Contacts of the strand formed by residues 229 - 237 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A THR* 3.3 30.4 - - + +
155A LEU 3.4 3.6 - - - -
156A HIS* 3.3 31.3 + - + +
207A ASP* 4.6 3.1 - - - +
227A GLY* 3.7 11.0 + - - +
228A GLN* 1.3 76.5 - - - +
230A ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 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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153A VAL 3.6 1.6 - - - +
154A THR* 3.1 7.7 - - - -
155A LEU 2.9 32.0 + - - -
162A PHE* 3.6 32.8 - - + -
206A VAL* 5.1 0.2 - - + -
207A ASP* 3.6 11.2 - - - +
226A CYS* 3.8 16.8 - - - -
227A GLY 4.0 1.8 - - - +
229A GLU* 1.3 75.5 - - - +
231A ALA* 1.3 58.7 + - - +
232A LEU* 3.8 9.7 + - + +
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Residues in contact with ALA 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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152A GLU* 3.9 28.7 - - + +
153A VAL 3.6 4.3 - - - -
154A THR* 4.3 8.3 - - - +
205A SER* 4.0 1.2 + - - +
206A VAL* 3.7 1.6 - - - -
207A ASP* 2.8 44.4 + - - +
208A GLY 4.8 0.5 + - - -
230A ALA* 1.3 69.4 - - - +
232A LEU* 1.3 62.5 + - - +
233A LEU 4.2 0.2 + - - -
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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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151A VAL 3.5 1.0 - - - +
152A GLU* 3.4 4.0 - - - -
153A VAL* 2.6 49.6 + - + +
155A LEU* 3.8 30.5 - - + -
162A PHE* 4.5 5.6 - - + -
164A PHE* 3.9 23.6 - - + -
197A ILE* 4.1 8.1 - - + -
203A LEU* 4.0 13.2 - - + -
205A SER 3.4 2.9 - - - -
206A VAL* 4.0 31.6 - - + -
223A LEU* 4.4 7.0 - - + -
230A ALA* 4.2 17.3 - - + +
231A ALA* 1.3 81.2 - - - +
233A LEU* 1.3 61.2 + - - +
234A ILE* 3.8 3.9 + - + +
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Residues in contact with LEU 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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150A THR* 4.1 26.0 - - + +
151A VAL 3.4 20.0 - - - +
152A GLU* 4.0 15.0 - - + +
203A LEU* 3.6 4.3 - - - +
204A LEU* 2.8 47.2 + - + -
205A SER* 2.9 32.4 + - - +
210A ARG* 6.5 0.4 - - - -
231A ALA 4.2 0.2 + - - -
232A LEU* 1.3 72.1 - - - +
234A ILE* 1.3 60.6 + - - +
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Residues in contact with ILE 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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150A THR* 3.1 6.4 - - - -
151A VAL* 2.8 43.1 + - + +
153A VAL* 3.9 20.4 - - + -
182A ILE* 4.5 9.6 - - + -
196A THR* 4.0 4.7 - - + -
197A ILE* 3.9 24.2 - - + -
201A ASP* 3.7 19.7 - - + +
202A ARG 3.0 12.8 - - - +
203A LEU* 4.0 16.2 - - + -
204A LEU* 4.6 1.6 - - - -
232A LEU* 4.7 5.8 - - + +
233A LEU* 1.3 78.6 - - - +
235A GLU* 1.3 63.8 + - - +
236A TYR* 3.5 28.7 - - + -
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Residues in contact with GLU 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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0A MET* 3.7 28.2 - - + +
149A ARG* 3.3 15.7 + - - +
150A THR* 4.2 10.9 - - - +
200A GLY 5.0 0.3 - - - +
201A ASP* 3.9 1.2 - - - -
202A ARG* 2.9 65.0 + - + +
204A LEU* 3.8 23.1 - - + +
234A ILE* 1.3 77.9 - - - +
236A TYR* 1.3 67.1 + - - +
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Residues in contact with TYR 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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0A MET* 3.7 17.3 - - + -
149A ARG 3.0 27.6 + - - +
151A VAL* 3.7 22.6 - - + +
196A THR* 3.4 20.3 - - + +
201A ASP* 3.4 25.4 - - - +
234A ILE* 3.5 32.8 - - + -
235A GLU* 1.3 80.6 - - - +
237A ASP* 1.3 70.5 + - - +
238A VAL* 3.1 24.3 + - + +
1245A SCN 2.7 38.0 + - - -
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Residues in contact with ASP 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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-1A SER* 2.7 39.8 + - - -
0A MET* 4.2 12.1 - - + +
236A TYR* 1.3 84.6 - - - +
238A VAL* 1.3 57.7 + - - +
239A SER* 4.0 2.6 + - - -
1245A SCN 4.2 5.0 - - - -
156B HIS* 6.0 2.4 - - - -
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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