Contacts of the strand formed by residues 242 - 247 (chain B) in PDB entry 4MZF
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 VAL 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B MET* 4.6 11.2 - - - -
156B LEU* 4.4 7.2 - - + -
235B GLN* 3.8 2.1 - - - +
236B VAL* 2.9 41.2 + - + +
239B LYS* 2.8 31.2 + - + +
241B SER* 1.3 78.8 - - - +
243B TYR* 1.3 66.1 + - - +
255B VAL* 3.6 29.4 - - + -
256B TYR 3.5 8.3 - - - +
257B ASP* 3.5 27.4 - - + +
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Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER* 3.4 7.8 - - - -
213B LEU* 3.2 48.0 + - + +
214B VAL* 3.9 2.2 - - + -
232B VAL* 3.4 23.8 - - + -
234B HIS 3.1 19.7 - - - +
235B GLN* 2.9 35.2 + - + -
236B VAL 4.7 0.4 - - - +
240B PRO 3.3 19.4 + - - -
241B SER* 3.4 18.8 - - - -
242B VAL* 1.3 74.3 - - - +
244B PHE* 1.3 66.1 + - - +
245B ILE* 4.4 3.9 - - + +
254B TYR 3.6 0.2 - - - +
255B VAL* 3.3 6.1 - - - +
256B TYR 3.0 31.6 + - - +
258B LEU* 3.6 24.9 - - + -
259B VAL* 6.5 0.4 - - + -
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Residues in contact with PHE 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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88B LEU* 4.6 14.1 - - + -
156B LEU* 4.2 9.0 - - + -
157B ALA* 6.3 0.2 - - + -
167B TYR* 3.9 23.1 - + - -
176B LEU* 3.7 28.0 - - + -
232B VAL* 3.7 2.4 - - - +
233B ILE* 2.9 38.1 + - + -
234B HIS* 2.9 40.4 + + + +
236B VAL* 3.7 23.3 - - + -
243B TYR* 1.3 76.9 - - - +
245B ILE* 1.3 63.3 + - - +
253B ILE* 3.6 21.1 - - + -
254B TYR 3.2 3.8 - - - -
255B VAL* 3.9 23.3 - - + -
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Residues in contact with ILE 245 (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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218B VAL* 3.6 31.6 - - + -
231B MET 3.4 11.0 - - - +
232B VAL* 4.2 13.2 - - + -
233B ILE* 4.7 1.8 - - - -
243B TYR* 4.4 5.8 - - + +
244B PHE* 1.3 79.7 - - - +
246B LYS* 1.3 67.5 + - - +
247B PHE* 3.9 19.3 - - + -
253B ILE* 3.7 4.7 - - - -
254B TYR* 2.7 48.4 + - + +
256B TYR* 3.8 28.9 - - + -
258B LEU* 4.2 26.0 - - + -
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Residues in contact with LYS 246 (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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86B LEU* 3.9 27.4 - - + -
99B GLY 3.5 22.9 - - - -
100B LEU* 5.5 0.2 - - - +
101B GLU* 6.3 0.2 - - - -
230B GLY* 3.2 1.0 - - - -
231B MET* 3.0 31.1 + - + +
233B ILE* 4.1 25.2 - - + +
245B ILE* 1.3 72.3 - - - +
247B PHE* 1.3 70.9 + - - +
248B ASP* 4.6 3.6 - - - +
249B ASP 4.7 1.6 - - - +
250B ASP 2.8 32.0 + - - +
251B PHE* 4.4 0.8 - - - +
252B HIS 4.1 10.8 - - - +
253B ILE* 4.2 12.1 - - + -
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Residues in contact with PHE 247 (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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218B VAL* 4.1 17.3 - - + -
220B TYR* 3.8 37.5 - + + -
228B ARG* 3.6 44.2 - - + +
229B THR 3.5 19.1 - - - -
230B GLY* 3.9 1.8 - - - -
245B ILE* 3.9 19.5 + - + -
246B LYS* 1.3 81.3 + - - +
248B ASP* 1.3 65.1 + - - +
250B ASP* 3.0 29.8 + - + +
252B HIS 4.8 2.4 + - - -
254B TYR* 3.4 42.8 - + + -
256B TYR* 4.6 7.4 - + - -
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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
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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