Contacts of the helix formed by residues 181 - 197 (chain A) in PDB entry 2BWJ
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 THR 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A GLY* 1.3 75.8 - - - +
182A PRO* 1.3 71.3 - - - +
183A GLU* 3.5 21.2 + - + +
184A ASP* 2.9 27.2 + - + +
185A VAL* 3.0 18.2 + - - +
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Residues in contact with PRO 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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26A THR* 5.6 4.0 - - - +
27A GLN* 2.8 33.2 + - - +
30A LYS* 3.6 9.7 + - - +
180A GLY 3.7 1.7 - - - +
181A THR* 1.3 83.2 - - + +
183A GLU* 1.3 75.1 + - - +
185A VAL* 3.4 3.5 + - + -
186A PHE* 2.9 17.3 + - - +
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Residues in contact with GLU 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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30A LYS* 4.7 4.8 + - - +
181A THR* 3.5 18.2 - - + +
182A PRO* 1.3 103.8 - - - +
184A ASP* 1.3 56.4 + - - +
186A PHE* 3.4 8.3 + - - +
187A LEU* 3.1 25.9 + - - +
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Residues in contact with ASP 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* 4.7 7.7 - - - -
181A THR* 2.9 26.1 + - + +
183A GLU* 1.3 74.8 - - - +
185A VAL* 1.3 65.1 + - - +
187A LEU* 3.3 19.4 + - - +
188A GLN* 2.7 52.6 + - - +
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Residues in contact with VAL 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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22A SER 5.6 0.9 - - - +
27A GLN* 3.8 26.0 - - + +
121A MET* 3.9 17.7 - - + -
176A ILE* 4.0 12.7 - - + +
177A ASN 3.6 19.7 - - - +
178A ALA* 3.7 13.5 - - + +
180A GLY 4.0 11.7 - - - +
181A THR 3.0 20.6 + - - +
182A PRO* 3.6 6.1 - - + +
184A ASP* 1.3 75.8 - - - +
186A PHE* 1.3 63.0 + - - +
188A GLN* 3.3 10.4 + - - +
189A LEU* 3.0 25.5 + - + +
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Residues in contact with PHE 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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27A GLN* 3.3 22.8 + - - +
30A LYS* 3.4 51.8 - - + +
31A LEU* 3.6 28.0 - - + -
34A LYS* 3.9 19.1 - - + -
182A PRO 2.9 15.1 + - - +
183A GLU* 3.6 7.2 - - - +
184A ASP 3.3 0.2 - - - -
185A VAL* 1.3 76.8 - - - +
187A LEU* 1.3 63.5 + - - +
189A LEU* 3.3 4.1 + - + +
190A CYS* 3.0 47.3 + - - -
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Residues in contact with LEU 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 GLU 3.1 13.9 + - - +
184A ASP* 3.5 24.0 - - - +
185A VAL 3.3 0.2 - - - -
186A PHE* 1.3 78.9 - - - +
188A GLN* 1.3 65.9 + - + +
190A CYS* 3.4 5.9 + - - +
191A THR* 2.9 40.9 + - - +
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Residues in contact with GLN 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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175A LYS 5.1 0.5 - - - +
176A ILE* 3.9 19.1 - - + +
177A ASN* 3.1 49.2 + - - +
184A ASP* 2.7 42.7 + - - +
185A VAL* 3.6 9.8 - - - +
187A LEU* 1.3 82.1 - - + +
189A LEU* 1.3 65.7 + - - +
191A THR* 3.5 7.0 + - - -
192A ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 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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16A ILE* 4.1 8.1 - - + -
27A GLN* 3.6 46.0 - - + +
31A LEU* 4.3 22.4 - - + -
119A ILE* 3.4 42.6 - - + -
121A MET* 4.6 7.4 - - + -
176A ILE* 4.1 9.2 - - + -
185A VAL* 3.0 22.5 + - + +
186A PHE* 3.5 6.1 - - - +
188A GLN* 1.3 77.0 - - - +
190A CYS* 1.3 57.7 + - - +
192A ALA* 3.2 6.1 + - - +
193A ILE* 3.0 34.4 + - + +
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Residues in contact with CYS 190 (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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31A LEU* 4.3 1.1 - - - -
34A LYS* 3.3 30.3 - - - -
35A TYR* 3.3 20.9 - - - +
186A PHE* 3.0 46.9 + - - +
187A LEU* 3.7 6.1 - - - +
189A LEU* 1.3 72.9 - - - +
191A THR* 1.3 61.5 + - - +
194A ASP* 2.9 42.1 + - - +
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Residues in contact with THR 191 (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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187A LEU* 2.9 28.5 + - - +
188A GLN* 3.6 9.0 - - - -
190A CYS* 1.3 77.1 - - - +
192A ALA* 1.3 61.8 + - - +
194A ASP* 3.9 4.5 - - - +
195A SER* 3.0 26.2 + - - -
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Residues in contact with ALA 192 (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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117A LEU* 4.2 9.9 - - + -
119A ILE* 5.0 2.7 - - + -
174A HIS* 3.6 33.3 + - + -
176A ILE* 4.2 9.6 - - + -
188A GLN 3.0 14.7 + - - +
189A LEU* 3.4 9.6 - - - +
191A THR* 1.3 75.1 - - - +
193A ILE* 1.3 61.0 + - + +
195A SER* 2.6 25.3 + - - -
196A ILE* 3.3 11.6 + - - +
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Residues in contact with ILE 193 (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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14A ILE* 4.2 7.4 - - + -
31A LEU* 3.6 39.5 - - + -
35A TYR* 3.8 27.6 - - + +
37A PHE* 4.2 20.4 - - + -
117A LEU* 3.8 21.3 - - + -
119A ILE* 4.1 11.9 - - + -
189A LEU 3.0 19.2 + - - +
190A CYS 4.0 2.9 - - - +
192A ALA* 1.3 74.5 - - - +
194A ASP* 1.3 60.8 + - - +
196A ILE 3.2 1.7 + - - -
197A PHE* 3.0 45.3 + - + +
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Residues in contact with ASP 194 (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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34A LYS* 4.8 6.2 + - - -
35A TYR* 2.6 33.0 + - - -
190A CYS* 2.9 28.0 + - - +
191A THR* 3.9 5.2 - - - +
193A ILE* 1.3 73.5 - - - +
195A SER* 1.3 59.8 + - - +
196A ILE 3.4 0.3 + - - -
197A PHE* 3.8 9.5 + - - +
198A LEU* 3.0 19.9 - - - +
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Residues in contact with SER 195 (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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174A HIS* 3.6 17.0 + - - -
191A THR* 3.0 17.6 + - - -
192A ALA* 2.6 22.0 + - - -
194A ASP* 1.3 77.4 - - - +
196A ILE* 1.3 64.5 + - - +
198A LEU* 3.8 13.2 - - - +
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Residues in contact with ILE 196 (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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116A GLN* 3.9 19.3 - - + +
117A LEU* 3.8 20.0 - - + -
172A GLN* 3.7 36.8 - - + +
174A HIS* 4.2 7.6 - - + +
192A ALA 3.5 12.6 - - - +
193A ILE 3.2 7.0 + - - +
194A ASP 3.2 0.2 - - - -
195A SER* 1.3 85.4 - - - +
197A PHE* 1.3 88.7 + - + +
198A LEU* 2.9 12.4 + - - -
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Residues in contact with PHE 197 (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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12A LYS* 3.5 53.4 - - + -
14A ILE* 3.7 32.3 - - + -
37A PHE* 5.1 1.6 - + + -
116A GLN* 3.8 33.2 - - + -
117A LEU* 4.7 3.6 - - + -
193A ILE* 3.0 36.4 + - + +
194A ASP* 4.0 6.5 - - - +
195A SER 3.7 0.2 - - - -
196A ILE* 1.3 96.0 - - + +
198A LEU* 1.3 72.4 - - - +
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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