Contacts of the strand formed by residues 259 - 264 (chain A) in PDB entry 2IDH
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 TRP 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 3.6 24.9 - - + +
256A PRO* 3.3 30.3 + - + +
257A ALA 3.7 10.1 - - - -
258A GLY* 1.3 79.7 + - - +
260A MET* 1.3 62.5 + - - +
270A TYR* 4.0 12.6 - - + -
271A TRP 3.3 32.3 - - - -
272A HIS* 3.4 44.8 + + + -
277A THR* 4.1 11.4 - - + -
279A GLN* 3.5 34.8 - - - -
283A PRO* 3.6 29.3 - - + +
264B ASP* 3.3 14.6 - - - +
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Residues in contact with MET 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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255A LEU* 3.6 4.9 - - - -
259A TRP* 1.3 75.8 - - - +
261A ARG* 1.3 63.3 + - - +
262A VAL* 4.0 2.8 + - + -
270A TYR* 3.5 5.8 - - - +
271A TRP* 2.8 69.2 + - + +
273A ILE* 3.7 23.3 - - + -
262B VAL* 3.7 30.5 - - + -
263B GLN 3.5 4.7 - - - +
264B ASP* 2.7 40.4 - - + +
269B TYR* 3.9 23.1 - - + +
273D ILE* 5.6 0.4 - - - -
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Residues in contact with ARG 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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202A SO4 2.5 43.5 + - - -
255A LEU* 3.3 12.3 - - + +
260A MET* 1.3 70.4 - - - +
262A VAL* 1.3 63.1 + - - +
263A GLN* 3.7 9.7 - - + +
268A THR* 3.6 28.3 - - + +
269A TYR 3.7 4.5 - - - +
270A TYR* 3.5 39.3 + - + -
261B ARG 3.7 1.0 - - - +
262B VAL* 3.3 4.5 - - - -
263B GLN* 2.8 64.1 + - + +
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Residues in contact with VAL 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 MET* 4.5 1.8 - - + +
261A ARG* 1.3 76.3 - - - +
263A GLN* 1.3 67.5 + - - +
264A ASP* 4.5 0.2 - - - +
267A GLY 3.8 0.5 - - - +
268A THR* 3.3 4.3 - - - +
269A TYR* 2.8 72.0 + - + +
271A TRP* 3.9 34.3 - - + -
302A PG4 4.7 4.5 - - - -
260B MET* 3.5 28.7 - - + -
261B ARG 3.3 3.8 - - - -
262B VAL* 4.0 15.3 - - + -
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Residues in contact with GLN 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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202A SO4 3.0 40.4 + - - -
261A ARG* 3.7 7.9 - - + +
262A VAL* 1.3 80.2 - - - +
264A ASP* 1.3 65.7 + - - +
267A GLY 3.2 10.3 - - - +
268A THR* 3.9 15.8 + - + +
255B LEU* 4.2 2.7 - - + +
260B MET* 3.7 0.9 - - - -
261B ARG* 2.7 62.2 + - + +
263B GLN* 3.2 30.3 - - - +
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Residues in contact with ASP 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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262A VAL* 4.5 0.9 - - - +
263A GLN* 1.3 77.5 - - - +
265A THR* 1.3 68.4 + - - +
266A SER* 2.6 44.6 + - - -
267A GLY* 3.0 11.9 + - - +
269A TYR* 2.5 32.4 + - - -
302A PG4 4.4 2.3 + - - -
255B LEU* 5.2 8.3 - - - -
257B ALA* 6.4 0.9 - - - -
259B TRP 3.9 19.7 - - - +
260B MET* 4.5 7.5 - - + +
273B ILE* 6.0 2.0 - - + +
274E PRO* 4.5 2.9 - - - +
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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