Contacts of the strand formed by residues 291 - 295 (chain D) in PDB entry 2XH2
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 ILE 291 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LEU* 4.5 6.3 - - + -
243D ILE* 3.4 22.0 - - + +
245D LEU* 4.1 19.3 - - + -
285D LEU* 3.9 40.4 - - + +
286D MET* 4.3 11.1 - - + +
289D TYR* 2.8 24.2 + - + +
290D PRO* 1.3 72.9 - - - +
292D VAL* 1.3 63.8 + - - +
293D SER 3.7 20.4 - - - +
294D ILE* 3.7 20.4 - - + -
315D ILE* 3.6 24.0 - - + +
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D PHE* 4.5 13.0 - - + -
172D ALA* 4.8 1.6 - - + -
242D LYS* 3.7 45.3 - - + -
243D ILE 2.9 20.2 + - - +
290D PRO 4.2 0.9 - - - +
291D ILE* 1.3 77.3 - - - +
293D SER* 1.3 61.2 + - - +
315D ILE* 3.8 12.7 - - + +
316D GLN* 3.4 21.3 + - - +
428D GLU* 5.6 3.1 - - - +
430D PHE* 3.9 31.4 - - + -
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Residues in contact with SER 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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150D PHE* 4.0 24.0 - - - -
243D ILE 3.7 0.6 + - - -
244D GLY* 3.3 4.4 - - - -
245D LEU 2.9 25.6 + - - -
291D ILE* 3.7 3.8 - - - +
292D VAL* 1.3 83.6 - - - +
294D ILE* 1.3 66.6 + - - +
315D ILE* 4.0 0.4 - - - +
316D GLN* 3.1 32.7 + - - +
318D VAL* 3.3 18.9 - - - +
370D MET* 4.2 4.0 - - - +
430D PHE* 5.0 0.7 - - - -
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Residues in contact with ILE 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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245D LEU* 3.5 17.9 - - + -
247D CYS* 3.5 30.3 - - - -
282D TYR* 4.3 19.7 - - + -
285D LEU* 6.4 0.7 - - + -
286D MET* 4.2 16.6 - - + -
291D ILE* 3.7 13.7 - - + -
293D SER* 1.3 80.4 + - - +
295D GLU* 1.3 61.9 + - - +
297D PRO* 4.0 17.2 - - + +
309D PHE* 4.5 6.3 - - + -
315D ILE* 3.6 21.3 - - + -
316D GLN 3.0 6.9 + - - -
317D ILE* 3.4 17.9 - - + +
318D VAL* 2.9 23.0 + - - +
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Residues in contact with GLU 295 (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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170D MET* 4.8 2.2 - - + +
245D LEU 2.8 17.4 + - - +
246D ASP* 3.0 14.9 - - - +
247D CYS* 2.9 24.6 + - - +
293D SER* 5.9 0.2 - - - +
294D ILE* 1.3 72.4 - - - +
296D ASP* 1.3 71.0 + - - +
297D PRO 3.2 3.2 - - - -
318D VAL* 3.3 26.7 - - + +
320D ASP* 3.0 21.3 - - + +
343D LEU* 3.6 9.4 - - - +
370D MET* 5.1 1.6 - - - +
396D LYS* 2.8 30.6 + - - -
1439D MG 2.0 33.3 - - - -
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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