Contacts of the helix formed by residues 169 - 180 (chain B) in PDB entry 2CT8
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 TYR 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B ASP* 2.8 40.1 + - - -
164B PHE* 3.9 20.6 - + - -
165B ARG 3.2 24.9 - - - -
166B LEU 2.7 17.8 + - - +
168B LYS* 1.3 78.1 - - + +
170B GLN* 1.3 62.6 + - - +
171B ASP 3.3 2.5 - - - -
172B LYS* 3.8 34.8 + - + -
173B LEU* 3.1 30.4 + - + +
270B ALA* 4.2 11.4 - - + -
273B MET* 3.6 44.2 - - + -
274B SER* 3.1 18.1 - - - -
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Residues in contact with GLN 170 (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 LEU 3.9 1.4 + - - -
167B SER 3.6 12.7 + - - +
168B LYS 3.5 2.4 - - - -
169B TYR* 1.3 78.7 - - - +
171B ASP* 1.3 66.7 + - - +
173B LEU* 3.6 2.6 - - - +
174B LEU* 3.1 35.3 + - + +
197B VAL* 3.4 33.3 + - + +
198B LYS* 4.6 2.6 - - - +
199B GLN* 4.5 6.3 - - - +
200B GLY 2.4 33.0 + - - +
201B LEU* 3.8 10.3 - - + +
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Residues in contact with ASP 171 (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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168B LYS 5.0 2.8 + - - +
169B TYR* 3.3 0.6 - - - +
170B GLN* 1.3 78.9 + - - +
172B LYS* 1.3 69.4 + - + +
173B LEU 3.0 1.6 - - - -
174B LEU* 2.9 24.5 + - - +
175B GLU* 2.9 13.8 + - - +
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Residues in contact with LYS 172 (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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168B LYS* 4.7 10.7 + - - +
169B TYR* 3.8 42.0 + - + +
171B ASP* 1.3 80.1 - - + +
173B LEU* 1.3 60.9 + - - +
175B GLU* 3.4 9.6 + - - +
176B LEU* 3.1 22.0 + - - +
273B MET* 3.8 24.5 - - + +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.6 4.7 - - + -
169B TYR* 3.1 25.8 + - + +
170B GLN* 3.6 4.7 - - - +
171B ASP 3.0 0.6 - - - -
172B LYS* 1.3 74.7 - - - +
174B LEU* 1.3 67.5 + - - +
176B LEU* 3.0 20.5 + - + +
177B TYR* 3.1 42.6 + - + +
197B VAL* 4.3 6.5 - - + -
201B LEU* 4.0 15.7 - - + -
265B THR 4.0 1.6 - - - +
266B VAL* 3.9 34.3 - - + +
269B PRO* 3.9 28.3 - - + -
270B ALA* 5.1 0.2 - - + -
273B MET* 3.9 13.0 - - + -
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Residues in contact with LEU 174 (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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170B GLN* 3.1 26.9 + - + +
171B ASP* 2.9 14.8 + - - +
173B LEU* 1.3 78.2 - - - +
175B GLU* 1.3 64.9 + - - +
177B TYR* 3.4 16.0 + - + +
178B GLU* 3.3 19.1 + - - +
194B ILE* 3.9 7.4 - - + +
197B VAL* 3.3 28.5 - - + -
198B LYS* 3.5 40.8 - - + -
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Residues in contact with GLU 175 (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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171B ASP 2.9 10.8 + - - +
172B LYS* 3.5 13.5 - - - +
174B LEU* 1.3 76.1 - - - +
176B LEU* 1.3 54.0 + - - +
178B GLU* 2.8 12.4 + - - +
179B LYS* 2.8 46.6 + - + +
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Residues in contact with LEU 176 (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 LYS 3.1 10.3 + - - +
173B LEU* 3.0 18.1 + - + +
175B GLU* 1.3 80.5 - - - +
177B TYR* 1.3 64.4 + - + +
179B LYS* 4.6 5.6 - - + +
180B ASN* 2.7 61.2 + - + +
183B PHE* 4.0 37.7 - - + -
269B PRO* 4.1 14.4 - - + -
273B MET* 5.3 3.8 - - - -
279B LEU* 4.1 29.4 - - + -
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Residues in contact with TYR 177 (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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173B LEU* 3.1 34.9 + - + +
174B LEU* 3.7 15.7 - - + +
176B LEU* 1.3 84.7 - - + +
178B GLU* 1.3 62.0 + - - +
180B ASN 3.2 4.6 - - - -
181B PRO* 3.2 27.5 - - - +
183B PHE* 4.2 5.6 - + - -
184B ILE* 3.4 31.4 - - + -
190B ARG* 5.0 7.4 + - - +
193B ILE* 3.7 14.5 - - + +
194B ILE* 3.9 35.9 - - + -
197B VAL* 3.8 29.3 - - + +
265B THR 2.8 26.7 + - - -
266B VAL* 3.9 1.2 - - - +
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Residues in contact with GLU 178 (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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174B LEU 3.3 9.8 + - - +
175B GLU* 2.8 12.3 + - - +
177B TYR* 1.3 79.0 - - - +
179B LYS* 1.3 65.1 + - - +
181B PRO* 3.8 11.8 - - - +
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Residues in contact with LYS 179 (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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175B GLU* 2.8 32.0 + - + +
176B LEU* 4.2 8.3 - - + +
178B GLU* 1.3 73.8 - - - +
180B ASN* 1.3 91.0 + - - +
181B PRO* 3.3 8.8 - - - +
279B LEU* 5.8 4.9 - - - +
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 2.7 38.2 + - + +
177B TYR* 3.2 8.9 - - - +
179B LYS* 1.3 121.2 - - - +
181B PRO* 1.3 60.0 - - - +
182B GLU* 3.0 10.6 + - - +
183B PHE* 3.1 23.0 + - + +
184B ILE* 5.4 0.3 - - - +
281B LYS* 6.0 3.8 - - - +
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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