Contacts of the strand formed by residues 240 - 244 (chain B) in PDB entry 1H4R
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 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLY 3.8 0.2 - - - +
236B VAL* 3.8 0.3 - - - -
237B ASP* 3.0 31.8 + - - +
239B LEU* 1.3 79.5 - - - +
241B LEU* 1.3 60.9 + - - -
242B HIS* 3.5 8.3 + - - -
256B PHE 3.2 13.7 - - - -
257B PRO* 4.3 0.2 - - - -
258B TRP* 3.1 26.5 - - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.2 12.8 - - + -
235B GLY 3.5 2.2 - - - +
236B VAL* 3.6 33.2 - - + -
240B GLY* 1.3 71.2 - - - -
242B HIS* 1.3 64.8 + - - +
243B ILE* 5.6 0.2 - - - -
255B SER* 3.5 0.2 - - - -
256B PHE* 2.8 43.3 + - + +
258B TRP* 3.5 29.4 - - + -
261B ILE* 4.1 14.8 - - + -
264B ILE* 4.2 16.2 - - + -
273B ILE* 3.8 33.7 - - + -
285B PHE* 5.8 0.7 - - + -
300B CYS* 3.7 8.7 - - - -
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B VAL* 5.6 0.4 - - + -
233B LEU 3.6 0.2 - - - +
234B LEU* 3.5 6.9 - - - +
235B GLY 2.9 37.1 + - - +
237B ASP* 2.8 41.2 + - - -
239B LEU* 4.5 9.6 - - + -
240B GLY* 3.5 19.7 + - - -
241B LEU* 1.3 76.0 + - - +
243B ILE* 1.3 67.8 + - - +
244B TYR* 3.7 24.6 - - + -
252B PRO* 3.7 14.6 - - + +
254B ILE 3.3 4.3 - - - -
255B SER* 2.8 34.0 + - - -
256B PHE 5.0 0.9 - - - -
257B PRO* 6.0 0.4 - - + -
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Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ILE* 4.3 9.6 - - + -
232B LEU* 3.9 32.3 - - + -
233B LEU 3.6 4.7 - - - +
234B LEU* 4.0 18.2 - - + -
241B LEU 5.6 0.2 - - - -
242B HIS* 1.3 80.6 - - - +
244B TYR* 1.3 63.3 + - - +
252B PRO* 3.4 1.1 - - - +
253B LYS* 2.8 30.4 + - + +
254B ILE* 2.8 37.0 + - + +
256B PHE* 4.4 11.4 - - + -
273B ILE* 5.0 2.9 - - + -
283B PHE* 3.8 37.9 - - + -
285B PHE* 5.2 0.4 - - + -
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Residues in contact with TYR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLU 4.9 3.5 + - - -
219B VAL* 3.9 19.2 - - - +
221B TYR* 3.8 26.5 + + - -
232B LEU* 3.6 10.3 - - - +
233B LEU* 2.8 51.1 + - + +
235B GLY* 3.8 13.7 - - - -
237B ASP* 5.3 0.3 + - - -
242B HIS* 3.7 25.8 - - + +
243B ILE* 1.3 77.1 - - - +
245B ASP* 1.3 64.3 + - - +
248B ASN 3.3 23.8 - - - +
249B ARG* 3.2 23.1 + - - -
250B LEU 4.1 1.0 + - - -
251B THR 3.9 0.9 - - - -
252B PRO* 3.5 41.1 - - + +
253B LYS* 4.5 0.4 - - - +
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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
------------------------------------------------------------
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