Contacts of the helix formed by residues 228 - 241 (chain A) in PDB entry 5H2U
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 HIS 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LEU* 1.3 78.3 - - - +
229A GLN* 1.3 60.2 + - - +
230A GLN* 3.1 38.3 + - + +
231A MET* 3.1 35.8 + - + +
232A LEU 2.9 23.7 + - - -
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Residues in contact with GLN 229 (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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223A ARG* 2.2 37.0 + - - +
227A LEU 3.8 0.4 + - - -
228A HIS* 1.3 73.9 - - - +
230A GLN* 1.3 54.0 + - - +
232A LEU* 3.4 6.0 - - - +
233A GLN* 2.8 61.0 + - + +
255A SER* 2.7 27.1 + - - -
256A VAL* 4.5 6.7 - - - +
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Residues in contact with GLN 230 (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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228A HIS* 3.1 25.4 + - + +
229A GLN* 1.3 77.8 - - - +
231A MET* 1.3 61.7 + - + +
233A GLN* 3.9 5.2 - - - +
234A SER* 3.2 22.6 + - - -
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Residues in contact with MET 231 (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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227A LEU* 4.4 25.1 - - + -
228A HIS* 3.1 30.7 + - + +
230A GLN* 1.3 75.7 - - + +
232A LEU* 1.3 61.1 + - - +
234A SER* 3.2 16.0 + - - +
235A GLU* 2.8 58.4 + - - +
335A ARG* 5.1 7.9 - - - +
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Residues in contact with LEU 232 (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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223A ARG* 3.3 29.6 - - - +
226A LEU* 3.6 37.9 - - + -
227A LEU* 4.1 7.5 - - - +
228A HIS 2.9 16.8 + - - +
229A GLN* 3.4 14.8 - - - +
231A MET* 1.3 75.1 - - - +
233A GLN* 1.3 62.6 + - - +
235A GLU* 3.2 5.5 + - - +
236A ILE* 3.1 37.8 + - + +
255A SER* 4.3 17.9 - - - +
260A VAL* 4.8 4.7 - - + -
262A ILE* 6.1 0.7 - - + -
336A LEU* 4.2 25.1 - - + +
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Residues in contact with GLN 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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185A GLU* 3.9 10.7 + - - +
229A GLN* 2.8 43.6 + - + +
230A GLN* 3.9 6.5 - - - +
232A LEU* 1.3 74.4 - - - +
234A SER* 1.3 62.0 + - - +
236A ILE* 3.3 11.1 + - - +
237A GLN* 3.3 46.5 + - + +
253A VAL* 5.5 0.2 - - - +
255A SER* 3.0 30.5 + - - -
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN 3.2 17.6 + - - -
231A MET* 3.2 20.9 + - - +
233A GLN* 1.3 78.7 - - - +
235A GLU* 1.3 62.1 + - - +
236A ILE 3.6 0.2 + - - -
237A GLN* 3.7 7.0 + - - +
238A ALA* 3.6 18.5 + - - +
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Residues in contact with GLU 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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227A LEU* 6.4 0.4 - - + -
231A MET* 2.8 38.9 + - - +
232A LEU 3.8 0.4 - - - +
234A SER* 1.3 77.0 + - - +
236A ILE* 1.3 59.7 + - - +
238A ALA* 3.5 10.4 + - - +
239A MET* 3.1 30.1 + - + +
308A TYR* 4.6 5.0 + - - +
332A GLY 5.0 1.8 - - - +
335A ARG* 3.4 38.8 + - + +
336A LEU* 3.5 26.5 - - + -
504A GOL 2.6 27.7 + - - -
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Residues in contact with ILE 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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184A CXM 4.6 5.8 - - - +
232A LEU* 3.1 40.3 + - + +
233A GLN* 3.7 11.2 - - - +
234A SER 3.3 0.2 - - - -
235A GLU* 1.3 76.4 - - - +
237A GLN* 1.3 74.3 + - - +
239A MET* 3.8 6.5 - - + +
240A LYS* 2.9 30.1 + - + +
250A LEU* 4.3 7.1 - - + +
253A VAL* 4.2 33.7 - - + -
255A SER* 4.1 22.2 - - - -
260A VAL* 6.1 0.4 - - + -
262A ILE* 5.4 7.0 - - + -
336A LEU* 4.3 16.8 - - + -
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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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184A CXM 5.5 0.6 + - - -
185A GLU* 6.4 0.4 - - - +
233A GLN* 3.3 29.6 + - + +
234A SER* 4.1 7.6 - - - +
235A GLU 3.4 0.2 - - - -
236A ILE* 1.3 94.0 - - - +
238A ALA* 1.3 62.1 + - - +
240A LYS* 3.0 35.8 + - - +
241A LYS* 3.3 37.0 + - - +
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Residues in contact with ALA 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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234A SER 3.6 10.7 + - - +
235A GLU* 3.5 14.7 + - - +
236A ILE 3.3 0.4 - - - -
237A GLN* 1.3 80.3 - - - +
239A MET* 1.3 60.6 + - - +
241A LYS* 3.6 21.0 + - - +
242A LEU* 3.8 12.1 - - - +
308A TYR* 4.2 16.8 - - + -
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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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235A GLU* 3.1 16.3 + - + +
236A ILE* 3.3 7.1 + - - +
238A ALA* 1.3 77.6 - - - +
240A LYS* 1.3 61.1 + - - +
241A LYS 3.5 0.3 + - - -
242A LEU* 3.6 10.9 + - - +
250A LEU* 3.7 31.2 + - + +
262A ILE* 5.4 2.0 - - - -
308A TYR* 3.5 19.7 + - - +
331A PHE* 3.4 48.5 - - + +
332A GLY 3.5 22.7 - - - +
333A LEU* 3.7 13.0 - - - +
336A LEU* 3.9 26.9 - - + -
501A 1N1 6.1 2.0 - - - -
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Residues in contact with LYS 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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184A CXM 3.6 42.0 - - - +
236A ILE* 2.9 18.8 + - + +
237A GLN* 3.0 48.7 + - - +
239A MET* 1.3 73.8 - - - +
241A LYS* 1.3 72.4 + - - +
242A LEU 3.2 6.9 + - - +
243A ARG* 5.3 7.8 + - - -
249A ALA* 6.1 0.3 - - - +
250A LEU* 3.9 21.2 + - + +
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Residues in contact with LYS 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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237A GLN* 3.3 27.3 + - - +
238A ALA* 3.6 13.4 + - - +
239A MET 3.3 0.8 - - - -
240A LYS* 1.3 87.7 - - + +
242A LEU* 1.3 64.5 + - + +
243A ARG* 3.6 6.8 + - - +
302A TYR* 4.1 4.0 + - - -
306A GLN* 5.7 2.1 + - - +
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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