Contacts of the strand formed by residues 302 - 306 (chain V) 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 LYS 302 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E LEU 5.1 8.1 + - - -
206E ASN* 5.3 10.6 + - - -
37V ASP* 3.7 17.5 - - + +
39V TYR* 5.3 1.8 - - + -
180V VAL* 4.0 11.0 - - + -
181V LYS* 2.9 62.3 - - + +
182V PHE* 3.9 11.7 - - + -
183V ASP* 2.7 40.6 + - - +
184V SER 3.2 7.4 + - - +
301V GLU* 1.3 95.4 - - + +
303V ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 303 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34V ILE* 5.3 0.9 - - + -
36V ALA* 4.2 9.9 - - + -
37V ASP 3.1 11.4 + - - +
38V VAL* 3.5 7.6 - - + -
39V TYR 2.9 25.1 + - - -
182V PHE* 3.7 9.0 - - - -
184V SER* 3.2 24.0 - - - +
186V VAL* 3.8 7.9 - - + -
290V LEU* 3.5 33.2 - - + -
294V ALA* 4.2 20.6 - - + -
299V LEU* 3.8 23.8 - - + +
300V GLY 4.0 13.9 - - - +
302V LYS* 1.3 84.9 - - - +
304V LEU* 1.3 63.1 + - - +
305V PHE 4.1 0.4 - - - -
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Residues in contact with LEU 304 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V ILE* 4.2 8.7 - - + -
39V TYR* 3.6 4.7 - - + +
40V ILE* 4.3 3.4 - - - -
41V LYS* 3.8 24.9 - - + +
174V ILE* 3.5 31.2 - - + -
182V PHE* 3.3 41.3 - - + -
184V SER 2.9 8.5 + - - -
185V ILE* 3.2 26.4 - - + +
186V VAL 2.8 25.6 + - - -
303V ILE* 1.3 74.5 - - - +
305V PHE* 1.3 79.0 + - - +
306V ILE* 4.3 6.3 - - + -
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Residues in contact with PHE 305 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38V VAL* 4.6 5.7 - - + +
39V TYR 2.8 15.5 + - - +
40V ILE* 3.2 20.6 - - + +
41V LYS 3.0 24.8 + - - -
186V VAL* 3.5 22.4 - - + +
187V VAL* 5.0 1.3 - - - -
188V ALA 5.2 0.4 - - - -
278V LEU* 4.1 13.5 - - + -
283V THR* 3.7 28.5 - - + -
286V ALA* 3.8 12.3 - - + -
287V PHE* 3.6 54.5 - + + -
290V LEU* 4.7 6.7 - - + -
303V ILE* 4.1 1.0 - - - +
304V LEU* 1.3 76.0 - - - +
306V ILE* 1.3 80.4 + - - +
307V HIS* 3.7 11.4 - - + -
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Residues in contact with ILE 306 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V LYS* 4.1 12.3 - - + +
43V ASP* 4.4 7.2 - - + +
167V TYR* 3.9 31.6 - - + +
170V ALA* 5.5 0.2 - - + -
174V ILE* 4.4 15.3 - - + -
185V ILE* 4.0 25.6 - - + -
186V VAL 2.9 10.0 + - - +
187V VAL* 3.8 19.9 - - + +
188V ALA 5.1 0.3 + - - -
198V LEU* 4.6 10.5 - - + -
304V LEU* 4.3 8.1 - - + -
305V PHE* 1.3 90.4 - - - +
307V HIS* 1.3 60.5 + - - +
308V THR* 3.1 35.8 + - + +
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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