Contacts of the strand formed by residues 259 - 266 (chain A) in PDB entry 2ABJ
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 MET 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A VAL* 5.5 0.7 - - + -
242A GLN* 4.1 8.3 - - + +
255A GLU* 3.2 12.8 - - - +
256A VAL* 2.8 48.2 + - + +
257A GLY 3.4 0.8 + - - -
258A THR* 1.3 77.1 - - - +
260A ASN* 1.3 61.0 + - - +
328A SER* 3.3 36.6 - - - +
329A SER 3.2 14.1 - - - +
333A CYS* 3.6 17.5 - - - -
336A CYS* 3.8 10.3 - - + -
420A PLP 3.8 0.7 - - - -
1401A CBC 3.4 65.3 - - + +
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Residues in contact with ASN 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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254A THR 5.4 0.2 - - - +
255A GLU* 3.8 9.6 - - - +
256A VAL 4.7 0.4 - - - -
259A MET* 1.3 73.8 - - - +
261A LEU* 1.3 60.5 + - - +
262A PHE* 3.9 2.2 + - + -
276A THR* 5.0 1.6 - - - +
283A ILE* 3.5 16.6 - - - +
284A LEU 2.9 18.1 + - - +
286A GLY* 3.3 30.7 - - - +
289A ARG* 3.4 28.2 - - + +
327A PHE 3.8 0.2 - - - +
328A SER* 3.1 9.2 - - - -
329A SER* 2.8 45.3 + - - +
420A PLP 3.4 16.1 - - - -
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Residues in contact with LEU 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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244A LEU* 4.6 5.6 - - + -
253A ILE* 3.8 32.1 - - + -
254A THR 3.5 27.0 + - - +
255A GLU* 4.2 3.6 - - - -
256A VAL* 3.2 28.5 - - + -
259A MET 3.9 0.4 + - - -
260A ASN* 1.3 74.7 - - - +
262A PHE* 1.3 70.6 + - - +
263A LEU* 4.6 1.1 - - + -
276A THR* 2.5 31.3 + - - -
277A PRO* 3.3 9.6 - - + +
309A LEU* 4.2 12.6 - - + -
326A MET* 3.6 31.9 - - + -
327A PHE 4.0 3.4 - - - +
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Residues in contact with PHE 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 ASN* 4.4 3.8 - - + -
261A LEU* 1.3 78.8 - - - +
263A LEU* 1.3 59.8 + - - +
274A LEU* 3.9 23.1 - - + -
275A ALA 3.5 2.0 - - - -
276A THR* 3.7 21.8 - - - -
289A ARG* 3.7 38.6 - - + -
292A ILE* 3.7 26.0 - - + -
293A LEU* 3.8 16.8 - - + -
325A GLU 4.8 0.2 - - - -
326A MET* 3.4 9.0 - - - +
327A PHE* 2.9 67.5 + + + +
329A SER* 3.3 28.7 - - - -
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Residues in contact with LEU 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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253A ILE* 4.9 1.8 - - + -
261A LEU* 4.4 2.2 - - + +
262A PHE* 1.3 74.4 - - - +
264A TYR* 1.3 63.0 + - - +
265A TRP* 3.6 42.2 + - + -
273A GLU 3.6 2.6 - - - +
274A LEU* 3.6 2.8 - - - -
275A ALA* 2.8 41.7 + - + +
309A LEU* 4.2 26.2 - - + -
313A ASP* 6.4 0.2 - - + -
314A LEU* 4.4 19.7 - - + -
323A VAL* 3.8 26.5 - - + -
325A GLU 3.5 15.7 - - - +
326A MET* 4.3 18.6 - - + -
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Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A PHE 4.3 0.2 - - - -
263A LEU* 1.3 70.9 - - - +
265A TRP* 1.3 61.6 + - - +
272A GLU* 2.3 45.5 + - + -
273A GLU 3.4 15.9 - - - -
274A LEU* 4.2 5.8 - - + -
302A PHE* 4.2 16.0 - + - -
323A VAL* 4.3 0.3 - - - -
324A ARG* 2.9 74.1 + - + +
325A GLU* 2.8 45.5 + - + +
327A PHE* 4.7 2.9 - - + -
358A LYS* 4.4 7.6 - - - -
359A LEU* 3.7 37.7 - - + -
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Residues in contact with TRP 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 LEU* 3.6 35.7 - - + -
264A TYR* 1.3 78.8 - - - +
266A ILE* 1.3 63.5 + - - +
267A ASN* 3.8 10.9 - - + +
268A GLU* 3.7 18.2 - - - -
272A GLU* 3.5 3.4 - - - +
273A GLU* 2.7 74.6 + - + +
275A ALA* 4.1 5.1 - - - +
307A ARG* 3.7 27.4 - - - -
309A LEU* 4.2 9.6 - - + -
313A ASP* 3.7 21.5 - - + -
314A LEU* 5.1 0.2 - - - -
317A ALA* 3.6 26.2 - - + -
322A ARG* 3.4 32.1 - - - +
323A VAL* 4.0 7.6 - - + -
324A ARG* 4.2 4.7 - - - +
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Residues in contact with ILE 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 TRP* 1.3 78.2 - - - +
267A ASN* 1.3 58.0 + - - +
270A GLY* 3.5 37.7 - - - +
271A GLU 3.4 1.8 - - - -
272A GLU* 3.8 30.3 - - + +
321A ASN 5.5 1.1 - - - +
322A ARG* 2.8 66.6 + - + +
324A ARG* 5.5 9.4 - - + -
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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