Contacts of the strand formed by residues 260 - 267 (chain A) in PDB entry 2JB3
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 GLU 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA* 4.4 3.4 - - + +
258A GLY 3.9 1.9 + - - +
259A ALA* 1.3 69.8 - - - +
261A VAL* 1.3 71.2 + - - +
262A THR* 3.3 13.8 - - + +
275A TYR* 3.2 2.5 - - - -
276A THR* 2.9 43.0 + - - +
420A LYS* 4.8 2.4 + - - +
421A TYR* 2.6 38.5 + - + +
1489A FAD 4.0 12.5 + - - +
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Residues in contact with VAL 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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18A LEU* 3.7 24.9 - - + -
41A LEU* 3.9 32.5 - - + -
259A ALA 4.4 0.4 - - - +
260A GLU* 1.3 74.9 - - - +
262A THR* 1.3 63.7 + - - +
263A SER 3.7 10.5 - - - +
273A VAL* 3.5 22.4 - - + -
274A GLU 3.6 5.8 - - - +
275A TYR* 3.8 3.1 - - + -
293A ILE* 4.3 3.1 - - + -
301A LEU* 3.3 21.9 - - + +
1489A FAD 3.0 39.7 + - + +
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Residues in contact with THR 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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260A GLU* 3.3 27.1 - - + +
261A VAL* 1.3 74.4 - - - +
263A SER* 1.3 63.3 + - - +
274A GLU* 2.9 21.4 + - - +
275A TYR* 4.2 1.6 + - - -
276A THR* 4.2 15.0 + - - +
281A LYS* 5.5 5.8 - - + +
300A ARG 4.9 0.3 - - - +
301A LEU* 3.6 10.5 - - - -
302A GLN* 2.9 33.5 + - - +
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Residues in contact with SER 263 (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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261A VAL* 3.7 3.5 - - - +
262A THR* 1.3 81.4 - - - +
264A MET* 1.3 61.9 + - - +
265A LYS* 3.9 17.2 - - - +
272A THR 4.4 1.0 + - - -
273A VAL* 3.2 11.0 - - - +
274A GLU* 3.0 57.9 + - - +
301A LEU* 4.3 1.3 - - - +
302A GLN* 3.2 29.7 + - - +
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Residues in contact with MET 264 (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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18A LEU* 3.9 26.0 - - + -
263A SER* 1.3 75.3 + - - +
265A LYS* 1.3 62.2 + - - +
271A VAL* 4.1 11.0 - - + -
272A THR 3.6 3.8 - - - -
273A VAL* 4.4 3.8 - - + +
289A ALA* 5.1 0.9 - - - -
291A CYS* 3.9 34.3 - - - -
298A VAL* 4.3 9.2 - - + -
301A LEU* 4.5 9.6 - - + -
302A GLN 2.9 9.2 + - - +
303A ASN* 3.2 26.6 - - + +
304A ASN* 3.8 1.9 + - - +
305A LEU* 4.2 26.4 - - + +
454A ILE* 3.9 38.0 - - + +
456A PHE* 4.4 2.0 - - + -
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Residues in contact with LYS 265 (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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263A SER* 3.9 20.6 - - - +
264A MET* 1.3 82.8 - - - +
266A ASN* 1.3 66.0 + - - +
267A VAL* 3.4 8.0 + - + +
271A VAL* 3.3 6.6 - - - +
272A THR* 2.9 37.0 + - - +
302A GLN* 4.4 7.0 + - - +
303A ASN* 3.9 27.1 - - - +
304A ASN* 3.5 20.4 - - + +
454A ILE* 4.7 0.4 - - - -
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Residues in contact with ASN 266 (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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265A LYS* 1.3 71.5 - - - +
267A VAL* 1.3 65.1 + - - +
270A GLY 3.7 11.6 + - - -
271A VAL* 3.9 0.6 - - - +
304A ASN* 2.9 36.8 + - - +
305A LEU* 5.3 0.3 - - - +
451A VAL* 3.0 27.5 + - - +
452A ASP* 3.5 18.5 - - + +
453A LYS* 3.2 31.7 - - - +
454A ILE* 3.2 22.3 - - - +
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Residues in contact with VAL 267 (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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265A LYS* 4.0 10.5 - - + +
266A ASN* 1.3 80.3 + - - +
268A SER* 1.3 69.1 + - - +
269A GLU* 3.8 23.3 - - + +
270A GLY* 2.9 33.3 + - - +
271A VAL 3.9 1.1 - - - +
272A THR* 3.3 34.5 - - - +
285A THR* 4.3 0.2 - - + -
453A LYS* 5.6 1.4 - - - +
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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
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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