Contacts of the strand formed by residues 183 - 188 (chain B) 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 LEU 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 4.1 16.4 - - + -
163B VAL* 3.9 21.3 - - + -
164B VAL* 4.5 0.2 - - + -
167B LEU* 4.6 2.7 - - + -
179B VAL* 3.3 42.4 + - + +
180B LEU* 3.4 31.7 + - + +
182B LYS* 1.3 79.5 - - - +
184B VAL* 1.3 59.0 + - - +
204B VAL* 4.0 7.0 - - + -
205B LYS* 3.6 27.6 + - - +
235B ILE* 3.6 20.4 - - + +
237B PHE* 3.6 24.9 - - + -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 1.3 77.9 - - - +
185B ALA* 1.3 74.2 + - - +
186B TYR* 3.4 30.0 - - + +
205B LYS* 3.4 9.6 - - + +
207B LYS* 3.8 31.6 - - + -
229B ASP* 4.3 1.1 - - + +
234B LEU* 4.2 21.3 - - + -
235B ILE 3.1 5.4 + - - +
236B PRO* 3.4 23.0 - - + +
237B PHE* 3.1 25.3 + - - -
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 4.8 3.6 - - + -
184B VAL* 1.3 74.4 - - - +
186B TYR* 1.3 69.0 + - - +
199B GLY* 6.1 0.2 - - - -
204B VAL* 4.5 6.1 - - + -
205B LYS 2.8 13.9 + - - +
206B LEU* 3.7 13.9 - - + -
207B LYS 2.9 24.4 + - - -
237B PHE* 3.9 17.5 - - + -
238B PHE* 3.2 27.6 - - + +
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Residues in contact with TYR 186 (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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184B VAL* 3.4 24.0 - - + +
185B ALA* 1.3 78.3 - - - +
187B ALA* 1.3 62.9 + - - +
206B LEU* 4.0 4.0 - - - +
207B LYS* 3.3 18.2 - - + +
209B ILE* 3.5 28.9 - - + -
222B LEU* 4.4 3.4 - - + -
225B ALA* 3.8 15.7 + - + -
226B LEU* 3.4 25.2 - - + +
229B ASP* 2.6 43.1 + - - +
236B PRO* 3.7 18.8 - - + +
237B PHE 5.7 0.2 - - - -
238B PHE* 2.8 13.1 + - - +
239B VAL* 3.3 26.8 - - + +
240B VAL* 2.9 27.4 + - - +
266B ILE* 5.4 0.2 - - + -
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Residues in contact with ALA 187 (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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186B TYR* 1.3 77.0 - - - +
188B SER* 1.3 64.1 + - - +
191B ALA* 3.6 21.8 - - + -
195B VAL* 3.7 24.5 - - + -
206B LEU* 4.1 6.2 - - + +
207B LYS 3.3 3.6 + - - -
208B ALA* 3.2 5.5 - - - -
209B ILE 2.7 22.5 + - - -
217B MET* 3.4 7.6 - - - -
240B VAL* 3.7 15.3 - - + +
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Residues in contact with SER 188 (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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187B ALA* 1.3 79.8 - - - +
189B ASP* 1.3 66.9 + - - +
190B GLN* 2.9 21.4 + - - +
191B ALA* 3.0 28.3 + - - +
208B ALA* 4.5 2.3 - - - +
209B ILE 3.6 7.0 - - - -
211B SER* 4.0 10.0 - - - -
215B PHE 4.6 0.5 + - - -
217B MET* 3.2 17.2 - - - +
240B VAL 4.2 2.2 + - - -
242B THR* 5.2 2.0 + - - -
252B ASP* 3.8 28.3 + - - -
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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