Contacts of the strand formed by residues 246 - 255 (chain B) in PDB entry 4HH3
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 GLU 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A GLU* 3.5 37.5 - - + +
166B SER* 5.7 1.2 + - - -
168B SER* 5.6 1.6 + - - -
242B ARG* 3.4 2.9 - - - -
243B ALA* 2.7 40.8 + - - +
244B ALA 4.5 4.0 - - - +
245B GLY* 1.3 85.0 - - - +
247B ARG* 1.3 63.9 + - - +
248B LEU* 3.7 11.8 + - + +
318C ARG* 5.8 4.5 + - - -
321C THR* 6.2 0.5 - - - +
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Residues in contact with ARG 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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166B SER* 4.0 1.7 + - - -
167B MET* 3.1 59.4 + - + +
168B SER* 3.4 31.7 + - - +
240B VAL* 6.0 0.7 - - + -
241B PHE 3.7 4.7 - - - +
242B ARG* 4.3 19.7 - - + +
245B GLY 3.9 0.6 + - - -
246B GLU* 1.3 73.9 + - - +
248B LEU* 1.3 64.0 + - - +
321C THR* 3.1 26.1 + - - +
322C SER* 3.9 16.6 - - - +
323C ARG* 3.5 51.7 - - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 3.8 22.9 - - - +
150A ARG* 3.8 18.6 - - + +
164B LEU* 4.5 5.8 - - + -
165B VAL 3.6 14.4 - - - +
166B SER* 4.1 10.5 - - - -
167B MET* 3.7 7.0 - - - +
173B VAL* 4.3 16.4 - - + -
240B VAL* 3.4 3.8 - - - -
241B PHE* 2.9 72.2 + - + -
243B ALA* 4.1 9.6 - - + -
246B GLU* 4.2 11.7 - - + +
247B ARG* 1.3 81.8 - - - +
249B LEU* 1.3 60.5 + - - +
250B LEU 4.2 0.2 - - - -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL 3.7 0.9 - - - +
164B LEU* 3.4 6.6 - - - +
165B VAL* 2.8 54.8 + - + +
167B MET* 3.9 13.2 - - + +
195B ILE* 5.5 0.2 - - + -
207B PHE* 5.4 2.2 - - + -
208B MET* 3.9 25.1 - - + -
211B MET* 4.0 20.9 - - + -
238B PRO* 3.7 27.8 - - + -
239B ARG 3.5 15.0 - - - +
240B VAL* 3.9 13.7 - - + +
248B LEU* 1.3 73.0 - - - +
250B LEU* 1.3 61.2 + - - +
251B CYS* 3.9 21.1 - - - -
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Residues in contact with LEU 250 (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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153A VAL* 3.8 26.0 - - + +
154A VAL* 4.6 7.4 - - + -
157A VAL* 4.3 13.2 - - + -
155B LEU* 6.1 0.4 - - + -
162B MET* 4.0 45.5 - - + -
163B VAL 3.5 11.0 - - - +
164B LEU* 3.7 27.8 - - + +
237B VAL 3.6 1.9 - - - +
238B PRO* 3.5 2.3 - - - +
239B ARG* 2.8 48.7 + - + +
241B PHE* 4.0 11.0 - - + -
248B LEU 4.2 0.8 - - - -
249B LEU* 1.3 73.3 - - - +
251B CYS* 1.3 65.5 + - - +
252B GLN* 4.1 0.8 + - + +
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Residues in contact with CYS 251 (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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162B MET* 3.3 7.1 - - - +
163B VAL* 2.7 47.5 + - + +
165B VAL* 4.6 9.9 - - - -
195B ILE* 5.3 7.9 - - - -
199B PHE* 6.4 0.9 - - - -
207B PHE* 5.8 0.9 - - - -
211B MET* 4.3 7.4 - - - -
236B VAL* 3.7 27.4 - - + -
237B VAL 3.5 4.0 - - - -
238B PRO* 5.0 0.9 - - - -
249B LEU* 3.9 26.9 - - - -
250B LEU* 1.3 79.1 - - - +
252B GLN* 1.3 58.8 + - - +
253B ILE* 4.0 8.8 + - + +
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Residues in contact with GLN 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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157A VAL* 3.4 22.4 + - + +
159A ARG* 3.3 23.3 - - - +
160B ASP* 2.7 40.5 + - - +
161B PRO 3.5 3.8 - - - +
162B MET* 4.2 9.8 - - + +
235B LEU 3.6 1.2 - - - +
236B VAL* 3.5 4.3 - - - -
237B VAL* 2.9 47.5 + - + +
239B ARG* 2.6 36.4 + - - +
250B LEU* 4.1 2.5 + - + +
251B CYS* 1.3 73.6 - - - +
253B ILE* 1.3 58.8 + - - +
254B ASP* 5.6 0.9 - - - +
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Residues in contact with ILE 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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159A ARG* 4.0 0.3 + - - -
161B PRO* 3.0 36.9 + - + +
163B VAL* 3.7 29.4 - - + -
179B ALA* 4.6 5.4 - - + -
182B LEU* 4.0 14.8 - - + -
183B LEU* 4.4 20.9 - - + -
199B PHE* 5.2 3.6 - - + -
234B LEU* 3.7 30.7 - - + -
235B LEU 3.4 8.3 - - - +
236B VAL* 4.4 14.8 - - + -
251B CYS* 4.0 13.2 - - + +
252B GLN* 1.3 78.8 - - - +
254B ASP* 1.3 75.3 + - - +
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Residues in contact with ASP 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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159A ARG* 2.9 43.2 + - - -
161B PRO* 4.7 3.1 - - - +
182B LEU* 4.3 4.7 - - - -
234B LEU* 3.3 5.5 - - - +
235B LEU* 2.7 49.0 + - + +
237B VAL* 5.7 4.9 - - - +
252B GLN* 5.6 1.0 - - - +
253B ILE* 1.3 78.0 - - - +
255B PRO* 1.3 76.4 - - + +
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Residues in contact with PRO 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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161B PRO* 6.0 0.4 - - + -
182B LEU* 4.1 25.7 - - + -
232B LYS* 6.1 1.8 - - + -
233B ARG 4.0 5.8 - - - +
234B LEU* 4.0 6.7 - - + -
235B LEU* 4.3 4.9 - - - +
254B ASP* 1.3 96.5 - - + +
256B ALA* 1.3 61.6 + - - +
257B ASP 5.2 2.2 - - - +
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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