Contacts of the helix formed by residues 234 - 244 (chain A) in PDB entry 4C8B
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 ASN 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A VAL* 3.7 2.7 - - - +
233A THR* 1.3 78.0 - - - +
235A PRO* 1.3 83.8 - - - +
236A LEU* 3.2 27.0 + - - +
237A GLN* 3.2 39.4 + - + +
238A ILE* 3.5 7.8 + - - +
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Residues in contact with PRO 235 (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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188A GLY 5.9 3.4 - - - +
190A ILE* 3.7 19.2 - - + +
233A THR 3.8 7.4 - - - +
234A ASN* 1.3 91.1 - - - +
236A LEU* 1.3 62.6 + - + +
237A GLN 3.3 0.2 - - - -
238A ILE* 3.2 16.2 + - + +
239A MET* 3.0 32.0 + - - +
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Residues in contact with LEU 236 (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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234A ASN* 3.2 20.3 + - - +
235A PRO* 1.3 78.8 - - + +
237A GLN* 1.3 60.2 + - + +
239A MET* 3.2 27.6 + - + +
240A TYR* 2.9 28.4 + - - +
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Residues in contact with GLN 237 (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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232A VAL* 4.5 10.7 - - + +
233A THR* 4.5 7.3 + - - -
234A ASN* 3.2 38.2 + - + +
236A LEU* 1.3 73.7 - - + +
238A ILE* 1.3 61.2 + - - +
240A TYR* 3.7 6.1 - - - +
241A SER* 2.9 34.5 + - - +
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Residues in contact with ILE 238 (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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188A GLY 6.0 0.7 - - - +
190A ILE* 3.5 19.7 - - + -
191A ILE* 4.2 15.9 - - + -
198A TYR* 5.1 0.2 - - - +
228A PRO 5.0 0.2 - - - +
229A PHE* 3.4 54.7 - - + +
232A VAL* 3.4 28.9 - - + +
234A ASN 3.5 3.6 + - - +
235A PRO* 3.2 19.6 + - + +
236A LEU 3.2 0.4 - - - -
237A GLN* 1.3 80.2 - - - +
239A MET* 1.3 61.7 + - - +
241A SER* 3.4 4.9 + - - -
242A VAL* 3.0 29.0 + - + +
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Residues in contact with MET 239 (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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190A ILE* 3.7 31.0 - - + -
193A MET* 5.9 1.3 - - + -
198A TYR* 3.3 59.6 - - + -
235A PRO* 3.0 18.0 + - - +
236A LEU* 3.2 32.3 + - + +
238A ILE* 1.3 74.7 - - - +
240A TYR* 1.3 57.4 + - - +
243A SER* 2.8 29.5 + - - -
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Residues in contact with TYR 240 (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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236A LEU 2.9 16.3 + - - +
237A GLN* 3.7 7.4 - - - +
239A MET* 1.3 76.9 - - - +
241A SER* 1.3 68.8 + - - +
243A SER* 2.9 27.2 - - - -
244A GLN* 2.9 40.7 + - + +
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Residues in contact with SER 241 (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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229A PHE* 5.1 8.7 - - - -
237A GLN* 2.9 22.4 + - - +
238A ILE* 3.8 6.5 - - - -
240A TYR* 1.3 79.2 - - - +
242A VAL* 1.3 62.3 + - - +
244A GLN* 3.3 6.8 + - - +
245A GLY 3.3 0.3 + - - -
246A HIS* 3.0 51.9 + - - +
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Residues in contact with VAL 242 (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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191A ILE* 6.0 2.5 - - - +
193A MET 4.7 0.9 - - - +
195A PRO* 3.8 16.8 - - + +
198A TYR* 3.4 24.9 - - - +
213A TYR* 3.4 25.8 - - + +
229A PHE* 3.9 23.3 - - + -
238A ILE* 3.0 25.0 + - + +
241A SER* 1.3 71.4 - - - +
243A SER* 1.3 68.9 + - - +
244A GLN 3.0 1.3 - - - -
245A GLY 2.9 11.1 + - - -
246A HIS 3.5 14.8 - - - +
247A ARG* 3.4 13.6 + - - +
275A GLN* 3.5 5.5 + - - +
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Residues in contact with SER 243 (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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195A PRO* 4.2 12.6 - - - -
198A TYR* 4.2 7.7 - - - -
239A MET 2.8 14.7 + - - -
240A TYR* 2.9 22.0 - - - -
242A VAL* 1.3 73.7 - - - +
244A GLN* 1.3 68.3 + - - -
275A GLN* 2.8 23.2 + - - -
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Residues in contact with GLN 244 (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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240A TYR* 2.9 49.2 + - + +
241A SER* 3.7 8.3 - - - +
242A VAL 3.0 0.6 - - - -
243A SER* 1.3 86.9 + - - +
245A GLY* 1.3 57.5 + - - +
246A HIS* 3.5 17.9 + - + +
275A GLN* 4.6 0.9 - - - -
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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