Contacts of the helix formed by residues 178 - 189 (chain A) in PDB entry 2BKA
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 ARG 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ASP* 2.9 39.5 + - - +
174A ARG* 3.3 16.3 + - + +
175A GLN* 3.3 28.3 + - - +
177A SER* 1.3 84.1 - - - +
179A PRO* 1.3 78.7 - - + +
180A GLY 3.0 5.4 + - - +
181A GLU* 3.0 16.6 + - - +
182A TRP* 3.9 2.1 + - - +
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Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER 4.9 0.2 - - - +
178A ARG* 1.3 90.0 - - + +
180A GLY* 1.3 60.7 + - - +
182A TRP* 3.1 27.9 + - + +
183A LEU* 3.1 22.5 + - + +
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLN 4.9 1.3 - - - -
178A ARG* 3.0 5.1 + - - +
179A PRO* 1.3 78.1 - - - +
181A GLU* 1.3 56.3 + - - +
183A LEU* 3.3 13.5 + - - +
184A VAL* 2.9 37.9 + - - +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLN 3.5 18.1 + - - +
176A GLU* 3.3 23.6 - - - +
177A SER* 5.0 0.6 - - - -
178A ARG 3.0 13.7 + - - +
180A GLY* 1.3 75.6 - - - +
182A TRP* 1.3 60.8 + - - +
184A VAL* 4.1 4.4 - - - +
185A ARG* 2.8 69.1 + - - +
193A ASP 4.6 8.7 - - - +
195A TRP* 4.4 1.8 - - + -
196A ALA* 4.1 26.7 - - + +
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Residues in contact with TRP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ARG 3.9 1.3 + - - +
179A PRO* 3.1 21.6 + - + +
181A GLU* 1.3 89.4 + - - +
183A LEU* 1.3 56.9 + - + +
185A ARG* 3.8 25.9 - - - +
186A LYS* 2.9 44.4 + - + +
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A PRO* 3.1 23.1 + - + +
180A GLY* 3.3 14.3 + - - +
182A TRP* 1.3 78.6 - - + +
184A VAL* 1.3 64.0 + - + +
186A LYS* 3.9 1.1 - - - +
187A PHE 3.1 17.5 + - - -
901A PE8 3.4 47.2 - - - +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLY* 2.9 22.3 + - - +
181A GLU* 4.1 4.5 - - - +
183A LEU* 1.3 76.9 - - + +
185A ARG* 1.3 64.0 + - - +
187A PHE* 3.2 7.3 + - - +
188A PHE* 3.1 44.2 + - + -
195A TRP* 3.8 16.4 - - + -
901A PE8 3.9 39.9 - - - +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLU* 2.8 53.8 + - - +
182A TRP* 3.8 29.4 - - - +
184A VAL* 1.3 77.3 - - - +
186A LYS* 1.3 68.0 + - - +
188A PHE* 3.1 12.1 + - - +
189A GLY 3.1 14.8 + - - +
191A LEU* 3.5 37.1 + - + +
192A PRO 3.4 24.0 + - - -
193A ASP* 3.6 24.5 + - - +
195A TRP* 3.8 24.4 - - + -
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TRP* 2.9 34.7 + - + +
183A LEU* 3.9 1.6 - - - +
185A ARG* 1.3 81.5 - - - +
187A PHE* 1.3 63.7 + - - +
189A GLY* 3.1 25.2 + - - +
190A SER* 5.3 9.7 + - - +
901A PE8 3.8 22.9 - - - +
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU 3.1 14.5 + - - +
184A VAL 3.4 9.0 - - - +
186A LYS* 1.3 78.4 - - - +
188A PHE* 1.3 85.5 + + - +
189A GLY 3.5 0.3 + - - -
901A PE8 3.6 60.5 - - - +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.1 37.6 + - + -
185A ARG 3.1 7.8 + - - +
186A LYS 3.1 0.8 - - - -
187A PHE* 1.3 101.7 - + - +
189A GLY* 1.3 54.6 + - - +
191A LEU* 3.7 21.0 - - + +
195A TRP* 3.6 23.3 - + + +
901A PE8 4.7 10.5 - - - -
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Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ARG* 3.1 14.7 + - - +
186A LYS* 3.1 25.6 + - - +
187A PHE 3.3 1.2 + - - -
188A PHE* 1.3 80.6 - - - +
190A SER* 1.3 61.4 + - - -
191A LEU* 3.3 8.6 + - - -
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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