Contacts of the strand formed by residues 229 - 237 (chain B) in PDB entry 2JIL
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 GLU 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B THR* 3.7 20.3 - - + +
155B LEU 3.5 3.8 - - - -
156B HIS* 3.5 34.8 - - + +
207B ASP* 4.0 4.9 - - - +
227B GLY* 3.8 8.4 - - - +
228B GLN* 1.3 76.8 - - - +
230B ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL 3.7 1.0 - - - +
154B THR* 3.2 6.6 - - - -
155B LEU* 2.9 34.7 + - - +
162B PHE* 3.6 29.2 - - + -
206B VAL* 5.0 0.2 - - + -
207B ASP* 3.1 19.5 - - - +
226B CYS* 4.0 7.0 - - - -
227B GLY 3.9 7.4 - - - +
229B GLU* 1.3 74.9 - - - +
231B ALA* 1.3 59.2 + - - +
232B LEU* 3.8 9.0 + - + +
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 4.3 21.3 - - + +
153B VAL 3.5 4.9 - - - -
154B THR* 4.1 13.0 - - + +
205B SER 4.1 0.7 - - - +
206B VAL* 3.8 0.5 - - - -
207B ASP* 2.9 34.4 + - - +
208B GLY 4.5 1.5 + - - +
230B ALA* 1.3 70.9 - - - +
232B LEU* 1.3 62.5 + - - +
233B LEU* 4.2 0.6 + - + +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B VAL 3.5 1.2 - - - +
152B GLU* 3.4 4.0 - - - +
153B VAL* 2.6 46.0 + - + +
155B LEU* 3.9 30.3 - - + -
162B PHE* 4.7 4.5 - - + -
164B PHE* 3.9 21.5 - - + -
197B ILE* 4.1 11.0 - - + -
203B LEU* 4.1 11.4 - - + -
205B SER 3.4 3.6 - - - +
206B VAL* 3.8 39.7 - - + -
223B LEU* 4.3 6.5 - - + -
230B ALA* 4.5 13.2 - - + +
231B ALA* 1.3 78.3 - - - +
233B LEU* 1.3 62.4 + - - +
234B ILE* 4.0 3.5 + - + -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B THR* 4.1 24.2 - - + -
151B VAL 3.4 2.7 - - - +
152B GLU* 3.7 38.4 - - + +
203B LEU* 3.6 4.3 - - - +
204B LEU* 2.8 35.9 + - + -
205B SER* 3.0 29.6 + - - +
210B ARG* 3.5 28.7 - - - +
231B ALA* 4.2 0.8 + - + +
232B LEU* 1.3 73.8 - - - +
234B ILE* 1.3 56.5 + - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B THR* 3.3 5.5 - - - +
151B VAL* 2.8 42.5 + - + +
153B VAL* 3.9 14.8 - - + -
182B ILE* 4.3 16.8 - - + -
196B THR* 4.0 5.2 - - + -
197B ILE* 3.9 23.6 - - + -
201B ASP* 3.7 19.5 - - + +
202B ARG 3.1 13.2 - - - +
203B LEU* 3.9 15.9 - - + -
204B LEU* 4.6 2.0 - - - -
232B LEU* 4.8 5.8 - - + +
233B LEU* 1.3 78.7 - - - +
235B GLU* 1.3 62.5 + - - +
236B TYR* 3.6 29.2 - - + -
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B MET* 3.4 24.1 - - + +
149B ARG 3.3 5.6 - - - +
150B THR* 4.0 0.3 + - - -
200B GLY 4.9 0.5 - - - +
201B ASP* 3.9 0.5 - - - -
202B ARG* 2.9 63.9 + - + +
204B LEU* 3.9 23.8 - - + +
234B ILE* 1.3 77.0 - - - +
236B TYR* 1.3 66.0 + - - +
1244B EDO 2.6 36.2 + - - +
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Residues in contact with TYR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.4 11.6 + - - -
178A ARG* 3.2 42.6 - - - +
1244A SCN 2.8 28.9 + - - -
0B MET* 3.4 14.0 - - - +
149B ARG 3.0 27.6 + - - +
151B VAL* 3.7 20.0 - - + +
196B THR* 3.4 6.8 - - + +
200B GLY 5.7 0.4 - - - +
201B ASP* 3.3 17.0 - - - +
234B ILE* 3.6 31.0 - - + -
235B GLU* 1.3 80.3 - - - +
237B ASP* 1.3 69.3 + - - +
238B VAL* 3.3 23.7 + - + +
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Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ARG* 5.3 0.5 + - - -
1244A SCN 4.3 4.7 - - - -
-1B SER* 2.8 39.4 + - - -
0B MET* 3.8 15.2 - - - -
236B TYR* 1.3 84.1 - - - +
238B VAL* 1.3 59.9 - - - +
239B SER* 4.0 1.4 + - - -
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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