Contacts of the helix formed by residues 292 - 307 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C PRO* 6.0 6.5 - - + -
289C VAL 5.0 1.1 - - - +
290C GLY* 3.8 6.7 - - - -
291C ASP 1.3 73.4 + - - +
293C ALA* 1.3 66.2 + - + +
294C GLY 3.7 0.2 + - - -
295C ASP* 3.8 6.0 + - - +
296C ALA* 3.6 19.2 + - - +
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 4.4 14.1 - - + +
257C PRO* 4.8 12.6 - - + -
261C MET* 3.9 24.1 - - + +
288C ALA* 4.3 5.2 - - + -
289C VAL 3.9 18.2 - - - +
290C GLY 4.4 0.4 - - - +
291C ASP* 3.4 1.6 - - - +
292C ALA* 1.3 77.7 - - + +
294C GLY* 1.3 67.5 + - - +
296C ALA* 3.4 2.4 + - - +
297C LEU* 2.8 26.7 + - - +
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Residues in contact with GLY 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ALA* 3.6 20.1 - - - +
290C GLY 3.3 10.7 + - - -
291C ASP* 3.6 0.4 - - - +
292C ALA 3.5 0.4 - - - -
293C ALA* 1.3 78.9 - - - +
295C ASP* 1.3 62.3 + - - +
297C LEU* 3.5 2.1 - - - +
298C VAL* 3.0 28.6 + - - +
390C VAL* 5.4 0.9 - - - -
392C ARG* 3.5 24.5 - - - -
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Residues in contact with ASP 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ASP* 3.5 21.3 - - - +
292C ALA 3.8 6.9 + - - +
293C ALA 3.3 0.4 - - - -
294C GLY* 1.3 75.1 - - - +
296C ALA* 1.3 58.0 + - - +
298C VAL* 3.4 2.6 + - - +
299C SER* 2.8 32.2 + - - -
392C ARG* 3.4 25.3 + - - +
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Residues in contact with ALA 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C MET* 4.4 15.9 - - + +
292C ALA 3.6 14.6 + - - +
293C ALA* 3.4 6.3 + - - +
294C GLY 3.4 0.6 - - - -
295C ASP* 1.3 74.8 - - - +
297C LEU* 1.3 59.5 + - - +
299C SER* 3.7 5.6 - - - -
300C LYS* 3.0 44.1 + - - +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 4.5 13.9 - - + -
261C MET* 4.0 19.7 - - - -
264C ALA* 5.5 0.4 - - + -
265C VAL* 3.9 20.8 - - + +
268C LEU* 4.0 20.9 - - + -
286C ALA* 3.8 26.9 - - + -
288C ALA* 4.6 8.5 - - + -
293C ALA 2.8 18.2 + - - +
294C GLY 3.5 2.7 - - - +
296C ALA* 1.3 74.6 - - - +
298C VAL* 1.3 61.3 + - - +
300C LYS* 4.0 0.5 - - - +
301C MET* 2.9 41.1 + - + +
388C LEU* 6.2 2.5 - - + -
390C VAL* 3.9 23.3 - - + -
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C GLY 3.0 16.7 + - - +
295C ASP* 4.0 2.7 - - - +
297C LEU* 1.3 75.8 - - + +
299C SER* 1.3 58.9 - - - +
301C MET* 4.0 5.3 - - - +
302C THR* 2.7 34.4 + - - +
347C VAL* 3.8 34.8 - - + -
368C LEU* 4.2 6.7 - - + -
370C ASP* 3.4 29.2 - - + +
390C VAL* 4.2 22.9 - - + -
392C ARG* 3.9 4.5 - - - +
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Residues in contact with SER 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ASP 2.8 18.6 + - - -
296C ALA* 3.7 8.3 - - - -
298C VAL* 1.3 81.1 - - - +
300C LYS* 1.3 70.3 + - - +
302C THR* 3.1 12.9 + - - -
303C GLN* 3.2 17.1 + - - +
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Residues in contact with LYS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C MET* 4.2 23.2 - - + +
262C ASP* 2.7 36.0 + - - +
265C VAL* 3.9 18.1 - - + +
296C ALA* 3.0 24.5 + - - +
299C SER* 1.3 83.5 - - - +
301C MET* 1.3 56.0 + - - +
303C GLN* 3.3 10.4 + - - +
304C ALA* 3.0 29.3 + - - +
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Residues in contact with MET 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL* 3.9 23.6 - - + +
268C LEU* 4.8 9.2 - - - -
269C LEU* 3.2 40.6 - - + -
273C PHE* 4.1 5.2 - - + -
297C LEU* 2.9 26.8 + - + +
298C VAL* 4.0 0.4 - - - +
300C LYS* 1.3 73.6 - - - +
302C THR* 1.3 59.2 + - - +
304C ALA* 3.2 1.7 + - + -
305C MET* 2.8 61.3 + - + +
368C LEU* 3.5 15.9 - - + -
388C LEU* 4.2 21.8 - - + -
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Residues in contact with THR 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C VAL* 2.7 21.3 + - - +
299C SER* 3.3 9.6 - - - -
301C MET* 1.3 76.1 - - - +
303C GLN* 1.3 61.8 + - + +
305C MET* 3.2 13.5 + - - +
306C GLN* 2.6 36.4 + - - +
347C VAL* 3.3 24.8 - - + +
348C VAL* 4.0 17.3 - - + -
368C LEU* 4.1 2.7 - - - +
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Residues in contact with GLN 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C SER* 3.2 16.2 + - - +
300C LYS* 3.4 13.5 - - - +
301C MET 3.2 0.4 - - - -
302C THR* 1.3 81.8 - - + +
304C ALA* 1.3 62.1 + - - +
306C GLN* 3.4 20.6 + - - +
307C LYS* 4.2 7.8 + - - +
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Residues in contact with ALA 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL* 4.1 13.5 - - + -
266C ASN* 6.1 0.2 - - - -
269C LEU* 3.9 35.0 - - + +
300C LYS 3.0 15.4 + - - +
301C MET 3.9 2.9 - - - +
303C GLN* 1.3 76.2 - - - +
305C MET* 1.3 60.2 + - - +
307C LYS* 3.4 26.3 + - + +
308C LEU* 4.0 3.6 + - - +
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Residues in contact with MET 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C LEU* 4.5 1.8 - - - -
273C PHE* 3.8 24.2 - - + -
301C MET* 2.8 53.9 + - + +
302C THR* 3.5 7.2 - - - +
303C GLN 3.2 0.4 - - - -
304C ALA* 1.3 71.3 - - - +
306C GLN* 1.3 65.3 + - - +
307C LYS 3.3 0.2 - - - -
308C LEU* 3.4 41.9 - - + +
348C VAL* 4.0 15.6 - - + +
366C GLY 3.9 20.0 - - - +
368C LEU* 3.5 35.4 - - + -
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Residues in contact with GLN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C THR* 2.6 42.4 + - - +
303C GLN* 3.6 13.4 + - - +
304C ALA 3.3 0.6 - - - -
305C MET* 1.3 78.3 + - - +
307C LYS* 1.3 62.3 + - + +
308C LEU 3.4 6.1 + - - +
348C VAL* 4.6 22.2 - - - +
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Residues in contact with LYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C GLN 4.4 8.7 - - - +
304C ALA* 3.4 17.0 + - + +
305C MET 3.3 0.8 - - - -
306C GLN* 1.3 77.1 - - + +
308C LEU* 1.3 63.4 - - - +
309C LYS* 3.5 21.0 + - - +
319C ASP* 3.9 3.5 - - - +
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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