Contacts of the helix formed by residues 231 - 242 (chain A) in PDB entry 4M04
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ARG* 3.2 12.9 + - - -
228A VAL* 2.8 23.7 + - - -
230A ARG* 1.3 79.8 - - - +
232A GLU* 1.3 65.7 + - - +
233A ARG* 4.2 7.0 - - - +
234A TYR* 3.1 17.9 + - - +
235A GLN* 3.2 21.3 + - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ARG 3.6 2.4 + - - -
231A SER* 1.3 73.8 - - - +
233A ARG* 1.3 64.2 + - - +
235A GLN* 3.9 6.5 - - - +
236A THR* 2.9 36.7 + - - +
255A TYR* 3.7 10.5 + - - +
260A ARG* 3.1 38.3 + - - +
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Residues in contact with ARG 233 (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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169A PHE* 3.2 24.8 + - + -
170A GLU* 2.8 34.1 + - - +
231A SER* 4.4 6.3 - - - +
232A GLU* 1.3 78.8 - - - +
234A TYR* 1.3 63.4 + - - +
236A THR* 4.1 0.5 - - - -
237A MET* 3.0 47.2 + - + +
252A ASP* 2.8 33.7 + - - -
255A TYR* 3.3 55.1 + - + +
256A ARG* 5.1 1.6 - - - +
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Residues in contact with TYR 234 (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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162A ILE* 3.3 29.5 - - + +
165A GLU* 2.6 38.3 + - + -
166A ALA* 4.3 5.4 - - + -
169A PHE* 3.7 25.1 - + - -
228A VAL* 3.1 35.7 - - + +
229A ARG* 3.9 19.5 - - + -
231A SER* 3.1 20.6 + - - +
233A ARG* 1.3 81.0 - - - +
235A GLN* 1.3 63.2 + - + +
238A LYS* 2.9 57.3 + - + +
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ARG 3.0 25.1 - - - +
230A ARG* 3.3 18.0 + - - +
231A SER 3.2 17.4 + - - +
232A GLU* 4.0 5.7 - - - +
234A TYR* 1.3 82.5 - - + +
236A THR* 1.3 58.4 + - - +
238A LYS* 3.6 4.1 + - - +
239A LEU* 3.0 27.7 + - - +
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Residues in contact with THR 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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232A GLU* 2.9 22.0 + - - +
235A GLN* 1.3 75.5 - - - +
237A MET* 1.3 60.0 + - - +
238A LYS 3.2 1.1 - - - -
239A LEU* 3.3 4.9 + - - +
240A PHE* 2.8 52.6 + - + +
255A TYR* 3.6 24.9 - - + -
259A LEU 3.9 0.2 - - - +
260A ARG* 3.6 42.0 + - - +
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Residues in contact with MET 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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169A PHE* 3.6 50.9 - - + +
233A ARG* 3.0 50.0 + - - +
236A THR* 1.3 75.4 - - - +
238A LYS* 1.3 52.0 + - - +
240A PHE* 4.5 0.9 - - - +
241A THR* 2.7 42.4 + - + +
248A VAL* 3.6 31.9 - - + +
251A ALA* 3.7 14.6 - - + +
252A ASP* 3.5 26.0 - - + +
255A TYR* 4.4 4.5 - - + -
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Residues in contact with LYS 238 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 2.7 32.9 + - - +
169A PHE* 3.7 13.6 - - + -
234A TYR* 2.9 42.5 + - + +
235A GLN* 3.8 5.4 - - - +
237A MET* 1.3 77.3 - - - +
239A LEU* 1.3 62.8 + - - +
241A THR* 3.3 3.0 + - - +
242A GLN* 3.2 51.9 + - + +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLN 3.0 18.1 + - - +
236A THR* 3.3 4.9 + - - +
238A LYS* 1.3 77.1 - - - +
240A PHE* 1.3 67.7 + - + +
242A GLN* 3.5 26.0 - - - +
243A ILE* 3.7 9.5 - - - +
260A ARG 3.7 22.4 - - - +
261A THR* 4.1 10.1 - - + -
262A LEU* 3.8 37.9 - - + +
283A HIS* 4.3 7.0 + - + -
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Residues in contact with PHE 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 THR* 2.8 35.6 + - + +
239A LEU* 1.3 83.3 - - + +
241A THR* 1.3 62.5 + - - +
243A ILE* 3.0 26.7 + - + +
246A VAL* 3.3 14.7 - - + +
251A ALA* 3.5 35.9 - - + -
254A TRP* 3.9 26.9 - + + -
255A TYR 4.5 0.9 - - - -
259A LEU* 3.7 16.4 - - + -
260A ARG 3.6 34.3 - - - -
261A THR 3.8 16.2 - - - -
262A LEU* 4.6 0.4 - - + -
265A LEU* 3.8 26.2 - - + -
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Residues in contact with THR 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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169A PHE* 3.7 23.8 - - + -
237A MET* 2.7 25.9 + - + +
238A LYS* 3.3 7.4 + - - -
240A PHE* 1.3 76.3 - - - +
242A GLN* 1.3 54.7 + - - +
246A VAL* 3.7 8.3 - - - -
247A GLY* 3.8 17.0 - - - +
248A VAL* 3.9 11.9 - - + +
251A ALA* 3.7 20.0 - - + -
707A NA 2.3 26.6 - - - -
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Residues in contact with GLN 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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238A LYS* 3.2 54.2 + - + +
239A LEU* 3.5 20.4 - - - +
240A PHE 3.1 0.8 - - - -
241A THR* 1.3 75.0 + - - +
243A ILE* 1.3 64.1 + - - +
244A PHE* 3.4 2.6 + - - -
283A HIS* 4.0 23.3 + - - +
286A LEU* 6.2 0.2 - - - +
287A SER* 5.3 2.9 + - - +
707A NA 4.1 0.7 - - - -
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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