Contacts of the strand formed by residues 290 - 294 (chain D) in PDB entry 2IHU
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 LEU 290 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ALA 4.8 2.0 - - - +
212D LEU* 3.7 14.6 - - + +
213D LEU* 3.6 36.1 - - + +
216D ALA* 3.9 17.3 - - + -
218D HIS 3.9 0.4 + - - -
219D PRO* 3.3 7.5 - - + +
220D VAL 3.0 26.3 + - - +
288D VAL* 3.6 4.7 - - - +
289D ASP* 1.3 82.1 + - - +
291D VAL* 1.3 63.2 + - - +
292D LEU* 4.0 22.0 - - + -
313D LYS* 4.5 0.4 - - - +
314D LYS* 3.3 33.2 - - + +
316D VAL* 4.0 22.7 - - + -
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Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D VAL* 3.8 7.2 - - + -
222D VAL* 3.7 27.4 - - + -
285D PHE* 5.2 0.7 - - + -
288D VAL* 4.0 16.8 - - + -
290D LEU* 1.3 75.5 - - - +
292D LEU* 1.3 63.1 + - - +
293D THR* 3.7 19.0 + - + +
307D TRP* 3.9 37.9 - - + -
313D LYS* 4.4 10.1 - - + -
314D LYS 2.9 13.6 + - - +
315D THR* 3.3 10.3 - - + -
316D VAL 2.9 24.3 + - - +
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Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ALA* 4.8 2.5 - - + +
213D LEU* 4.8 5.6 - - + -
219D PRO* 4.4 9.9 - - + -
220D VAL 3.0 20.5 + - - +
221D LEU* 3.6 23.9 - - + -
222D VAL 2.9 25.8 + - - -
245D ILE* 5.4 2.2 - - + -
290D LEU* 4.0 25.4 - - + -
291D VAL* 1.3 71.9 - - - +
293D THR* 1.3 62.2 + - - +
294D VAL* 3.3 10.0 + - + +
316D VAL* 3.5 34.1 - - + +
318D ILE* 4.4 2.7 - - + -
342D PHE* 4.7 9.6 - - + -
346D PHE* 4.1 30.1 - - + -
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Residues in contact with THR 293 (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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222D VAL* 3.3 13.5 - - + -
291D VAL* 3.8 17.0 - - + +
292D LEU* 1.3 67.9 - - - +
294D VAL* 1.3 59.7 + - - +
295D GLY 3.5 0.3 + - - -
296D TYR* 3.4 31.2 + - + +
307D TRP* 3.7 29.4 - - + -
316D VAL 2.8 11.7 + - - -
317D ARG* 3.4 3.6 - - - -
318D ILE* 3.0 26.9 + - - +
329D TYR* 2.8 27.3 + - - +
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Residues in contact with VAL 294 (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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221D LEU* 3.8 26.5 - - + -
222D VAL 2.8 11.5 + - - +
223D VAL* 3.6 9.3 - - + -
224D GLY 3.1 24.4 + - - -
227D ALA* 4.0 4.4 - - - +
236D ILE* 3.9 21.8 - - + -
292D LEU* 3.7 13.2 - - + +
293D THR* 1.3 68.9 - - - +
295D GLY* 1.3 61.2 + - - +
318D ILE* 4.1 20.6 - - + -
339D VAL* 3.6 26.7 - - + -
342D PHE* 4.9 7.2 - - + -
343D VAL* 4.9 5.8 - - + -
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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