Contacts of the strand formed by residues 184 - 189 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I PHE* 3.7 5.5 - - - +
183I ASP* 1.3 77.8 - - - +
185I ILE* 1.3 72.4 + - - +
186I VAL* 4.2 0.6 - - - +
210I ARG* 3.3 26.9 - - - +
212I VAL* 3.8 13.2 - - - +
299I LEU* 2.5 39.1 + - - +
302I LYS 3.5 1.7 + - - +
303I ILE* 3.9 9.4 - - - +
304I LEU 3.3 18.1 + - - -
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Residues in contact with ILE 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I VAL* 6.2 1.3 - - + -
174I ILE* 5.2 11.7 - - + -
182I PHE* 4.5 7.6 - - + -
184I SER* 1.3 78.9 - - - +
186I VAL* 1.3 57.9 + - - +
187I VAL 4.0 0.5 + - - -
198I LEU* 3.9 18.2 - - + +
202I LEU* 4.0 19.1 - - + -
209I ILE* 3.3 29.4 - - + -
210I ARG 2.5 11.6 + - - +
211I PRO* 3.4 2.8 - - - +
212I VAL 2.5 29.3 + - - +
304I LEU* 3.6 31.6 - - + +
306I ILE* 3.8 29.6 - - + -
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Residues in contact with VAL 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I SER* 4.7 0.9 - - - +
185I ILE* 1.3 71.2 - - - +
187I VAL* 1.3 61.0 + - - +
212I VAL* 2.6 37.7 - - + +
214I ILE* 5.5 3.8 - - + -
286I ALA 5.3 2.5 - - - +
290I LEU* 3.7 23.6 - - + +
299I LEU* 4.0 19.7 - - + -
303I ILE* 4.2 11.0 - - + -
304I LEU 3.1 12.6 + - - +
305I PHE* 3.4 27.8 - - + -
306I ILE* 3.5 21.1 + - - +
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Residues in contact with VAL 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ILE 4.0 0.2 + - - -
186I VAL* 1.3 73.9 - - - +
188I ALA* 1.3 69.0 + - - +
194I THR* 3.1 29.4 - - + -
195I LEU* 3.4 45.1 - - + +
198I LEU* 3.4 19.7 - - + -
212I VAL 2.5 10.3 + - - +
213I GLY* 2.9 25.4 - - - -
214I ILE* 2.9 7.7 + - - +
286I ALA* 4.9 0.2 - - - -
305I PHE* 5.3 1.1 - - - -
306I ILE* 4.1 19.5 - - + +
308I THR* 4.5 6.7 - - + -
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Residues in contact with ALA 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I VAL* 1.3 83.3 - - - +
189I ALA* 1.3 59.2 + - - +
194I THR* 4.7 0.7 - - - -
214I ILE* 3.8 11.5 - - - +
216I VAL* 4.0 14.1 - - + -
282I TYR* 4.3 7.9 - - - -
283I THR* 4.5 0.9 - - + +
286I ALA* 3.4 24.1 - - + +
305I PHE* 5.1 2.3 - - + -
306I ILE 5.2 2.2 + - - +
308I THR* 4.5 5.6 - - + +
1091I 5PA 3.2 39.3 + - + +
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Residues in contact with ALA 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I VAL 3.4 1.7 + - - +
188I ALA* 1.3 74.4 - - - +
190I GLY* 1.3 60.1 + - - +
192I GLY* 4.7 7.4 - - - -
195I LEU* 4.0 32.3 - - + -
214I ILE 3.3 8.3 + - - +
215I ALA* 3.7 5.4 - - - -
216I VAL* 3.4 25.9 + - - +
217I GLY 4.4 0.3 + - - -
223I MET* 4.0 10.8 - - + +
248I LEU* 4.1 15.7 - - + -
1091I 5PA 3.4 7.4 - - - +
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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
------------------------------------------------------------
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