Contacts of the strand formed by residues 235 - 242 (chain A) in PDB entry 1JS3
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 ILE 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL* 4.2 12.8 - - + -
166A ARG* 4.1 20.9 - - - +
167A LEU* 3.4 33.2 - - + -
182A LYS* 2.7 36.8 + - + +
183A LEU* 3.6 8.6 - - + -
184A VAL* 3.1 20.1 + - - -
233A GLY 4.6 3.1 - - - +
234A LEU* 1.3 78.6 - - - +
236A PRO* 1.3 76.0 - - + +
237A PHE* 3.2 2.4 + - - +
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Residues in contact with PRO 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 5.0 4.2 + - - -
184A VAL* 3.4 12.1 - - + +
186A TYR* 3.7 17.9 - - + +
226A LEU* 3.4 36.3 - - + +
229A ASP* 5.1 0.9 - - + -
230A LYS* 3.7 26.7 - - + -
234A LEU 3.6 9.4 - - - +
235A ILE* 1.3 90.5 - - + +
237A PHE* 1.3 58.6 + - - +
238A PHE 3.9 0.2 - - - -
264A GLU* 5.1 2.5 - - + +
265A ASP 5.0 1.7 - - - +
266A ILE* 3.5 22.8 - - + +
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Residues in contact with PHE 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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156A LEU* 3.7 16.8 - - + -
159A ALA* 3.7 19.7 - - - +
160A ARG* 3.5 26.5 - - + -
163A VAL* 3.7 27.3 - - + +
183A LEU* 3.6 27.4 - - + -
184A VAL 3.1 28.9 + - - -
185A ALA* 3.9 14.1 - - + -
204A VAL* 3.9 29.2 - - + -
235A ILE 3.2 2.4 + - - +
236A PRO* 1.3 75.5 - - - +
238A PHE* 1.3 76.2 + - + +
265A ASP 5.1 1.5 - - - +
266A ILE* 3.7 9.8 - - - +
267A TRP* 3.0 23.4 + - - +
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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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152A THR* 3.9 11.0 - - + -
155A ALA* 3.7 2.0 - - + -
156A LEU* 3.6 53.4 - - + -
159A ALA* 3.6 10.1 - - + -
184A VAL 4.0 0.2 + - - -
185A ALA* 3.2 10.5 - - + +
186A TYR* 2.8 27.6 + - - +
195A VAL* 5.5 2.9 - - + -
206A LEU* 6.2 0.4 - - + -
237A PHE* 1.3 104.2 - + + +
239A VAL* 1.3 64.6 + - - +
240A VAL* 3.3 31.2 - - + -
266A ILE* 3.6 2.4 - - - +
267A TRP* 3.4 38.4 - + - -
269A HIS* 3.6 15.7 - + + -
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Residues in contact with VAL 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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186A TYR* 3.3 26.7 - - + +
217A MET* 4.4 13.7 - - + -
222A LEU* 4.3 10.1 - - + -
238A PHE* 1.3 79.6 - - - +
240A VAL* 1.3 73.0 + - - +
241A ALA 4.3 0.4 - - - +
257A VAL* 4.3 13.7 - - + -
261A CYS* 3.8 18.6 - - - -
266A ILE* 3.6 19.7 - - + -
267A TRP 2.8 7.5 + - - +
268A LEU* 3.5 14.3 - - + +
269A HIS* 2.8 28.8 + - - +
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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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152A THR* 4.3 4.7 - - + -
186A TYR 2.9 11.7 + - - +
187A ALA* 3.7 23.6 - - + +
188A SER 4.2 1.7 + - - -
195A VAL* 4.1 29.6 - - + -
217A MET* 4.0 7.6 - - - +
238A PHE* 3.3 37.0 - - + -
239A VAL* 1.3 74.3 - - - +
241A ALA* 1.3 63.1 + - - +
242A THR* 3.9 7.0 + - - +
269A HIS* 3.3 16.6 - - + +
271A ASP* 3.9 27.1 - - + -
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Residues in contact with ALA 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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217A MET* 5.1 2.2 - - - -
239A VAL* 3.9 2.7 + - + -
240A VAL* 1.3 73.0 - - - +
242A THR* 1.3 60.9 + - - +
252A ASP* 3.5 13.7 - - + -
254A LEU* 3.4 33.2 - - + -
257A VAL* 5.0 7.6 - - + -
268A LEU* 4.0 15.9 - - + -
269A HIS 2.9 8.1 + - - +
270A VAL* 3.4 4.7 - - + +
271A ASP* 2.8 26.0 + - - +
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Residues in contact with THR 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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188A SER* 5.2 1.2 - - - -
191A ALA* 4.0 25.6 - - - +
192A HIS 4.8 0.6 + - - +
195A VAL* 5.5 0.2 - - - +
240A VAL* 4.3 10.0 + - - +
241A ALA* 1.3 75.3 - - - +
243A LEU* 1.3 64.3 + - - +
244A GLY 3.9 1.0 + - - -
245A THR* 3.7 38.6 - - + +
250A SER 4.1 1.0 - - - +
251A PHE* 3.8 1.9 - - - -
252A ASP* 2.6 43.0 + - - -
271A ASP* 3.3 14.3 + - - +
601A PLP 4.0 17.7 - - + -
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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