Contacts of the helix formed by residues 231 - 243 (chain A) in PDB entry 3U86
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 ASP 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A HIS* 3.9 8.7 - - + +
229A ARG 3.9 1.2 + - - -
230A CYS* 1.3 74.1 - - - +
232A ARG* 1.3 66.4 + - - +
233A LYS* 3.1 14.6 + - + +
234A MET* 2.9 42.0 + - - +
235A GLU* 3.1 15.2 + - - -
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Residues in contact with ARG 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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30A GLU 5.0 2.2 - - - +
31A GLU* 2.2 55.6 + - - +
32A PRO* 3.9 22.2 - - + -
34A LEU* 3.8 12.6 - - - +
162A VAL* 3.9 13.7 + - - +
165A CYS* 5.8 0.4 - - - +
166A GLN* 3.7 28.9 - - - +
170A LEU 4.1 13.3 + - - -
171A ARG* 4.1 10.5 + - - +
173A VAL 2.8 28.3 + - - -
174A HIS* 3.7 23.1 + - - +
231A ASP* 1.3 74.3 - - - +
233A LYS* 1.3 65.1 + - + +
235A GLU* 2.9 32.6 + - - +
236A VAL* 3.3 18.8 + - - +
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Residues in contact with LYS 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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27A LEU* 2.8 35.3 + - + +
28A GLY 5.3 0.2 - - - -
29A ARG 3.7 11.5 + - - -
30A GLU* 4.9 3.4 - - - +
32A PRO* 3.6 29.2 - - + -
231A ASP* 3.0 12.2 + - - +
232A ARG* 1.3 79.6 - - + +
234A MET* 1.3 62.4 + - + +
236A VAL* 3.4 9.5 + - - +
237A ALA* 3.3 17.2 + - - +
267A LEU* 4.3 7.3 - - - +
272A HIS* 3.7 43.8 + - + +
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Residues in contact with MET 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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228A MET* 4.3 17.5 - - + -
229A ARG 4.1 6.3 - - - +
230A CYS* 3.9 28.7 - - - -
231A ASP* 2.9 40.7 + - - +
233A LYS* 1.3 75.0 - - + +
235A GLU* 1.3 61.2 + - - +
236A VAL 3.1 0.4 - - - -
237A ALA* 3.1 10.5 + - + +
238A PHE* 2.9 27.4 + - - +
272A HIS* 4.5 15.0 - - + +
275A ARG* 4.3 35.0 - - + +
276A TYR* 4.1 12.5 - - + -
313A TYR* 4.3 8.3 - - - +
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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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34A LEU* 3.4 17.7 - - + +
159A PHE* 3.7 18.6 - - + -
162A VAL* 3.9 9.9 - - + +
174A HIS* 3.2 19.4 - - - +
175A LEU* 3.0 38.5 + - + -
230A CYS* 3.6 14.1 - - + +
231A ASP 3.1 16.1 + - - +
232A ARG* 2.9 37.6 + - - +
233A LYS 3.2 0.2 - - - -
234A MET* 1.3 77.0 - - - +
236A VAL* 1.3 60.2 + - - +
238A PHE* 3.5 9.0 - - - +
239A MET* 3.4 16.1 + - - +
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Residues in contact with VAL 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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23A PHE* 3.8 30.3 - - + -
27A LEU* 3.8 35.4 - - + -
32A PRO* 4.1 6.7 - - + -
34A LEU* 3.9 15.3 - - + -
37A LEU* 4.1 14.4 - - + -
232A ARG 3.3 14.9 + - - +
233A LYS 3.5 7.9 - - - +
234A MET 3.1 0.2 - - - -
235A GLU* 1.3 76.5 - - - +
237A ALA* 1.3 65.4 + - - +
239A MET* 3.3 9.5 - - + +
240A VAL* 3.1 26.6 + - + +
267A LEU* 4.5 5.2 - - + -
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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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233A LYS 3.3 9.1 + - - +
234A MET* 3.1 13.1 + - - +
236A VAL* 1.3 76.8 - - - +
238A PHE* 1.3 65.5 + - - +
240A VAL* 3.1 5.4 + - - +
241A CYS* 3.0 24.1 + - - -
264A LEU* 4.9 0.9 - - + +
267A LEU* 3.7 24.6 - - + +
272A HIS 5.1 2.9 - - - +
273A LEU* 4.2 12.1 - - + -
276A TYR* 3.7 23.6 - - + -
279A ALA* 5.1 1.1 - - + -
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Residues in contact with PHE 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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141A GLN* 6.5 0.2 - - + -
155A SER* 4.1 19.3 - - - -
156A GLY* 5.6 1.1 - - - -
159A PHE* 4.0 34.8 - + + -
175A LEU* 4.0 10.5 - - + -
177A LEU* 3.4 42.4 - - + -
182A ALA* 5.6 0.9 - - + -
234A MET 2.9 12.1 + - - +
235A GLU* 3.5 12.1 - - - +
237A ALA* 1.3 74.5 - - - +
239A MET* 1.3 55.7 + - - +
241A CYS* 2.7 25.1 + - - +
242A ALA* 2.8 21.6 + - + +
276A TYR* 3.7 18.7 - - - +
32B PHE* 4.7 4.3 - + - -
33B PRO* 3.3 38.5 - - + +
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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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23A PHE* 3.4 13.7 - - + -
34A LEU* 4.0 7.9 - - - +
37A LEU* 3.3 33.9 - - + -
38A SER* 3.8 16.2 - - - +
41A LEU* 3.3 29.8 - - + +
159A PHE* 3.3 40.4 - - + -
235A GLU 3.4 5.7 + - - +
236A VAL* 3.3 12.3 - - + +
238A PHE* 1.3 81.5 - - - +
240A VAL* 1.3 61.3 + - - +
242A ALA* 3.1 19.0 + - - +
243A ILE* 3.1 15.4 + - - +
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Residues in contact with VAL 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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23A PHE* 4.3 19.1 - - + -
41A LEU* 4.7 1.1 - - + -
236A VAL* 3.1 16.4 - - + +
237A ALA 3.1 7.9 + - - +
238A PHE 3.1 0.2 + - - -
239A MET* 1.3 75.7 - - + +
241A CYS* 1.3 51.9 + - - +
243A ILE* 3.2 13.7 - - + +
260A GLN* 2.7 47.1 + - + +
263A LEU* 3.5 35.9 - - + -
264A LEU* 3.9 14.1 - - + +
267A LEU* 3.9 17.5 - - + -
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Residues in contact with CYS 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 ALA 3.0 13.8 + - - +
238A PHE* 2.7 18.3 + - - +
240A VAL* 1.3 68.7 - - - +
242A ALA* 1.3 57.9 + - - +
243A ILE 3.0 8.5 - - - +
260A GLN* 3.2 15.9 + - - +
264A LEU* 4.5 7.4 - - - -
276A TYR* 4.2 10.5 - - - +
279A ALA* 3.7 35.0 - - - -
282A ASN* 3.8 15.4 - - - +
33B PRO* 3.8 7.8 - - + +
34B GLY* 3.8 28.0 + - - +
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Residues in contact with ALA 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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141A GLN* 2.8 44.0 + - + +
238A PHE* 2.8 18.3 + - + +
239A MET* 3.1 14.8 + - - +
241A CYS* 1.3 73.1 - - - +
243A ILE* 1.3 63.5 + - - +
244A ASN* 3.2 2.9 + - - +
33B PRO* 3.5 26.7 - - + -
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Residues in contact with ILE 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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41A LEU* 3.8 34.3 - - + -
45A GLU* 3.7 13.5 - - - +
141A GLN* 4.3 0.7 - - - +
239A MET 3.1 11.9 + - - +
240A VAL* 3.2 23.1 - - - +
241A CYS 3.0 9.2 - - - +
242A ALA* 1.3 78.8 - - - +
244A ASN* 1.3 64.8 + - - +
245A PRO* 3.4 10.4 - - + +
256A LEU* 4.1 30.7 - - + +
259A LEU* 4.5 11.9 - - + -
260A GLN* 3.5 24.6 + - + +
263A LEU* 4.5 4.9 - - + -
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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