Contacts of the helix formed by residues 251 - 261 (chain B) in PDB entry 6B0Z
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 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B SER* 3.7 27.1 - - - +
211B THR 3.1 14.0 + - - +
212B LYS* 3.6 40.6 - - + -
249B ARG 3.6 0.6 + - - -
250B LEU* 1.3 72.7 - - + +
252B ASP* 1.3 78.1 + - - +
255B VAL* 3.0 31.2 + - + +
267B TRP* 3.8 20.4 - - + -
269B CYS* 5.9 1.1 - - + -
271B ASN* 5.5 9.0 - - + +
277B GLN* 5.9 5.2 - - - +
277D GLN* 4.5 17.5 - - - +
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Residues in contact with ASP 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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214B THR* 5.8 0.2 + - - -
250B LEU* 3.1 12.9 - - + +
251B ILE* 1.3 89.1 + - - +
253B ASP* 1.3 67.9 + - - +
255B VAL* 3.5 9.2 + - - +
256B ALA* 3.5 10.0 + - - +
277D GLN* 2.6 30.8 - - - +
280D SER* 3.7 20.8 + - - +
283D GLN* 5.4 1.7 - - - +
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Residues in contact with ASP 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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249B ARG* 4.9 12.0 - - - -
250B LEU* 3.0 32.2 + - + +
252B ASP* 1.3 80.5 - - - +
254B MET* 1.3 58.0 + - - +
256B ALA* 3.1 8.5 + - - +
257B GLN* 2.8 30.4 + - + +
283D GLN* 5.5 7.0 + - - +
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Residues in contact with MET 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B TYR* 3.8 34.3 - - + -
210B SER* 4.0 10.8 - - - -
249B ARG* 3.9 22.9 - - + +
250B LEU 2.8 15.9 + - - +
251B ILE 3.8 3.8 - - - +
252B ASP 3.3 0.2 - - - -
253B ASP* 1.3 74.5 - - - +
255B VAL* 1.3 60.1 - - - +
257B GLN* 3.9 16.2 - - - +
258B ALA* 2.8 32.5 + - + +
265B PHE* 3.6 33.7 - - + -
267B TRP* 3.4 38.6 - - + +
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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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251B ILE* 3.0 36.1 + - + +
252B ASP 3.7 5.6 - - - +
253B ASP 3.3 0.2 - - - -
254B MET* 1.3 77.0 - - - +
256B ALA* 1.3 62.0 + - - +
258B ALA* 3.9 0.2 - - - +
259B MET* 3.2 25.7 + - - +
267B TRP* 4.6 6.3 - - + -
502B C81 3.4 27.5 - - + +
277D GLN* 4.7 7.6 - - - +
280D SER* 3.9 27.8 - - - +
281D VAL* 3.9 17.7 - - + +
504D C81 4.5 12.8 - - + -
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Residues in contact with ALA 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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252B ASP 3.5 7.4 + - - +
253B ASP* 3.1 10.1 + - - +
255B VAL* 1.3 78.6 - - - +
257B GLN* 1.3 64.3 + - - +
259B MET* 3.3 2.8 + - - +
260B LYS* 3.1 31.9 + - + +
280D SER 4.1 4.7 - - - +
283D GLN* 4.0 32.3 - - + +
284D GLY* 3.9 20.8 - - - +
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Residues in contact with GLN 257 (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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208B TYR* 3.2 49.1 + - - -
249B ARG* 2.8 33.2 + - - -
253B ASP* 2.8 19.9 + - + +
254B MET* 3.8 14.3 - - - +
256B ALA* 1.3 74.7 - - - +
258B ALA* 1.3 63.7 + - - +
260B LYS* 3.1 8.8 + - - +
261B SER* 3.0 24.0 + - - -
265B PHE* 5.7 1.4 - - + -
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Residues in contact with ALA 258 (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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124B TRP* 2.9 22.4 + - + -
254B MET* 2.8 22.6 + - + +
255B VAL 3.9 3.8 - - - +
257B GLN* 1.3 73.9 - - - +
259B MET* 1.3 61.5 + - - +
261B SER* 3.2 11.6 + - - -
265B PHE* 3.9 28.0 - - + -
267B TRP* 4.0 21.5 - - + -
502B C81 4.6 11.7 - - + -
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Residues in contact with MET 259 (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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121B VAL* 3.4 43.2 - - + +
123B GLY* 5.9 0.3 - - - -
124B TRP* 4.1 7.5 + - - +
255B VAL* 3.2 17.9 + - - +
257B GLN 3.2 0.2 - - - -
258B ALA* 1.3 75.8 - - - +
260B LYS* 1.3 60.2 + - - +
261B SER 3.4 1.3 + - - +
502B C81 3.7 25.8 - - - -
120D LEU* 4.3 6.5 - - + -
281D VAL* 3.5 54.5 - - + +
284D GLY* 3.7 20.7 - - - +
285D TYR* 3.8 21.8 - - + +
504D C81 4.5 3.8 - - - -
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Residues in contact with LYS 260 (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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256B ALA* 3.1 17.7 + - + +
257B GLN* 3.1 9.5 + - - +
259B MET* 1.3 75.3 - - - +
261B SER* 1.3 61.3 + - - +
262B GLU 4.2 0.2 + - - -
283D GLN* 3.5 31.5 + - - +
284D GLY* 3.7 14.6 - - - +
286D GLY* 5.4 2.7 - - - +
501D NDP 4.3 15.8 + - - -
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Residues in contact with SER 261 (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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123B GLY* 3.8 8.3 - - - +
124B TRP* 3.3 18.9 - - - -
257B GLN* 3.0 14.3 + - - -
258B ALA* 3.2 13.6 + - - -
259B MET 4.3 2.1 - - - +
260B LYS* 1.3 82.2 - - - +
262B GLU* 1.3 69.6 + - - +
263B GLY 2.8 15.3 + - - -
265B PHE* 3.3 25.6 - - - -
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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