Contacts of the strand formed by residues 249 - 256 (chain B) in PDB entry 1MHP
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 LYS 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLN 4.0 8.3 + - - +
147B LEU* 3.6 11.7 - - + -
148B ASP* 2.9 28.4 + - - +
247B GLY 4.3 0.4 + - - -
248B VAL* 1.3 75.3 - - - +
250B LYS* 1.3 65.2 + - - +
251B VAL* 3.9 14.0 + - + -
277B ASN* 2.5 40.9 + - + +
279B GLN* 3.0 45.2 - - + +
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASP* 3.6 8.1 - - + +
238B PHE* 3.6 55.3 + - + +
244B ALA* 5.8 3.1 - - + -
245B ARG 6.0 0.4 - - - +
248B VAL 3.5 14.8 - - - +
249B LYS* 1.3 79.5 - - - +
251B VAL* 1.3 60.8 + - - +
276B GLU* 4.0 33.5 + - - +
277B ASN 3.7 5.2 + - - +
278B ILE* 3.2 22.0 - - + -
279B GLN 2.8 24.9 + - - -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.9 28.7 - - + -
148B ASP 3.0 7.1 + - - +
149B ILE* 3.2 18.1 - - + +
150B VAL 2.8 27.0 + - - +
238B PHE* 3.5 4.3 - - - -
249B LYS* 4.2 11.2 - - + -
250B LYS* 1.3 77.9 - - - +
252B MET* 1.3 65.4 + - - +
253B VAL* 4.5 1.3 - - + -
279B GLN* 3.4 20.0 - - + +
281B PHE* 4.0 19.7 - - + -
335B ILE* 3.9 24.2 - - + -
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Residues in contact with MET 252 (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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150B VAL 3.3 4.7 - - - +
152B VAL* 3.7 20.2 - - + -
230B ILE* 3.3 39.0 - - + +
233B ALA* 3.7 22.0 - - + -
234B ARG 4.1 4.9 - - - +
238B PHE* 3.9 17.3 - - + -
251B VAL* 1.3 73.9 - - - +
253B VAL* 1.3 65.0 + - - +
254B ILE* 3.4 21.0 - - + +
273B CYS* 4.2 9.4 - - - -
278B ILE* 3.7 21.9 - - + +
279B GLN 2.7 11.0 + - - +
280B ARG* 3.4 6.1 - - + -
281B PHE* 2.9 27.7 + - - +
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Residues in contact with VAL 253 (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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149B ILE* 4.2 20.4 - - + -
150B VAL 3.0 7.1 + - - -
151B ILE* 3.5 19.5 - - + +
152B VAL 2.7 31.6 + - - +
168B PHE* 5.0 1.3 - - + -
172B LEU* 5.0 10.8 - - + -
251B VAL* 4.5 7.2 - - + -
252B MET* 1.3 77.8 - - - +
254B ILE* 1.3 58.8 + - - +
255B VAL* 4.5 7.0 - - + -
281B PHE* 3.3 17.9 - - + +
283B ILE* 4.2 21.8 - - + -
331B LEU* 4.3 20.2 - - + -
335B ILE* 5.0 4.3 - - + -
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Residues in contact with ILE 254 (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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152B VAL* 3.6 19.7 - - + +
190B TYR* 4.6 2.7 - - - +
226B THR* 4.5 15.5 - - + -
230B ILE* 4.0 22.0 - - + -
252B MET* 3.4 34.1 - - + +
253B VAL* 1.3 73.2 - - - +
255B VAL* 1.3 72.4 + - - +
256B THR* 4.2 17.7 - - + -
280B ARG* 4.7 5.8 - - + -
281B PHE 2.8 21.4 + - - +
282B SER* 3.4 8.6 - - - -
283B ILE* 2.8 29.7 + - - +
303B ILE* 6.2 0.2 - - + -
306B ILE* 4.1 19.3 - - + -
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Residues in contact with VAL 255 (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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152B VAL 3.2 5.2 + - - +
153B LEU* 3.6 29.8 - - + -
154B ASP* 3.0 26.5 + - - +
159B ILE* 5.9 1.3 - - + -
165B VAL* 5.9 5.4 - - + -
168B PHE* 4.1 19.1 - - + -
190B TYR* 3.9 1.9 + - - -
253B VAL* 4.5 7.2 - - + +
254B ILE* 1.3 83.0 - - - +
256B THR* 1.3 67.2 + - - +
283B ILE* 3.8 13.0 - - + -
285B ILE* 3.6 22.7 - - + -
324B LEU* 4.0 22.4 - - + -
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Residues in contact with THR 256 (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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154B ASP* 2.9 17.6 + - - -
159B ILE* 4.7 1.8 - - - -
190B TYR* 3.2 21.2 + - - +
226B THR* 4.0 7.2 + - + +
254B ILE* 4.2 12.1 - - + -
255B VAL* 1.3 77.4 - - - +
257B ASP* 1.3 63.5 + - - +
258B GLY 3.3 17.8 + - - +
283B ILE 3.2 9.9 + - - +
284B ALA* 3.4 7.4 - - - -
285B ILE* 2.9 26.6 + - - +
299B PHE* 3.9 1.6 - - - -
303B ILE* 3.8 28.5 - - + -
306B ILE* 5.5 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
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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