Contacts of the strand formed by residues 283 - 287 (chain B) in PDB entry 1JQO
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 ILE 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.3 17.5 - - + +
172B LEU* 5.0 5.8 - - + -
256B VAL* 4.4 24.0 - - + -
259B PHE* 4.5 8.1 - - + -
260B LEU* 4.7 11.9 - - + -
281B SER* 3.8 15.7 - - - -
282B LEU* 1.3 90.4 - - + +
284B ARG* 1.3 62.8 + - - +
285B PHE* 3.6 23.3 - - + -
445B THR* 3.9 9.7 - - + +
691B LEU* 3.7 29.4 - - + +
694B PHE* 5.6 2.2 - - + -
695B THR* 3.9 18.8 - - + +
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B THR* 4.7 17.5 - - + +
170B VAL 3.2 4.1 + - - +
171B ASP* 3.5 26.0 - - + +
172B LEU* 3.0 27.9 + - - +
279B ASN 5.2 0.8 + - - -
281B SER* 2.7 34.8 + - - -
283B ILE* 1.3 75.0 + - - +
285B PHE* 1.3 79.5 + - - +
286B SER* 4.8 0.9 - - - +
444B PHE 3.4 13.9 + - - -
445B THR* 4.5 14.1 + - - +
452B LYS* 4.9 20.0 - - + +
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Residues in contact with PHE 285 (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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172B LEU* 3.6 10.1 - - + -
174B PHE* 3.5 33.2 - + + -
248B ILE* 4.4 5.4 - - + -
252B VAL* 3.2 36.3 - - + -
256B VAL* 4.0 8.7 - - + -
283B ILE* 3.6 23.3 - - + -
284B ARG* 1.3 86.3 - - - +
286B SER* 1.3 66.5 + - - +
445B THR* 4.5 7.2 + - + +
446B PHE* 4.2 13.2 - + + -
450B LEU 4.5 4.9 - - - +
451B VAL* 3.5 33.6 - - + -
452B LYS* 3.5 4.0 + - - +
681B PHE* 4.0 14.8 - + - -
691B LEU* 4.0 22.4 - - + -
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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
----------------------------------------------------------
171B ASP* 2.7 31.5 + - - -
172B LEU 3.1 6.1 + - - +
173B VAL* 3.1 7.5 - - - -
174B PHE* 2.7 36.3 + - - +
284B ARG* 4.8 1.7 - - - +
285B PHE* 1.3 77.2 + - - +
287B SER* 1.3 55.6 + - - +
451B VAL* 4.2 3.1 - - - -
452B LYS* 3.5 21.2 - - - +
454B ASP* 4.4 2.9 - - - -
669B ARG* 3.3 21.7 + - - -
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Residues in contact with SER 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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174B PHE* 3.3 6.7 - - - -
245B MET* 5.1 2.5 - - - +
286B SER* 1.3 75.8 - - - +
288B TRP* 1.3 75.7 + - - +
289B MET* 2.9 43.9 + - - +
451B VAL* 3.6 22.0 - - - +
452B LYS 2.8 8.5 + - - +
453B LEU* 3.4 9.4 - - - +
454B ASP* 3.1 25.3 + - - +
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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