Contacts of the helix formed by residues 292 - 306 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E PRO* 6.3 4.0 - - + -
289E VAL 5.1 0.4 - - - +
290E GLY* 3.8 5.6 - - - -
291E ASP* 1.3 75.5 + - - +
293E ALA* 1.3 68.8 + - + +
295E ASP* 3.2 14.6 + - - +
296E ALA* 3.3 12.0 + - - +
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Residues in contact with ALA 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E VAL* 4.1 15.3 - - + +
256E MET 5.2 0.2 - - - +
257E PRO* 5.1 10.0 - - + +
261E MET* 4.0 23.0 - - + +
288E ALA* 4.3 5.6 - - + -
289E VAL 3.6 13.7 - - - +
290E GLY 3.5 8.1 - - - +
291E ASP* 3.4 1.0 - - - +
292E ALA* 1.3 76.6 - - - +
294E GLY* 1.3 53.3 + - - +
296E ALA* 2.9 8.3 + - - +
297E LEU* 2.7 37.1 + - + +
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Residues in contact with GLY 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E ALA* 3.3 22.2 - - - +
290E GLY 2.9 13.7 + - - -
291E ASP* 3.4 3.5 - - - +
292E ALA 3.3 0.2 + - - -
293E ALA* 1.3 73.1 - - - +
295E ASP* 1.3 58.0 + - - +
297E LEU* 4.0 3.8 - - - +
298E VAL* 3.1 32.4 + - - +
390E VAL* 5.3 0.9 - - - -
392E ARG* 3.1 21.3 + - - -
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Residues in contact with ASP 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E ASP* 3.5 22.3 - - - +
292E ALA 3.2 8.7 + - - +
293E ALA 3.2 0.6 - - - -
294E GLY* 1.3 72.9 - - - +
296E ALA* 1.3 63.4 + - - +
298E VAL* 3.6 3.1 + - - +
299E SER* 2.9 29.8 + - - -
371E HIS* 5.6 0.5 + - - -
392E ARG* 2.9 26.1 + - - +
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Residues in contact with ALA 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E MET* 4.3 21.5 - - + -
292E ALA 3.3 9.4 + - - +
293E ALA* 2.9 9.7 + - - +
295E ASP* 1.3 77.1 - - - +
297E LEU* 1.3 64.7 + - - +
299E SER* 2.9 7.4 + - - -
300E LYS* 2.9 35.0 + - - +
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Residues in contact with LEU 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E VAL* 4.3 13.7 - - + -
261E MET* 3.7 24.8 - - - -
264E ALA* 5.3 1.6 - - + -
265E VAL* 4.0 13.0 - - + +
268E LEU* 3.9 23.6 - - + -
286E ALA* 3.8 28.0 - - + +
288E ALA* 4.2 19.7 - - + -
293E ALA* 2.7 19.9 + - + +
294E GLY* 4.0 5.4 - - - +
296E ALA* 1.3 72.5 - - - +
298E VAL* 1.3 58.4 + - + +
300E LYS* 4.2 0.3 - - - -
301E MET* 2.9 40.3 + - + +
388E LEU* 6.3 1.1 - - + -
390E VAL* 4.6 15.3 - - + -
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Residues in contact with VAL 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E GLY 3.1 19.4 + - - +
295E ASP* 4.0 3.8 - - - +
296E ALA 3.3 0.4 - - - -
297E LEU* 1.3 78.3 - - + +
299E SER* 1.3 61.9 + - - +
301E MET* 4.0 4.7 - - - +
302E THR* 2.6 39.4 + - - +
347E VAL* 4.1 22.0 - - + -
368E LEU* 4.2 6.0 - - + +
370E ASP* 3.6 34.8 - - + +
390E VAL* 4.2 19.7 - - + -
392E ARG* 3.8 4.5 - - - +
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Residues in contact with SER 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E ASP 2.9 19.3 + - - -
296E ALA* 2.9 9.5 + - - -
298E VAL* 1.3 80.2 - - - +
300E LYS* 1.3 65.0 + - - +
302E THR* 3.6 4.9 - - - -
303E GLN* 3.3 24.5 + - - +
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Residues in contact with LYS 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E MET* 4.1 25.3 - - + +
262E ASP* 2.6 36.0 + - - +
265E VAL* 3.9 18.0 - - + +
296E ALA* 2.9 23.9 + - - +
299E SER* 1.3 74.7 - - - +
301E MET* 1.3 59.9 + - - +
303E GLN* 3.2 11.0 + - - +
304E ALA* 3.0 30.1 + - - +
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Residues in contact with MET 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E VAL* 3.8 25.9 - - + +
268E LEU* 4.5 11.9 - - - -
269E LEU* 3.3 41.1 - - + -
273E PHE* 4.2 4.3 - - + -
297E LEU* 2.9 28.1 + - + +
298E VAL* 4.0 2.9 - - - +
300E LYS* 1.3 74.5 - - - +
302E THR* 1.3 57.8 + - - +
304E ALA* 4.3 1.3 - - + -
305E MET* 3.0 53.7 + - + +
368E LEU* 3.9 10.8 - - + -
388E LEU* 3.8 26.0 - - + -
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Residues in contact with THR 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E VAL* 2.6 24.0 + - - +
299E SER* 3.6 5.6 - - - -
301E MET* 1.3 76.7 - - - +
303E GLN* 1.3 61.1 + - + +
305E MET* 3.5 12.5 + - - +
306E GLN* 2.9 33.8 + - - +
347E VAL* 3.3 25.0 - - + +
348E VAL* 3.8 21.8 - - + -
368E LEU* 3.6 4.3 - - - +
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Residues in contact with GLN 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E SER* 3.3 15.8 + - - +
300E LYS* 3.2 12.4 + - - +
302E THR* 1.3 78.0 - - + +
304E ALA* 1.3 64.1 + - - +
305E MET 3.3 0.7 + - - -
306E GLN* 3.3 25.1 + - - +
307E LYS* 4.2 8.1 + - - +
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Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E VAL* 4.0 15.0 - - + -
269E LEU* 3.8 32.1 - - + +
300E LYS 3.0 16.6 + - - +
301E MET* 4.0 3.6 - - + +
303E GLN* 1.3 77.1 - - - +
305E MET* 1.3 61.6 + - - +
307E LYS* 3.4 27.0 + - + +
308E LEU* 4.1 3.5 + - - +
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Residues in contact with MET 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E LEU* 4.6 1.6 - - - -
273E PHE* 3.8 23.8 - - + -
301E MET* 3.0 55.4 + - + +
302E THR* 3.6 9.0 - - - +
303E GLN 3.1 0.6 - - - -
304E ALA* 1.3 75.7 - - - +
306E GLN* 1.3 64.4 + - - +
307E LYS 3.3 0.4 - - - -
308E LEU* 3.5 39.8 - - + +
348E VAL* 4.0 25.6 - - + +
366E GLY 4.4 7.4 - - - -
368E LEU* 3.6 36.3 - - + -
388E LEU* 5.0 0.2 - - + -
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Residues in contact with GLN 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E THR* 2.9 38.8 + - - +
303E GLN* 3.3 17.3 + - - +
304E ALA 3.3 1.2 - - - -
305E MET* 1.3 76.0 + - - +
307E LYS* 1.3 62.0 + - + +
308E LEU 3.2 10.5 + - - +
348E VAL* 4.8 15.2 - - - +
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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