Contacts of the helix formed by residues 187 - 203 (chain A) in PDB entry 1BK6
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 VAL 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A SER* 1.3 75.0 - - - +
188A GLU* 1.3 68.6 + - + +
190A LYS* 3.4 11.9 + - + +
191A GLU* 2.9 24.2 + - + +
228A LYS* 4.2 30.3 - - + +
231A LEU* 3.9 24.2 - - + +
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Residues in contact with GLU 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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145A GLU* 5.7 0.2 - - - +
146A MET* 5.5 3.1 - - - +
149A LEU* 3.5 33.8 - - + +
186A SER* 3.4 10.8 + - - +
187A VAL* 1.3 77.1 - - + +
189A VAL* 1.3 63.6 + - - +
191A GLU* 3.1 23.2 - - - +
192A GLN* 3.2 6.1 + - - +
228A LYS* 5.9 5.8 - - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 3.7 26.7 - - + +
148A GLN* 4.6 6.3 - - + +
149A LEU* 3.8 29.4 - - + +
152A ALA* 5.6 0.2 - - - +
181A LEU* 4.0 34.0 - - + +
185A GLY* 3.8 15.5 - - - -
186A SER* 3.3 23.6 + - - +
187A VAL 3.2 0.4 - - - -
188A GLU* 1.3 74.8 - - + +
190A LYS* 1.3 67.9 + - - +
192A GLN* 3.0 6.1 + - - +
193A ALA* 3.0 19.1 + - - +
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Residues in contact with LYS 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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181A LEU 3.7 14.6 - - - +
182A LEU* 3.1 28.6 + - + +
183A TYR 3.9 9.3 + - - -
185A GLY 3.2 18.6 - - - -
186A SER 3.0 21.9 + - - +
187A VAL* 3.4 11.9 + - + +
189A VAL* 1.3 75.4 - - - +
191A GLU* 1.3 64.1 + - - +
193A ALA* 3.0 7.4 + - - +
194A ILE* 2.9 28.1 + - - +
223A LEU* 3.8 27.3 - - + +
231A LEU* 4.2 11.9 - - + -
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Residues in contact with GLU 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 VAL* 2.9 15.8 + - + +
188A GLU* 3.1 17.7 - - - +
190A LYS* 1.3 76.7 - - - +
192A GLN* 1.3 61.7 + - + +
194A ILE* 3.4 5.5 - - - +
195A TRP* 3.3 33.0 + - - +
228A LYS* 5.8 3.8 - - - +
230A SER* 3.4 14.0 - - - +
231A LEU* 3.4 38.0 - - + +
234A THR* 2.9 29.4 + - - +
131C LYS* 5.2 6.2 + - - -
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Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 3.3 37.0 - - + +
152A ALA* 4.2 14.6 - - + -
153A TRP* 3.7 12.0 - - + +
156A THR* 3.4 32.4 + - - +
188A GLU 3.2 2.0 + - - +
189A VAL 3.0 8.8 + - - +
191A GLU* 1.3 83.1 - - + +
193A ALA* 1.3 58.3 + - - +
195A TRP* 3.2 12.6 + - - +
196A ALA 2.9 24.4 + - - -
131C LYS* 2.8 44.6 + - - +
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Residues in contact with ALA 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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152A ALA* 5.0 1.5 - - - +
178A PHE* 3.5 39.8 - - + +
181A LEU* 4.1 14.6 - - + -
182A LEU* 3.9 9.0 - - + -
189A VAL 3.0 11.9 + - - +
190A LYS* 3.0 7.6 + - - +
192A GLN* 1.3 74.7 - - - +
194A ILE* 1.3 60.9 + - - +
196A ALA* 3.3 3.1 + - - +
197A LEU* 3.0 34.1 + - - +
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Residues in contact with ILE 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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182A LEU* 3.9 14.5 - - + +
190A LYS 2.9 13.4 + - - +
191A GLU 3.4 14.1 - - - +
193A ALA* 1.3 76.9 - - - +
195A TRP* 1.3 61.7 + - - +
197A LEU* 3.6 5.3 + - + -
198A GLY 3.0 13.2 + - - -
220A ILE* 3.8 31.6 - - + -
223A LEU* 3.9 13.7 - - + -
231A LEU* 4.1 13.0 - - + -
234A THR* 3.5 20.9 - - + -
235A ALA* 3.8 16.4 - - - +
238A THR* 2.8 46.1 + - + +
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Residues in contact with TRP 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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156A THR* 4.6 6.5 - - - -
191A GLU* 3.3 26.0 + - - +
192A GLN* 3.2 18.8 + - - +
193A ALA 3.1 0.6 - - - -
194A ILE* 1.3 80.3 - - - +
196A ALA* 1.3 67.9 + - - +
198A GLY* 3.0 11.3 + - - -
199A ASN* 3.2 19.1 + - - +
234A THR* 3.8 24.0 - - + -
237A TRP* 3.9 8.9 - + - -
129C LYS* 3.0 41.5 + - + +
130C ARG 3.5 24.5 - - - -
131C LYS* 3.6 37.7 - - + +
132C VAL 5.1 0.7 - - - -
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Residues in contact with ALA 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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156A THR* 3.0 36.5 - - + +
159A ALA* 5.0 1.6 - - + +
178A PHE* 3.4 33.0 - - + -
192A GLN 2.9 7.7 + - - +
193A ALA 3.6 6.7 - - - +
195A TRP* 1.3 76.0 - - - +
197A LEU* 1.3 63.4 + - - +
199A ASN* 3.0 17.4 + - - +
200A VAL* 3.1 16.2 + - - +
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Residues in contact with LEU 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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175A VAL* 4.2 23.1 - - + -
178A PHE* 3.9 31.4 - - + -
179A ILE* 4.2 12.3 - - + -
182A LEU* 3.8 28.9 - - + -
193A ALA 3.0 23.0 + - - +
194A ILE* 3.7 11.0 - - + +
196A ALA* 1.3 75.3 - - - +
198A GLY* 1.3 56.8 - - - +
200A VAL* 3.9 5.0 - - + +
201A ALA* 2.9 34.3 + - - +
211A VAL* 4.3 20.4 - - + +
216A ALA* 4.9 6.3 - - + -
220A ILE* 5.2 2.0 - - + -
238A THR* 4.2 8.7 - - + -
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Residues in contact with GLY 198 (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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194A ILE 3.0 7.1 + - - -
195A TRP 3.0 10.1 + - - -
197A LEU* 1.3 77.0 - - - +
199A ASN* 1.3 55.0 + - - +
201A ALA* 3.7 1.7 + - - +
202A GLY* 3.1 21.0 + - - -
237A TRP* 3.8 13.4 - - - -
238A THR* 3.4 28.7 + - - -
241A ASN* 3.2 14.4 + - - -
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Residues in contact with ASN 199 (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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156A THR 3.3 22.8 + - - -
159A ALA* 3.3 25.4 - - + +
160A SER* 4.0 3.1 - - - -
166A THR* 4.7 0.2 - - - +
195A TRP* 3.2 21.6 + - - -
196A ALA* 3.0 8.3 + - - +
198A GLY* 1.3 74.6 - - - +
200A VAL* 1.3 66.0 + - - +
202A GLY* 3.2 2.1 + - - -
203A ASP* 3.2 17.0 + - - +
237A TRP* 3.7 3.3 - - - -
127C LYS 4.8 0.4 - - - -
128C LYS* 3.4 22.0 + - + +
129C LYS 2.8 45.4 + - - -
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Residues in contact with VAL 200 (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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159A ALA* 4.6 9.4 - - + -
166A THR* 4.2 13.5 - - + -
169A VAL* 5.4 3.6 - - + -
170A VAL* 3.9 29.2 - - + -
175A VAL* 4.3 13.9 - - + -
178A PHE* 5.1 9.0 - - + -
196A ALA 3.1 14.9 + - - +
197A LEU* 3.9 7.9 - - - +
199A ASN* 1.3 76.2 - - - +
201A ALA* 1.3 64.8 + - - +
202A GLY 3.0 1.0 + - - -
203A ASP* 3.0 12.6 + - - +
207A TYR* 3.2 34.2 - - + +
210A TYR* 5.2 2.0 - - + -
211A VAL* 3.9 17.5 - - + -
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Residues in contact with ALA 201 (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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197A LEU 2.9 17.7 + - - +
198A GLY* 4.2 4.0 - - - +
200A VAL* 1.3 76.9 - - - +
202A GLY* 1.3 57.4 + - - +
203A ASP 3.4 0.4 + - - -
204A SER 4.0 3.1 - - - +
207A TYR 4.4 1.8 - - - -
208A ARG* 3.7 32.5 - - - +
211A VAL* 4.3 6.9 - - + +
238A THR* 5.1 1.8 - - + +
241A ASN* 4.0 16.9 - - + +
242A LEU* 3.7 33.0 - - + +
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Residues in contact with GLY 202 (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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198A GLY 3.1 14.0 + - - -
199A ASN 3.2 5.8 + - - -
200A VAL 3.0 1.6 - - - -
201A ALA* 1.3 78.3 - - - +
203A ASP* 1.3 63.1 + - - +
204A SER* 4.8 0.4 - - - -
241A ASN* 4.0 11.7 - - - -
127C LYS* 3.8 26.6 + - - +
128C LYS* 4.3 5.6 - - - +
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Residues in contact with ASP 203 (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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163A SER* 2.9 39.9 + - - +
166A THR* 4.3 4.7 - - + -
199A ASN 3.2 5.0 + - - +
200A VAL 3.0 12.1 + - - +
202A GLY* 1.3 82.0 - - - +
204A SER* 1.3 73.4 + - - +
207A TYR* 3.7 21.6 - - + -
128C LYS* 2.5 36.5 + - - +
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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