Contacts of the strand formed by residues 267 - 272 (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 GLY 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A VAL 3.8 0.5 - - - +
263A GLN* 3.2 5.4 - - - +
264A ASP* 3.0 30.1 + - - +
265A THR 3.3 1.0 - - - -
266A SER* 1.3 82.6 + - - +
268A THR* 1.3 63.7 + - - -
269A TYR* 4.0 5.6 - - - -
280A TRP* 4.5 6.5 - - - -
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Residues in contact with THR 268 (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 4.0 5.7 + - - -
261A ARG* 3.6 48.2 - - + +
262A VAL 3.3 6.3 - - - +
263A GLN* 3.9 19.6 + - + +
267A GLY* 1.3 73.9 + - - -
269A TYR* 1.3 62.1 + - - +
270A TYR* 4.8 6.4 - - - +
280A TRP* 3.2 23.9 - - - +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 3.7 3.5 - - - +
262A VAL* 2.8 56.8 + - + +
264A ASP* 2.5 29.6 + - - -
266A SER* 3.4 22.0 - - - -
267A GLY 4.0 7.4 - - - -
268A THR* 1.3 78.1 - - - +
270A TYR* 1.3 70.9 + - - +
271A TRP* 5.7 0.4 - - + -
278A THR* 3.6 20.2 - - - -
279A GLN 3.5 14.6 - - - +
280A TRP* 3.9 13.2 - + + +
302A PG4 3.0 27.4 + - - -
272E HIS* 3.8 14.8 - + - -
274E PRO* 3.5 20.9 - - + +
275E THR* 4.3 4.3 - - + -
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Residues in contact with TYR 270 (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* 4.2 17.9 - - + -
259A TRP* 4.0 16.2 - - + -
260A MET 3.5 5.4 - - - +
261A ARG* 3.5 49.3 + - + -
268A THR* 4.8 5.2 - - + +
269A TYR* 1.3 81.0 - - - +
271A TRP* 1.3 62.0 - - - +
277A THR 3.6 0.3 - - - +
278A THR* 3.2 8.4 + - - -
279A GLN 2.8 37.5 + - - +
280A TRP 3.2 26.7 - - - -
281A GLU 3.8 6.7 - - - +
282A PRO* 3.8 24.0 - - + +
283A PRO* 3.7 22.2 - - + -
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Residues in contact with TRP 271 (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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258A GLY 4.0 0.2 - - - +
259A TRP* 3.3 7.5 - - - -
260A MET* 2.8 74.0 + - + +
262A VAL* 3.9 20.2 - - + -
269A TYR* 5.7 0.7 - - + -
270A TYR* 1.3 75.2 - - - +
272A HIS* 1.3 72.6 + - - +
273A ILE* 3.6 34.4 + - + +
276A GLY* 3.9 17.1 - - - -
277A THR 3.3 9.0 - - - -
278A THR* 4.6 7.4 - - + +
302A PG4 4.0 34.4 + - - +
262B VAL* 5.3 1.8 - - + -
271B TRP* 3.6 32.3 - + - -
273D ILE* 3.8 15.3 - - + -
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Residues in contact with HIS 272 (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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258A GLY 3.6 6.5 - - - -
259A TRP* 3.4 52.4 + + + -
271A TRP* 1.3 73.4 + - - +
273A ILE* 1.3 58.4 + - - +
274A PRO* 3.3 19.9 - - + +
275A THR* 2.6 32.3 + - + +
276A GLY* 2.9 31.0 + - - -
277A THR* 2.8 14.9 + - - +
276C GLY 3.1 26.7 - - - -
277C THR* 4.9 1.6 - - - -
278C THR* 3.2 21.1 + - - -
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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