* 1.3 61.8 + - + +
267F GLN 4.0 0.3 - - - -
268F LEU* 3.1 34.7 + - + +
297F LEU* 5.5 0.4 - - + -
415F PHE* 3.9 41.3 - - + -
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Residues in contact with VAL 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F MET* 2.7 28.2 + - + +
262F ASP* 3.9 4.9 - - - +
264F ALA* 1.3 68.7 - - - +
266F ASN* 1.3 69.3 + - - +
268F LEU* 3.0 18.3 + - - +
269F LEU* 3.0 13.6 + - + +
297F LEU* 4.1 26.2 - - + +
300F LYS* 3.8 41.1 - - + +
301F MET* 3.8 23.2 - - + +
304F ALA* 4.3 10.5 - - + -
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Residues in contact with ASN 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F ASP 3.0 18.5 + - - +
263F ASN* 3.9 9.6 - - - +
265F VAL* 1.3 78.6 - - - +
267F GLN* 1.3 64.9 + - - +
269F LEU* 3.4 30.3 - - - +
270F GLY 3.9 2.8 + - - -
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Residues in contact with GLN 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480E ARG* 3.3 20.9 + - - +
263F ASN* 3.1 39.9 + - - +
264F ALA 4.2 2.0 - - - +
266F ASN* 1.3 79.4 - - + +
268F LEU* 1.3 59.5 + - - +
270F GLY* 3.7 2.2 + - - -
271F ALA* 3.3 25.3 + - - +
415F PHE* 3.7 14.3 - - + -
437F ASN 3.1 24.5 + - - +
438F ILE* 4.6 4.9 - - - +
439F PRO* 3.4 27.2 - - + +
440F LEU* 5.9 0.2 - - - +
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Residues in contact with LEU 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F ALA* 4.4 2.5 - - + -
255F VAL* 4.8 5.2 - - + -
264F ALA 3.1 25.0 + - - +
265F VAL* 3.0 7.9 + - - +
267F GLN* 1.3 75.7 - - - +
269F LEU* 1.3 58.0 + - - +
271F ALA* 3.7 2.0 - - - -
272F ALA* 2.9 34.1 + - - +
273F PHE* 4.6 0.3 - - - -
283F LEU* 3.9 44.4 - - + +
286F ALA* 4.5 16.4 - - + -
297F LEU* 4.0 26.0 - - + -
301F MET* 4.6 9.9 - - - -
388F LEU* 4.9 10.9 - - + +
415F PHE* 4.3 17.7 - - + -
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Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F VAL 3.0 8.0 + - - +
266F ASN* 3.4 28.7 - - - +
268F LEU* 1.3 76.9 - - - +
270F GLY* 1.3 57.3 + - - +
273F PHE* 3.1 46.7 + - + +
274F GLY 3.8 0.5 + - - -
301F MET* 3.3 29.1 - - + +
304F ALA* 3.8 30.5 - - + +
305F MET* 4.4 0.7 - - - -
308F LEU* 3.9 32.0 - - + +
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Residues in contact with GLY 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F ASN 3.9 3.6 + - - -
267F GLN 3.7 5.2 + - - -
268F LEU 3.4 0.4 - - - -
269F LEU* 1.3 78.9 - - - +
271F ALA* 1.3 52.3 + - - +
274F GLY* 2.9 17.0 + - - -
279F ARG* 2.8 29.0 + - - -
440F LEU* 4.8 4.3 - - - -
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Residues in contact with ALA 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F GLN 3.3 19.2 + - - +
268F LEU* 3.9 5.6 - - - +
269F LEU 3.3 0.2 - - - -
270F GLY* 1.3 80.0 - - - +
272F ALA* 1.3 61.2 + - - +
274F GLY 4.4 0.5 + - - +
279F ARG* 3.7 7.1 + - - -
282F ALA* 3.5 11.3 - - - +
283F LEU* 3.2 31.2 + - + -
439F PRO* 3.6 24.5 - - + -
440F LEU* 4.0 17.4 - - + +
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Residues in contact with ALA 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F LEU* 2.9 17.8 + - + +
271F ALA* 1.3 79.9 - - - +
273F PHE* 1.3 74.0 + - + +
277F GLY* 3.5 19.5 - - - -
282F ALA* 4.7 2.6 - - - +
283F LEU 3.4 24.0 - - - +
284F SER* 6.0 0.2 - - - -
385F GLY 4.7 0.3 - - - +
386F PRO* 4.4 3.3 - - - +
387F VAL 4.6 7.5 + - - +
388F LEU* 3.7 26.5 - - + -
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Residues in contact with PHE 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F LEU* 3.1 33.8 + - + +
272F ALA* 1.3 83.8 - - + +
274F GLY* 1.3 68.1 + - - +
276F SER* 3.0 17.8 + - - -
277F GLY 3.2 5.0 + - - +
301F MET* 4.2 7.4 - - + -
305F MET* 3.5 43.5 - - + -
308F LEU* 3.9 15.9 - - + -
320F PHE* 3.6 27.5 - - + -
366F GLY* 4.1 4.9 - - - -
367F THR 3.5 24.9 - - - -
386F PRO* 3.8 29.2 - - + -
387F VAL 4.3 0.4 - - - -
388F LEU* 4.1 17.5 - - + -
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Residues in contact with GLY 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ASP* 4.5 4.0 - - - -
269F LEU 3.8 0.8 + - - -
270F GLY* 2.9 26.6 + - - -
271F ALA 4.8 0.3 - - - +
272F ALA 3.6 0.8 - - - +
273F PHE* 1.3 77.3 - - - +
275F SER* 1.3 63.9 + - - -
277F GLY* 3.0 19.2 + - - -
278F GLU 4.3 0.3 + - - -
279F ARG* 3.5 18.9 + - - +
319F ASP 5.3 3.1 - - - -
320F PHE* 5.1 2.0 - - - -
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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