Contacts of the helix formed by residues 186 - 191 (chain B) in PDB entry 6APL
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 PHE 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B ASN* 4.2 9.0 - - - -
182B VAL* 4.1 13.2 - - + +
183B ILE 3.1 7.3 + - - +
184B LYS 3.6 13.7 - - - -
185B GLY* 1.3 86.0 - - - +
187B GLU* 1.3 61.8 + - - +
188B ARG* 3.2 5.4 - - - +
189B ASP* 3.0 22.4 + - + +
190B VAL* 2.9 30.9 + - + +
214B LEU 4.4 7.2 - - - -
337B TYR* 3.3 44.9 - + + -
338B PHE* 3.4 37.5 - - + -
339B GLU 5.5 0.4 - - - -
340B ARG* 5.6 9.4 - - - -
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY* 3.9 2.6 - - - -
183B ILE* 3.2 18.4 + - + +
184B LYS* 3.3 14.9 + - - +
185B GLY* 3.2 20.5 + - - -
186B PHE* 1.3 84.3 + - - +
188B ARG* 1.3 60.5 + - - +
191B GLY* 2.7 37.3 + - - -
192B THR* 3.6 27.9 - - + +
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Residues in contact with ARG 188 (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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164B ARG* 3.2 65.5 - - + +
166B GLY* 3.1 20.1 + - - -
167B PRO* 4.2 3.2 - - - +
185B GLY 5.0 8.8 + - - +
186B PHE* 4.7 5.2 - - - -
187B GLU* 1.3 80.8 + - - +
189B ASP* 1.3 65.0 + - - +
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Residues in contact with ASP 189 (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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160B LEU* 3.3 21.2 - - - +
161B ASN* 4.0 9.0 - - - +
162B GLY 3.1 13.7 + - - -
163B SER* 3.2 9.7 + - - -
164B ARG* 2.8 55.5 + - - +
165B GLN* 3.4 12.8 + - - +
166B GLY 3.4 12.3 + - - -
169B ILE* 3.9 1.6 - - - +
186B PHE* 3.0 21.0 + - + +
188B ARG* 1.3 85.3 + - - +
190B VAL* 1.3 67.3 + - + +
191B GLY 3.7 0.4 - - - -
337B TYR* 5.6 0.4 - - + -
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Residues in contact with VAL 190 (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 VAL* 4.4 5.2 - - + -
160B LEU* 3.9 21.5 - - + -
166B GLY* 4.3 0.4 - - - -
169B ILE* 3.5 22.3 - - - +
177B ARG* 2.8 35.4 + - - +
182B VAL 3.8 21.5 - - - +
183B ILE* 4.7 2.5 - - - -
186B PHE 2.9 22.4 + - - +
189B ASP* 1.3 80.2 - - + +
191B GLY* 1.3 66.4 + - - +
337B TYR* 3.6 35.2 - - + +
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Residues in contact with GLY 191 (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 GLY* 3.7 11.3 - - - -
169B ILE* 4.8 0.2 - - - -
170B ASP* 3.6 18.4 - - - -
177B ARG* 3.3 7.4 + - - -
183B ILE* 3.8 9.9 - - - +
187B GLU* 2.7 30.6 + - - -
190B VAL* 1.3 78.1 - - - +
192B THR* 1.3 68.9 + - - +
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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