Contacts of the helix formed by residues 186 - 195 (chain B) in PDB entry 4BPK
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 GLY 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B ILE 3.4 0.2 + - - -
183B GLN 4.0 4.6 + - - -
184B GLU 3.6 3.0 + - - -
185B ASN* 1.3 77.0 - - - +
187B GLY* 1.3 60.6 + - - +
189B ASP* 2.9 4.2 - - - +
190B THR* 2.5 26.7 + - - -
1196B CD 2.6 24.6 - - - -
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Residues in contact with GLY 187 (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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137B TRP* 3.5 6.4 - - - -
182B ILE* 2.7 30.6 + - - -
183B GLN* 4.0 15.4 + - - +
185B ASN 3.4 0.6 - - - -
186B GLY* 1.3 82.3 - - - +
188B TRP* 1.3 65.3 + - - -
189B ASP* 3.1 6.3 - - - -
190B THR* 3.1 9.9 + - - -
191B PHE 3.5 3.5 + - - -
1196B CD 4.2 0.9 - - - -
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Residues in contact with TRP 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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5A ASN* 4.2 15.2 + - - -
8A LEU* 3.5 25.7 - - + +
26B GLN* 4.3 2.7 - - - +
86B VAL* 3.8 30.1 - - + -
90B LEU* 4.3 10.1 - - + -
137B TRP* 3.9 15.0 - + - -
140B ILE* 3.7 23.6 - - + -
144B PHE* 3.8 17.5 - + - -
174B LEU* 4.3 5.4 - - + -
179B GLU* 5.0 4.0 + - - -
182B ILE* 3.8 35.0 - - + +
183B GLN* 4.9 2.2 + - - -
187B GLY* 1.3 71.5 - - - -
189B ASP* 1.3 58.3 + - - +
191B PHE* 3.0 43.2 + + - +
192B VAL* 2.9 31.1 + - - +
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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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26B GLN* 3.5 27.4 + - + +
186B GLY 2.9 9.2 - - - +
187B GLY* 3.9 4.9 - - - -
188B TRP* 1.3 78.7 + - - +
190B THR* 1.3 65.6 + - - +
192B VAL* 3.3 9.7 + - - +
193B GLU* 3.0 24.4 + - - +
1196B CD 2.4 31.9 - - - -
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Residues in contact with THR 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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137B TRP* 4.9 2.0 - - - +
185B ASN 3.9 12.8 - - - +
186B GLY* 2.5 34.1 + - - -
187B GLY 3.1 5.8 + - - -
189B ASP* 1.3 81.3 + - - +
191B PHE* 1.3 59.7 + - - +
193B GLU* 3.0 29.0 + - - +
194B LEU* 2.8 40.9 + - + +
1196B CD 4.2 0.2 - - - -
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Residues in contact with PHE 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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86B VAL* 4.9 1.3 - - + -
89B ALA* 3.9 10.5 - - + -
90B LEU* 3.9 30.3 - - + -
93B ALA* 3.7 25.1 - - + -
137B TRP* 3.7 46.7 - + + -
140B ILE* 6.2 0.2 - - + -
141B VAL* 3.9 17.7 - - + -
187B GLY 3.5 2.8 + - - -
188B TRP* 3.0 32.4 + + + +
190B THR* 1.3 77.4 - - - +
192B VAL* 1.3 64.4 + - + +
194B LEU* 3.2 4.5 + - - +
195B TYR* 2.9 33.1 + - + +
20D TYR* 3.6 28.5 - + - -
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Residues in contact with VAL 192 (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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26B GLN* 5.3 1.1 - - + +
85B ALA* 4.0 21.1 - - + +
86B VAL* 3.6 39.0 - - + +
89B ALA* 4.2 12.8 - - + -
188B TRP 2.9 18.4 + - - +
189B ASP* 3.5 9.9 - - - +
191B PHE* 1.3 80.7 - - + +
193B GLU* 1.3 62.7 + - - +
195B TYR* 3.6 14.0 + - - +
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Residues in contact with GLU 193 (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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189B ASP 3.0 12.3 + - - +
190B THR* 3.0 35.7 + - - +
192B VAL* 1.3 79.5 - - - +
194B LEU* 1.3 72.8 + - - +
195B TYR 4.3 3.1 - - - -
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Residues in contact with LEU 194 (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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137B TRP* 3.4 37.2 - - + +
190B THR* 2.8 30.4 + - + +
191B PHE* 3.8 4.3 - - - +
193B GLU* 1.3 84.0 - - + +
195B TYR* 1.3 65.7 + - - +
19D GLN 4.4 11.7 - - - +
20D TYR* 4.0 40.6 - - + +
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Residues in contact with TYR 195 (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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89B ALA* 4.2 24.7 - - + -
92B GLU* 3.0 49.1 + - + +
93B ALA* 3.9 16.2 - - + -
96B GLU* 3.4 29.2 - - - +
191B PHE* 2.9 21.0 + - + +
192B VAL 4.1 10.8 - - - +
193B GLU 3.4 3.7 - - - -
194B LEU* 1.3 82.8 - - - +
19D GLN* 5.1 2.0 - - - -
20D TYR* 4.0 22.3 - + + -
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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