Contacts of the strand formed by residues 259 - 264 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C GLN 4.6 0.2 - - - +
264C ASP* 4.6 4.9 - - - +
255D LEU* 4.1 19.7 - - + +
256D PRO* 3.1 38.4 + - + +
257D ALA 3.9 5.2 - - - -
258D GLY* 1.3 77.8 + - - +
260D MET* 1.3 67.9 + - - +
270D TYR* 3.8 17.3 - - + -
271D TRP 3.3 32.1 - - - -
272D HIS* 3.4 45.2 + + + -
277D THR* 4.0 13.5 - - + -
279D GLN* 3.6 28.0 - - + -
283D PRO* 3.4 33.9 - - + +
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Residues in contact with MET 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ILE* 5.1 2.7 - - + -
264B ASP* 5.3 4.5 - - - +
262C VAL* 3.1 37.0 - - + -
263C GLN 3.3 8.1 - - - +
264C ASP* 3.7 29.8 - - - +
269C TYR* 3.2 29.8 - - + +
255D LEU* 4.4 2.0 - - - -
258D GLY 5.9 0.4 - - - -
259D TRP* 1.3 77.4 - - - +
261D ARG* 1.3 60.8 + - - +
262D VAL* 3.9 1.5 + - + -
270D TYR* 3.4 10.2 - - - +
271D TRP* 2.8 50.2 + - + +
273D ILE* 3.9 30.1 - - + -
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Residues in contact with ARG 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ARG 3.6 1.2 - - - +
262C VAL* 3.4 3.1 - - - -
263C GLN* 2.7 76.5 + - + +
201D SO4 3.2 38.8 + - - -
255D LEU* 4.2 10.1 - - + +
260D MET* 1.3 71.6 - - - +
262D VAL* 1.3 62.5 + - - +
263D GLN* 4.4 4.3 - - + +
268D THR* 3.4 34.0 + - + +
269D TYR 3.5 4.3 - - - -
270D TYR* 3.5 31.2 + - + -
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Residues in contact with VAL 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C MET* 3.7 26.9 - - + -
261C ARG 3.3 5.8 - - - +
262C VAL* 4.4 11.4 - - + -
260D MET* 4.5 2.9 - - + +
261D ARG* 1.3 78.1 - - - +
263D GLN* 1.3 67.7 + - - +
267D GLY 3.8 0.7 - - - +
268D THR* 3.3 5.4 - - - +
269D TYR* 2.8 72.5 + - + +
271D TRP* 4.0 39.3 - - + -
305D PG4 5.1 1.3 - - - +
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Residues in contact with GLN 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C LEU* 3.7 3.9 - - - +
260C MET* 3.4 1.7 - - - -
261C ARG* 2.1 91.9 + - + +
263C GLN* 5.3 5.5 + - - +
201D SO4 3.3 34.0 + - - -
261D ARG* 4.2 6.2 - - + +
262D VAL* 1.3 73.8 - - - +
264D ASP* 1.3 67.9 + - - +
267D GLY 3.4 7.4 - - - +
268D THR* 2.9 34.6 + - + +
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Residues in contact with ASP 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C LEU* 4.8 9.0 - - - -
257C ALA* 6.4 0.4 - - - -
259C TRP 3.6 20.2 - - - +
260C MET* 4.3 11.6 - - + +
261C ARG* 6.0 0.7 - - - +
273C ILE* 6.0 0.9 - - - +
263D GLN* 1.3 79.4 - - - +
265D THR* 1.3 66.6 + - - +
266D SER* 2.5 42.7 + - - -
267D GLY* 3.0 18.0 + - - +
269D TYR* 2.6 30.2 + - - -
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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