Contacts of the helix formed by residues 254 - 263 (chain B) in PDB entry 6O81
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 PRO 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B ASP* 4.5 0.3 - - - +
144B VAL* 3.9 22.7 - - + +
145B ARG 3.5 22.7 - - - +
146B SER* 3.9 3.1 - - - +
147B ASP* 3.5 21.8 - - - +
148B PHE* 3.7 13.5 - - + -
172B ARG* 5.7 3.8 - - - +
253B SER* 1.3 84.6 - - - +
255B GLN* 1.3 65.2 + - + +
256B VAL 3.2 0.9 - - - -
257B ALA* 3.3 19.5 + - + +
258B GLN* 3.7 13.6 + - - +
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Residues in contact with GLN 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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172B ARG* 3.2 35.8 - - - +
177B ASN* 3.6 23.6 + - - +
180B VAL* 3.8 18.5 - - + +
253B SER* 3.1 6.1 - - - -
254B PRO* 1.3 77.8 - - + +
256B VAL* 1.3 59.6 + - - +
257B ALA 3.2 0.2 - - - -
258B GLN* 3.2 14.9 + - + +
259B LEU* 2.9 33.4 + - + +
285B ASN* 4.2 13.9 + - - +
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.5 12.6 - - + -
148B PHE* 4.1 9.2 - - + -
180B VAL* 3.7 22.4 - - + +
181B MET* 3.8 26.7 - - + -
252B CYS* 3.6 22.9 - - + -
253B SER 3.3 16.6 - - - +
255B GLN* 1.3 75.7 - - - +
257B ALA* 1.3 61.7 + - - +
259B LEU* 3.4 7.5 + - - +
260B PHE* 2.9 39.0 + - + -
272B PHE* 4.0 18.6 - - + -
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Residues in contact with ALA 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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135B LEU* 3.5 32.4 - - + +
138B VAL* 4.9 8.5 - - + -
139B ASP* 3.7 19.1 - - + +
144B VAL* 5.9 1.6 - - + -
148B PHE* 5.4 2.5 - - + -
254B PRO* 3.3 13.9 + - + +
255B GLN 3.2 0.4 - - - -
256B VAL* 1.3 80.8 - - + +
258B GLN* 1.3 59.0 + - - +
260B PHE* 3.3 6.1 + - - +
261B THR* 2.9 33.4 + - - +
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Residues in contact with GLN 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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139B ASP* 2.8 23.8 + - - +
254B PRO* 3.7 17.3 + - - +
255B GLN* 3.2 16.5 + - + +
257B ALA* 1.3 78.1 - - - +
259B LEU* 1.3 57.6 + - + +
261B THR* 2.6 22.8 + - - -
262B ASP* 2.9 23.4 + - - +
75S ARG* 2.7 42.8 + - + +
352S ARG* 3.5 18.2 + - - +
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Residues in contact with LEU 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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180B VAL* 5.2 4.7 - - + -
255B GLN* 2.9 23.2 + - + +
256B VAL* 3.4 7.2 + - - +
258B GLN* 1.3 76.9 - - + +
260B PHE* 1.3 58.5 + - - +
262B ASP* 3.9 15.3 - - + +
263B ASN* 3.0 39.8 + - - +
266B TYR* 4.5 3.2 - - + -
272B PHE* 4.1 27.1 - - + -
276B LEU* 4.4 12.1 - - + -
283B LEU* 4.0 31.2 - - + -
285B ASN* 3.7 26.7 - - + +
75S ARG 5.5 1.3 - - - +
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Residues in contact with PHE 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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131B LEU* 4.6 4.5 - - + -
132B GLY* 3.6 32.1 - - - +
135B LEU* 3.6 30.7 - - + -
136B ARG* 2.5 36.4 + - - +
181B MET* 6.1 0.7 - - + -
256B VAL* 2.9 26.7 + - + +
257B ALA* 3.7 7.0 - - - +
258B GLN 3.2 0.2 - - - -
259B LEU* 1.3 76.8 - - - +
261B THR* 1.3 60.5 + - - +
263B ASN 3.0 9.7 - - - +
266B TYR* 3.3 39.7 - + + -
268B THR 3.4 25.6 - - - -
269B ARG* 5.0 0.7 - - - -
272B PHE* 3.6 31.2 - + + -
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Residues in contact with THR 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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136B ARG* 3.8 24.9 - - + +
139B ASP* 3.5 26.0 - - + +
257B ALA 2.9 16.5 + - - +
258B GLN* 2.6 22.5 + - - -
260B PHE* 1.3 75.9 - - - +
262B ASP* 1.3 63.0 + - - +
264B PHE* 3.2 27.7 - - - -
75S ARG* 2.7 25.6 + - - +
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Residues in contact with ASP 262 (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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258B GLN* 2.9 18.6 + - - +
259B LEU* 3.9 16.1 - - + +
260B PHE 3.3 0.2 - - - -
261B THR* 1.3 79.6 - - - +
263B ASN* 1.3 71.1 + - - +
264B PHE* 3.4 14.4 + - - -
283B LEU* 5.8 2.3 - - + +
75S ARG* 2.9 58.1 + - - +
76S ASN* 5.1 8.2 - - + +
405S MET* 4.6 6.2 - - - +
451S TRP* 5.5 1.0 + - - -
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Residues in contact with ASN 263 (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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136B ARG* 3.5 2.9 + - - -
259B LEU* 3.0 23.0 + - - +
260B PHE* 3.0 19.3 - - - +
262B ASP* 1.3 81.7 + - - +
264B PHE* 1.3 62.7 + - - +
265B ASP* 3.4 15.7 + - - +
266B TYR* 3.3 40.9 + - + +
283B LEU* 4.9 17.5 - - - +
446S ARG* 3.2 24.1 - - - +
451S TRP* 4.5 5.4 - - - +
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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