Contacts of the strand formed by residues 184 - 188 (chain U) in PDB entry 1J0B
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 SER 184 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182U PHE* 3.4 5.6 - - - +
183U ASP* 1.3 78.0 - - - +
185U ILE* 1.3 74.2 + - - +
186U VAL* 4.4 0.5 - - - +
209U ILE* 4.2 0.9 - - - -
210U ARG* 3.1 33.4 - - - +
212U VAL* 4.2 11.4 - - - -
299U LEU* 3.7 31.5 + - - +
302U LYS 3.7 1.0 + - - -
303U ILE* 3.8 9.7 - - - +
304U LEU 3.2 16.8 + - - -
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Residues in contact with ILE 185 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171U VAL* 6.1 2.0 - - + -
174U ILE* 4.7 12.3 - - + -
182U PHE* 4.3 7.9 - - + -
184U SER* 1.3 85.8 - - - +
186U VAL* 1.3 62.0 + - - +
198U LEU* 3.6 33.5 - - + +
202U LEU* 4.5 11.4 - - + -
209U ILE* 4.1 18.6 - - + -
210U ARG 2.7 11.1 + - - +
212U VAL 2.9 25.5 + - - +
304U LEU* 3.0 46.7 - - + +
306U ILE* 3.7 13.7 - - + -
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Residues in contact with VAL 186 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184U SER* 4.4 1.1 - - - +
185U ILE* 1.3 76.6 - - - +
187U VAL* 1.3 58.6 + - - +
212U VAL* 3.4 28.3 - - + +
214U ILE* 4.9 6.7 - - + -
286U ALA 5.1 2.2 - - - +
290U LEU* 3.6 28.0 - - + -
293U LEU* 5.9 0.2 - - + -
299U LEU* 4.1 18.4 - - + -
303U ILE* 3.8 17.3 - - + -
304U LEU 3.0 6.5 + - - -
305U PHE* 3.2 26.1 - - + -
306U ILE 2.8 31.2 + - - -
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Residues in contact with VAL 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186U VAL* 1.3 76.9 - - - +
188U ALA* 1.3 83.4 + - - +
189U ALA 3.3 0.7 + - - -
194U THR* 3.9 24.5 - - + -
195U LEU* 4.4 9.9 - - + +
198U LEU* 4.0 24.5 - - + -
212U VAL 3.1 6.7 + - - +
213U GLY* 3.7 3.5 - - - -
214U ILE* 3.4 15.4 + - - +
305U PHE* 4.6 2.2 - - - -
306U ILE* 3.7 18.2 - - + +
308U THR* 3.3 34.8 - - + +
1211U 5PA 5.3 0.2 - - + -
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Residues in contact with ALA 188 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187U VAL* 1.3 96.3 - - - +
189U ALA* 1.3 58.5 + - - +
190U GLY 4.3 0.7 - - - -
214U ILE* 3.3 18.2 - - - +
216U VAL* 3.6 10.3 - - + -
282U TYR* 3.3 21.5 - - + +
283U THR* 4.3 2.4 - - + +
286U ALA* 3.3 24.2 - - + +
305U PHE* 4.7 1.4 - - - -
308U THR* 5.0 1.1 - - - +
1211U 5PA 3.9 25.8 + - + +
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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