Contacts of the helix formed by residues 230 - 242 (chain A) in PDB entry 5UQ9
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A ILE* 5.5 0.2 - - - +
224A ASN* 3.0 12.4 + - - +
228A LEU 2.9 6.7 + - - -
229A ASP* 1.3 76.1 + - - +
231A PHE* 1.3 62.7 + - - +
232A LEU* 3.9 5.5 + - - +
233A ILE* 3.1 33.3 + - - +
234A GLU* 3.3 16.9 + - - +
331A LYS* 3.7 16.3 + - - -
368A ILE 5.5 0.7 - - - -
369A ARG 3.7 2.2 - - - -
370A SER* 3.5 23.3 - - - +
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Residues in contact with PHE 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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230A SER* 1.3 72.9 - - - +
232A LEU* 1.3 62.0 + - - +
234A GLU* 3.1 27.5 + - - +
235A ILE* 2.9 55.7 + - + +
367A ILE* 3.8 22.4 - - + +
369A ARG* 3.1 64.5 + - + +
449B TYR* 4.7 8.3 - + - -
450B PHE* 4.2 23.1 - + + -
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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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191A GLU* 4.5 1.8 - - + +
194A ASP* 3.6 33.2 - - + +
195A MET* 3.8 25.1 - - + +
198A ILE* 3.8 13.0 - - + -
230A SER* 3.5 5.7 + - - +
231A PHE* 1.3 79.4 - - + +
233A ILE* 1.3 53.8 + - - +
235A ILE* 3.3 24.6 - - + +
236A THR* 2.5 38.8 + - - -
367A ILE* 3.7 37.6 + - + +
368A ILE* 4.8 6.5 - - + -
446B GLN* 4.6 4.7 - - - +
450B PHE* 4.1 9.2 - - + -
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.7 26.5 - - + -
220A PHE* 3.2 53.0 - - + +
223A TRP* 4.8 4.5 - - + -
224A ASN* 3.7 18.6 - - + +
228A LEU* 3.9 15.9 - - + +
230A SER* 3.1 24.7 + - - +
232A LEU* 1.3 73.1 - - - +
234A GLU* 1.3 65.7 + - - +
236A THR* 3.4 3.5 + - - -
237A ALA* 3.1 22.3 + - - +
327A LEU* 4.2 14.1 - - + -
331A LYS* 6.0 0.7 - - - +
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Residues in contact with GLU 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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224A ASN* 3.2 25.3 + - - +
230A SER 3.3 5.4 + - - +
231A PHE* 3.1 35.9 + - + +
233A ILE* 1.3 78.7 - - - +
235A ILE* 1.3 62.6 + - + +
237A ALA* 3.3 5.2 + - - +
238A ASN* 3.2 38.7 + - - +
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Residues in contact with ILE 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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231A PHE* 2.9 39.2 + - + +
232A LEU* 3.3 35.4 - - + +
234A GLU* 1.3 75.8 - - + +
236A THR* 1.3 65.1 + - - +
238A ASN* 3.2 8.7 + - - +
239A ILE* 2.8 36.1 + - + +
446B GLN* 4.3 15.0 - - + -
449B TYR* 3.4 39.0 - - + +
450B PHE* 3.7 22.2 - - + -
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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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198A ILE* 3.7 24.8 - - + +
220A PHE* 4.0 23.3 - - + -
232A LEU 2.5 24.2 + - - -
233A ILE* 3.6 9.0 - - - -
234A GLU 3.2 0.2 - - - -
235A ILE* 1.3 78.1 - - - +
237A ALA* 1.3 61.2 + - - +
239A ILE* 3.4 6.8 + - - +
240A LEU* 3.1 27.3 + - + +
442B LEU* 4.1 17.9 - - + +
446B GLN* 3.0 22.0 + - - +
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Residues in contact with ALA 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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217A ALA* 3.4 30.9 - - - +
220A PHE* 4.0 10.5 - - + +
221A GLU* 4.1 19.3 - - + +
233A ILE 3.1 12.9 + - - +
234A GLU* 3.7 9.0 - - - +
235A ILE 3.3 0.2 - - - -
236A THR* 1.3 78.1 - - - +
238A ASN* 1.3 64.8 + - - +
240A LEU 3.5 0.7 + - - -
241A LYS* 3.2 31.3 + - - +
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Residues in contact with ASN 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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221A GLU* 5.4 2.1 - - - +
234A GLU* 3.2 34.8 + - - +
235A ILE* 3.2 6.3 + - - +
237A ALA* 1.3 78.0 - - - +
239A ILE* 1.3 64.4 + - - +
241A LYS* 3.4 16.2 + - - +
242A PHE* 3.1 23.6 + - - +
449B TYR* 3.5 29.7 + - + +
469B TRP* 5.6 1.1 - - - +
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Residues in contact with ILE 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 ILE* 2.8 21.9 + - + +
236A THR* 3.9 4.7 - - - +
238A ASN* 1.3 74.0 - - - +
240A LEU* 1.3 66.0 + - - +
242A PHE* 3.1 18.2 + - - +
250A LEU* 5.9 0.3 - - - +
251A LEU* 3.9 25.9 + - + +
442B LEU* 4.2 4.0 - - + -
445B ALA* 3.4 51.6 - - + +
446B GLN* 3.7 19.3 - - + +
449B TYR* 3.5 25.1 - - + -
469B TRP* 3.8 20.1 - - + -
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Residues in contact with LEU 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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202A TYR* 3.5 29.2 - - + -
213A GLN* 3.7 25.4 + - - +
214A ASP* 4.4 0.3 - - - +
216A MET* 3.9 7.6 - - + -
217A ALA* 3.6 31.4 - - + +
220A PHE* 3.6 36.8 - - + -
236A THR* 3.1 22.4 + - + +
238A ASN 3.3 0.2 - - - -
239A ILE* 1.3 77.9 - - - +
241A LYS* 1.3 60.8 + - - +
242A PHE 4.4 0.2 - - - +
249A HIS* 3.3 22.0 + - - +
251A LEU* 3.7 21.1 - - + -
442B LEU* 4.9 2.5 - - + -
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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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214A ASP* 4.1 15.9 - - + +
217A ALA* 3.5 29.2 - - + -
218A GLN* 4.2 14.1 - - - +
221A GLU* 2.8 42.9 + - - +
237A ALA* 3.2 20.0 + - - +
238A ASN* 3.8 14.1 + - - +
239A ILE 3.2 0.2 - - - -
240A LEU* 1.3 75.1 - - - +
242A PHE* 1.3 63.9 + - - +
243A GLN* 3.2 15.6 + - - +
249A HIS* 4.3 3.0 - - - -
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Residues in contact with PHE 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 ASN 3.1 13.2 + - - +
239A ILE 3.1 16.5 + - - +
241A LYS* 1.3 76.3 - - - +
243A GLN* 1.3 79.1 + - - +
244A ASP* 4.7 3.8 - - - -
249A HIS* 3.7 8.7 - - - +
250A LEU* 3.5 41.0 + - + -
467B THR* 3.6 26.0 - - + -
468B ASN* 5.6 2.5 - - + -
469B TRP* 3.5 52.9 - + + -
470B THR 5.7 0.2 - - - -
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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