Contacts of the strand formed by residues 285 - 291 (chain B) in PDB entry 1JQE
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 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLU* 3.9 20.0 - - - +
31B CYS* 3.9 20.9 - - + -
32B MET* 3.8 28.3 - - + -
143B GLN* 3.7 22.7 - - - +
171B ILE* 4.5 4.7 - - + -
172B VAL 3.8 4.5 - - - +
173B VAL* 4.1 14.4 - - + -
174B SER* 4.2 0.4 - - - -
218B TYR 3.8 0.2 - - - +
219B ASP* 3.3 4.5 - - - +
220B LEU 3.0 32.9 + - - +
283B ASN* 3.4 20.6 - - - +
284B THR* 1.3 78.5 - - - +
286B SER* 1.3 62.0 + - - +
287B PHE* 3.8 20.6 - - + -
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Residues in contact with SER 286 (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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170B ILE 3.7 1.0 - - - +
171B ILE* 3.3 25.8 - - - +
172B VAL* 2.8 16.1 + - - -
174B SER* 3.1 10.6 - - - +
201B SER* 3.0 37.9 + - - -
217B CYS* 3.8 7.9 - - - -
218B TYR 3.3 4.0 - - - -
219B ASP* 2.6 20.0 + - - -
285B LEU* 1.3 73.8 - - - +
287B PHE* 1.3 63.9 + - - +
288B ILE* 4.0 3.8 - - - +
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Residues in contact with PHE 287 (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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31B CYS* 4.0 17.3 - - - -
32B MET* 4.1 10.3 - - + -
35B PHE* 3.3 63.0 - + + -
169B LEU* 4.5 2.5 - - + -
170B ILE 3.7 3.8 - - - -
171B ILE* 3.4 33.9 - - + -
217B CYS* 3.2 0.7 - - - -
218B TYR* 2.6 57.7 + - + +
220B LEU* 3.8 31.0 - - + -
285B LEU* 3.8 26.0 - - + -
286B SER* 1.3 75.1 - - - +
288B ILE* 1.3 59.9 + - - +
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Residues in contact with ILE 288 (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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168B MET 3.5 1.4 - - - +
169B LEU* 3.4 4.7 - - - +
170B ILE* 2.8 48.6 + - + +
172B VAL* 4.9 2.7 - - + -
201B SER* 4.5 8.7 - - - -
204B LEU* 3.8 39.7 - - + -
205B THR* 4.5 9.4 - - + -
208B LEU* 3.7 25.1 - - + -
215B TYR* 4.1 14.1 - - + -
216B GLU 3.2 9.2 - - - +
217B CYS* 3.6 23.3 - - + -
286B SER 4.7 1.8 - - - -
287B PHE* 1.3 78.1 - - - +
289B VAL* 1.3 63.1 + - - +
290B ILE* 4.0 7.1 + - + +
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Residues in contact with VAL 289 (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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43B ILE* 3.6 29.6 - - + -
167B LYS* 3.9 23.6 - - + +
168B MET 3.4 6.7 - - - +
169B LEU* 4.2 12.3 - - + -
215B TYR* 3.1 4.7 - - - -
216B GLU* 2.8 38.6 + - + +
218B TYR* 3.5 30.5 - - + +
288B ILE* 1.3 75.7 - - - +
290B ILE* 1.3 64.1 + - - +
291B GLU* 3.8 21.7 + - - +
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Residues in contact with ILE 290 (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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155B LEU* 4.6 0.9 - - + -
159B HIS* 3.8 11.7 - - + -
162B LEU* 4.1 0.7 - - + +
167B LYS* 3.4 7.8 - - - +
168B MET* 2.8 70.8 + - + +
170B ILE* 3.8 24.9 - - + -
208B LEU* 3.7 26.2 - - + -
213B LEU* 4.3 11.7 - - + -
214B LYS 3.5 9.0 - - - +
215B TYR* 3.8 14.8 - - + -
288B ILE* 4.2 5.2 - - + -
289B VAL* 1.3 76.3 - - - +
291B GLU* 1.3 74.9 + - - +
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Residues in contact with GLU 291 (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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159B HIS* 3.2 19.1 + - - -
162B LEU* 4.1 1.8 - - - -
165B ASN* 5.6 1.0 - - - +
166B ALA 4.2 2.5 - - - +
167B LYS* 2.9 44.8 + - - +
214B LYS* 3.1 31.6 + - + +
215B TYR* 5.5 1.1 - - - -
289B VAL* 3.8 14.1 - - - +
290B ILE* 1.3 76.7 - - - +
292B ALA* 1.3 70.0 + - - +
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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