Contacts of the strand formed by residues 258 - 262 (chain A) in PDB entry 5J3S
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.7 32.8 - - + -
116A LEU* 3.5 30.3 - - + -
149A PHE* 4.3 3.3 - - + -
220A LEU* 4.3 14.6 - - + -
221A CYS 3.1 12.8 + - - +
222A LEU* 3.8 11.7 - - + -
223A MET* 3.2 23.4 + - - +
257A VAL* 1.3 79.3 - - - +
259A PHE* 1.3 65.0 + - - +
318A ILE* 4.3 6.7 - - + -
319A PHE 3.3 8.3 - - - +
320A PHE* 3.9 27.6 - - + -
327A ILE* 6.0 0.9 - - + -
356A LEU* 4.5 8.7 - - + -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 6.3 0.7 - - + -
223A MET* 3.7 25.4 - - + -
224A THR* 3.9 3.6 - - - -
225A SER* 3.8 39.0 - - - -
227A LEU* 4.5 7.9 - - + -
241A LEU* 6.2 0.7 - - + -
244A VAL* 3.9 23.8 - - + -
248A MET* 3.8 23.8 - - + +
257A VAL* 4.1 1.2 - - - +
258A ILE* 1.3 74.1 - - - +
260A ALA* 1.3 77.8 + - - +
261A GLY* 4.3 2.9 - - - -
263A THR* 4.0 22.9 - - + -
317A ARG 4.7 1.6 - - - -
318A ILE* 3.2 5.2 - - - +
319A PHE* 2.8 64.9 + + + +
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.7 3.6 - - + -
118A THR* 3.1 23.6 - - - +
149A PHE* 3.8 21.3 - - + +
223A MET 3.2 4.9 + - - +
224A THR* 2.9 28.3 + - - -
259A PHE* 1.3 86.5 - - - +
261A GLY* 1.3 57.8 + - - +
317A ARG 3.3 8.3 - - - -
318A ILE* 3.9 15.9 - - + -
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR* 3.6 7.9 - - - +
151A GLN* 3.4 18.2 - - - -
225A SER 3.7 9.2 - - - -
259A PHE* 4.3 3.4 - - - -
260A ALA* 1.3 76.6 - - - +
262A ASP* 1.3 65.8 + - - -
263A THR* 3.1 17.6 + - - +
316A ASP* 4.1 5.4 - - - -
317A ARG 3.2 17.4 + - - -
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASN* 3.5 10.7 + - + -
151A GLN* 3.6 14.9 + - + +
225A SER 3.4 5.9 + - - +
226A HIS* 3.4 40.1 + - - +
227A LEU* 3.2 24.3 + - - +
261A GLY* 1.3 68.4 - - - -
263A THR* 1.3 59.4 + - - +
264A ASN* 3.4 17.5 + - - +
315A PHE* 3.3 25.6 - - - +
316A ASP* 3.7 13.4 + - - +
349A HIS* 3.5 16.3 + - - -
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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