Contacts of the helix formed by residues 282 - 293 (chain A) in PDB entry 4V0P
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 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A TRP* 3.4 10.5 - - - -
278A LEU* 5.9 1.8 - - - -
281A THR* 1.3 83.6 + - - +
283A TYR* 1.3 65.7 + - - +
284A VAL* 3.6 8.0 + - - +
285A LYS* 3.3 32.6 + - - +
286A VAL* 3.1 25.1 + - - +
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Residues in contact with TYR 283 (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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209A ILE* 4.1 6.6 - - - +
210A ALA* 4.0 24.7 - - + -
213A GLY* 2.7 33.5 + - - -
214A ASP* 3.6 21.9 + - - -
273A TRP* 3.4 51.3 - + + +
278A LEU* 5.4 5.8 - - + -
282A SER* 1.3 73.3 - - - +
284A VAL* 1.3 66.8 + - + +
286A VAL* 3.2 3.1 + - - +
287A LEU* 3.1 33.5 + - + +
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Residues in contact with VAL 284 (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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282A SER* 3.3 7.7 + - - +
283A TYR* 1.3 78.8 - - + +
285A LYS* 1.3 61.3 + - + +
287A LEU* 3.4 4.5 + - - +
288A HIS* 2.9 37.8 + - + +
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Residues in contact with LYS 285 (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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182A LEU* 3.8 11.3 - - + +
280A GLU 5.6 1.6 + - - +
281A THR* 3.5 27.9 - - - +
282A SER* 3.3 21.4 + - - +
284A VAL* 1.3 79.4 - - + +
286A VAL* 1.3 57.6 + - - +
288A HIS* 3.6 6.7 + - - +
289A HIS* 2.9 29.3 + - - +
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Residues in contact with VAL 286 (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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182A LEU* 3.7 20.6 - - + -
203A ILE* 4.1 13.0 - - + +
206A LEU* 4.4 7.2 - - + -
207A ALA* 3.8 37.9 - - + +
210A ALA* 5.1 0.7 - - + -
273A TRP* 3.5 21.5 - - + -
281A THR* 3.8 9.0 - - + +
282A SER 3.1 18.1 + - - +
283A TYR 3.7 3.6 - - - +
285A LYS* 1.3 75.2 - - - +
287A LEU* 1.3 66.7 + - + +
289A HIS* 3.1 7.4 + - - +
290A MET* 3.0 23.0 + - - +
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Residues in contact with LEU 287 (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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207A ALA* 3.9 13.2 - - + +
210A ALA* 3.9 32.5 - - + +
211A ARG* 3.7 38.8 + - + +
283A TYR* 3.1 24.0 + - + +
284A VAL* 4.1 3.6 - - - +
286A VAL* 1.3 75.5 - - - +
288A HIS* 1.3 61.6 + - - +
290A MET* 3.5 5.2 + - - +
291A VAL* 3.2 27.1 + - - +
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Residues in contact with HIS 288 (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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284A VAL* 2.9 24.9 + - + +
285A LYS* 3.7 7.4 + - - +
287A LEU* 1.3 75.5 - - - +
289A HIS* 1.3 61.0 + - - +
291A VAL* 3.2 10.5 + - + +
292A LYS* 2.9 46.9 + - + +
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Residues in contact with HIS 289 (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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159A GLN 4.8 1.4 + - - -
165A GLU* 3.6 9.2 + - - -
181A CYS* 3.6 37.8 - - + +
182A LEU* 3.8 22.7 + - + +
203A ILE* 3.9 27.0 - - + +
285A LYS 2.9 19.4 + - - +
286A VAL* 3.3 5.2 - - - +
288A HIS* 1.3 79.7 + - - +
290A MET* 1.3 58.6 + - - +
292A LYS* 3.2 18.8 + - - +
293A ILE* 3.0 67.1 + - + +
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Residues in contact with MET 290 (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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160A LEU* 4.5 9.0 - - + -
203A ILE* 3.8 27.6 - - - -
204A ILE* 4.1 25.4 - - + -
207A ALA* 3.8 22.2 - - + -
211A ARG* 3.8 21.1 - - - +
286A VAL 3.0 14.2 + - - +
287A LEU* 3.8 7.6 - - - +
288A HIS 3.3 0.2 - - - -
289A HIS* 1.3 84.2 - - - +
291A VAL* 1.3 62.1 - - + +
293A ILE* 3.6 17.7 - - + +
294A SER* 3.3 24.4 + - - -
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Residues in contact with VAL 291 (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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287A LEU 3.2 16.6 - - - +
288A HIS* 3.2 11.2 + - + +
289A HIS 3.2 0.2 - - - -
290A MET* 1.3 77.3 - - + +
292A LYS* 1.3 65.8 + - - +
294A SER* 2.9 22.0 + - - -
296A GLY* 3.2 15.8 + - - -
297A PRO* 4.0 32.8 - - + -
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Residues in contact with LYS 292 (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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159A GLN* 3.9 11.4 - - - +
165A GLU* 3.4 25.5 + - - -
288A HIS* 2.9 32.3 + - + +
289A HIS* 3.2 24.8 + - - +
291A VAL* 1.3 79.6 - - - +
293A ILE* 1.3 62.1 + - + +
294A SER 3.4 0.5 + - - -
295A GLY* 3.4 10.0 + - - -
296A GLY* 4.2 3.9 + - - +
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Residues in contact with ILE 293 (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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156A SER* 5.2 9.9 + - - +
159A GLN* 3.9 39.7 - - + +
160A LEU* 3.7 49.5 - - + +
203A ILE* 6.0 0.2 - - + -
289A HIS* 3.0 57.0 + - + +
290A MET* 3.6 19.5 - - + +
292A LYS* 1.3 79.7 - - + +
294A SER* 1.3 59.5 + - - +
295A GLY 3.3 3.8 - - - -
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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