Contacts of the helix formed by residues 292 - 305 (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 ALA 292 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257F PRO* 6.1 5.4 - - + -
289F VAL 5.0 1.1 - - - +
290F GLY* 4.0 5.6 - - - -
291F ASP 1.3 73.6 + - - +
293F ALA* 1.3 67.7 + - + +
295F ASP* 3.6 6.9 + - - +
296F ALA* 3.3 20.9 + - - +
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Residues in contact with ALA 293 (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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255F VAL* 4.2 15.9 - - + +
256F MET 4.7 4.5 - - - +
257F PRO* 5.0 5.8 - - + -
261F MET* 3.8 23.9 - - + +
288F ALA* 4.2 6.5 - - + -
289F VAL 3.8 18.8 - - - +
291F ASP* 3.5 1.4 - - - +
292F ALA* 1.3 75.9 - - + +
294F GLY* 1.3 59.1 + - - +
295F ASP 3.1 0.2 + - - -
296F ALA* 3.1 1.7 + - - -
297F LEU* 2.7 37.3 + - - +
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Residues in contact with GLY 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F ALA* 3.5 20.8 - - - +
290F GLY 3.5 8.5 + - - -
291F ASP* 3.5 4.5 - - - +
292F ALA 3.5 1.2 - - - -
293F ALA* 1.3 78.3 - - - +
295F ASP* 1.3 59.3 + - - +
297F LEU* 3.8 1.9 - - - +
298F VAL* 3.3 20.4 + - - +
390F VAL* 5.5 1.1 - - - -
392F ARG* 3.3 33.7 + - - -
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Residues in contact with ASP 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ASP* 4.0 15.7 - - - +
292F ALA 3.6 9.0 + - - +
293F ALA 3.1 0.6 - - - -
294F GLY* 1.3 77.2 - - - +
296F ALA* 1.3 57.1 + - - +
298F VAL* 4.1 1.7 - - - +
299F SER* 3.0 31.9 + - - -
392F ARG* 2.9 27.1 + - - +
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Residues in contact with ALA 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F MET* 3.9 21.1 - - + +
292F ALA 3.3 13.4 + - - +
293F ALA* 3.1 4.6 + - - +
295F ASP* 1.3 76.4 - - - +
297F LEU* 1.3 61.2 + - - +
299F SER* 4.1 6.1 - - - -
300F LYS* 3.3 35.3 + - - +
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Residues in contact with LEU 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F VAL* 4.3 15.5 - - + -
261F MET* 4.0 22.6 - - + -
264F ALA* 5.5 0.7 - - + -
265F VAL* 4.1 13.5 - - + +
268F LEU* 4.0 23.1 - - + -
286F ALA* 3.8 35.2 - - + +
288F ALA* 4.5 7.6 - - + -
293F ALA 2.7 21.1 + - - +
294F GLY 3.8 3.4 - - - +
296F ALA* 1.3 71.2 - - - +
298F VAL* 1.3 61.3 + - - +
300F LYS* 3.5 1.2 + - - +
301F MET* 2.8 39.3 + - + +
388F LEU* 6.1 2.0 - - + -
390F VAL* 4.3 18.4 - - + -
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Residues in contact with VAL 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLY 3.3 19.1 + - - +
295F ASP* 4.1 2.5 - - - +
297F LEU* 1.3 72.6 - - + +
299F SER* 1.3 62.5 + - - +
301F MET* 4.1 5.1 - - - +
302F THR* 2.5 39.6 + - - +
347F VAL* 4.0 29.2 - - + -
368F LEU* 4.3 6.7 - - + -
370F ASP* 3.5 28.0 - - + +
390F VAL* 3.9 24.2 - - + -
392F ARG* 3.8 2.9 - - - +
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Residues in contact with SER 299 (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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295F ASP 3.0 21.7 + - - -
296F ALA* 4.1 6.5 - - - -
298F VAL* 1.3 81.4 - - - +
300F LYS* 1.3 65.3 + - - +
302F THR* 3.2 11.3 + - - -
303F GLN* 3.3 17.6 + - - +
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Residues in contact with LYS 300 (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* 4.2 20.8 - - + +
262F ASP* 2.9 38.2 + - - +
265F VAL* 3.8 17.6 - - + +
296F ALA* 3.3 26.2 + - - +
299F SER* 1.3 80.9 - - - +
301F MET* 1.3 63.6 + - - +
303F GLN* 3.4 9.7 + - - +
304F ALA* 3.2 24.4 + - - +
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Residues in contact with MET 301 (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* 3.8 26.0 - - + +
268F LEU* 4.6 10.8 - - - -
269F LEU* 3.3 41.1 - - + -
273F PHE* 4.2 4.3 - - + -
297F LEU* 2.8 27.5 + - + +
298F VAL* 4.1 0.4 - - - +
300F LYS* 1.3 74.0 - - - +
302F THR* 1.3 60.6 + - - +
304F ALA* 4.5 0.2 - - + -
305F MET* 3.0 57.6 + - + +
368F LEU* 3.5 17.9 - - + -
388F LEU* 4.3 20.0 - - + -
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Residues in contact with THR 302 (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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298F VAL* 2.5 25.2 + - - +
299F SER* 3.2 6.3 + - - -
301F MET* 1.3 77.4 - - - +
303F GLN* 1.3 61.9 + - + +
305F MET* 3.5 5.3 + - - +
306F GLN* 3.1 39.5 + - - +
347F VAL* 3.5 24.2 - - + +
348F VAL* 3.8 21.5 - - + -
368F LEU* 3.9 4.1 - - - +
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Residues in contact with GLN 303 (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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299F SER* 3.3 14.6 + - - +
300F LYS* 3.7 11.7 - - - +
301F MET 3.3 0.2 - - - -
302F THR* 1.3 77.5 - - + +
304F ALA* 1.3 66.9 + - - +
306F GLN* 3.2 28.9 + - - +
307F LYS* 4.1 5.8 + - - +
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Residues in contact with ALA 304 (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* 4.3 10.5 - - + -
269F LEU* 3.8 32.4 - - + +
300F LYS 3.2 14.0 + - - +
301F MET 4.2 2.5 - - - +
303F GLN* 1.3 80.1 - - - +
305F MET* 1.3 56.3 + - - +
306F GLN 3.3 0.2 - - - -
307F LYS* 3.2 35.2 + - + +
308F LEU* 4.1 3.3 + - - +
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Residues in contact with MET 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F LEU* 4.4 1.3 - - - -
273F PHE* 3.5 32.1 - - + -
301F MET* 3.0 45.3 + - + +
302F THR* 3.8 6.3 - - - +
303F GLN 3.1 0.4 - - - -
304F ALA* 1.3 74.3 - - - +
306F GLN* 1.3 64.7 + - - +
307F LYS 3.3 0.2 - - - -
308F LEU* 3.4 38.9 - - + +
348F VAL* 4.1 20.1 - - + +
366F GLY 3.8 21.8 - - - +
367F THR 4.2 2.0 - - - -
368F LEU* 3.6 21.5 - - + -
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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