Contacts of the helix formed by residues 296 - 305 (chain A) in PDB entry 4Z30
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 SER 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A LEU* 6.5 0.7 - - - -
295A ILE* 1.3 74.1 - - - +
297A PRO* 1.4 65.4 - - - -
298A GLU* 3.6 7.9 + - - +
299A GLN* 2.5 62.2 + - - +
300A TRP* 2.9 11.9 + - - -
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Residues in contact with PRO 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ILE 4.4 0.2 - - - +
296A SER* 1.4 84.9 - - - +
298A GLU* 1.3 55.8 + - - +
300A TRP* 3.5 10.3 - - + +
301A SER* 2.8 31.9 + - - -
311A LYS* 3.6 31.5 - - + +
314A MET* 4.1 5.5 - - + +
315A GLN* 3.9 26.0 - - + +
318A ILE* 4.0 14.8 - - + -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A SER* 2.8 11.0 + - - +
297A PRO* 1.3 73.6 - - - +
299A GLN* 1.3 63.6 + - + +
301A SER* 3.6 6.0 + - - -
302A SER* 3.1 22.3 + - - -
307A ASP 4.9 0.2 - - - +
308A LEU* 5.3 11.3 - - + +
311A LYS* 4.7 9.3 - - + +
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 5.3 4.4 - - - +
171A GLN* 3.0 31.4 + - - +
173A PRO* 5.8 4.4 - - + +
176A LEU* 3.9 11.1 - - + +
294A ARG 4.6 0.5 - - - +
295A ILE* 3.3 20.5 - - + -
296A SER* 2.5 51.2 + - - +
298A GLU* 1.3 71.3 - - + +
300A TRP* 1.3 51.7 + - - +
302A SER* 3.1 8.4 + - - -
303A LEU* 2.7 44.9 + - + +
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Residues in contact with TRP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.6 26.7 - - + -
284A ILE* 3.5 34.3 - - + -
285A VAL* 3.5 25.1 - - + +
288A ALA* 3.6 24.5 - - + -
295A ILE* 3.5 32.3 + - + +
296A SER 2.9 17.0 + - - -
297A PRO 3.5 8.5 - - - +
299A GLN* 1.3 76.2 - - - +
301A SER* 1.3 63.5 + - - +
303A LEU* 3.0 7.2 + - + +
304A LEU* 3.0 53.2 + - + +
314A MET* 3.9 19.1 - - + -
318A ILE* 3.3 31.8 - - + +
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A PRO 2.8 21.7 + - - -
298A GLU* 3.9 5.4 - - - -
300A TRP* 1.3 72.4 - - - +
302A SER* 1.3 62.6 + - - +
305A TYR* 3.2 23.4 + - - +
306A GLY 3.3 3.5 + - - -
307A ASP* 2.6 27.1 + - - +
308A LEU* 3.3 5.8 - - - -
310A HIS* 2.7 35.7 + - - +
311A LYS* 3.7 15.5 - - - -
314A MET* 4.1 3.7 - - - +
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PRO* 5.1 0.7 - - - +
298A GLU 3.1 13.8 + - - -
299A GLN* 3.1 11.1 + - - -
301A SER* 1.3 78.7 - - - +
303A LEU* 1.3 63.8 + - - +
306A GLY* 3.2 19.6 + - - -
307A ASP 3.3 15.8 + - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 6.2 2.9 - - + -
177A SER* 3.7 31.0 - - - -
180A LEU* 4.0 21.1 - - + -
181A TRP* 4.1 23.4 - - + +
191A PHE* 3.8 13.5 - - - -
194A PRO* 4.0 7.8 - - - +
295A ILE* 4.2 17.9 - - + -
299A GLN* 2.7 32.1 + - + +
300A TRP* 3.0 8.9 + - + +
302A SER* 1.3 78.3 - - - +
304A LEU* 1.3 69.7 + - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A TRP* 4.0 17.7 - - + -
191A PHE* 3.4 27.3 - - + -
194A PRO* 3.4 17.5 - - - +
277A ARG* 3.2 25.4 + - - +
281A ASP* 3.9 34.1 - - + +
284A ILE* 4.4 10.3 - - + -
300A TRP* 3.0 39.5 + - + +
303A LEU* 1.3 85.1 - - + +
305A TYR* 1.3 66.4 + - + +
314A MET* 4.2 14.6 - - + -
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PRO* 3.5 16.7 - - - +
198A GLU* 6.2 1.6 - - - -
273A TYR* 4.8 3.8 - + - -
277A ARG* 3.3 45.7 - - + +
281A ASP* 2.4 31.9 + - - -
301A SER* 3.2 13.4 + - - +
304A LEU* 1.3 85.9 - - + +
306A GLY* 1.3 63.5 + - - +
307A ASP* 4.0 9.5 - - - +
310A HIS* 3.6 60.1 - + + +
313A HIS* 3.7 10.2 + + - -
314A MET* 4.5 9.0 - - - -
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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