Contacts of the helix formed by residues 186 - 197 (chain B) in PDB entry 6BSL
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 SER 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B ASP* 2.6 27.3 + - - -
147B ASP* 3.4 35.4 - - - -
148B SER* 3.7 0.2 - - - -
181B GLN* 4.7 0.7 - - - +
184B ARG* 3.4 4.1 + - - -
185B LEU* 1.3 75.4 - - - +
187B LYS* 1.3 64.8 + - - +
188B GLY 3.3 1.1 + - - -
189B ASP* 2.9 24.0 + - - -
190B ILE* 3.0 25.2 + - - +
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Residues in contact with LYS 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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186B SER* 1.3 73.7 - - - +
188B GLY* 1.3 58.0 + - - +
190B ILE* 3.4 9.5 + - + +
191B ALA* 3.0 29.3 + - - +
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Residues in contact with GLY 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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142B GLU* 3.0 19.6 - - - +
145B ASP* 3.4 20.6 + - - -
186B SER* 3.2 3.2 + - - -
187B LYS* 1.3 76.9 - - - +
189B ASP* 1.3 60.0 + - - +
191B ALA* 4.4 0.7 - - - -
192B GLN* 2.9 29.7 + - - +
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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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38B TRP* 5.0 1.1 - - - -
101B PHE* 3.6 21.4 - - + -
145B ASP* 3.6 0.5 + - - +
148B SER* 2.6 26.5 + - - -
149B ILE* 2.8 37.4 + - - +
150B MET* 4.5 0.5 - - - +
185B LEU* 3.7 16.5 - - + -
186B SER* 2.9 34.6 + - - +
188B GLY* 1.3 74.5 - - - +
190B ILE* 1.3 58.4 + - - +
192B GLN* 4.6 3.6 + - - +
193B ALA* 3.0 30.0 + - - +
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Residues in contact with ILE 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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38B TRP* 6.3 0.2 - - - -
41B HIS* 3.5 46.0 - - + +
42B THR* 4.7 2.5 - - + -
185B LEU* 4.0 26.5 - - + +
186B SER 3.0 18.8 + - - +
187B LYS* 3.7 8.1 - - + +
189B ASP* 1.3 72.5 - - - +
191B ALA* 1.3 66.6 + - - +
193B ALA* 3.3 5.7 + - - +
194B ARG* 3.0 56.4 + - - +
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Residues in contact with ALA 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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142B GLU* 3.5 25.8 - - - +
187B LYS 3.0 18.7 + - - +
188B GLY* 4.4 0.7 - - - -
190B ILE* 1.3 78.7 - - - +
192B GLN* 1.3 61.2 + - - +
194B ARG* 3.4 8.5 + - - +
195B LYS* 3.0 32.4 + - - +
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Residues in contact with GLN 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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1B ALA* 2.7 43.6 + - - +
2B ALA* 3.9 2.1 + - + -
101B PHE* 3.2 45.6 - - + +
102B TRP 5.6 0.2 + - - -
140B LEU* 3.7 20.1 - - + +
142B GLU* 3.7 24.4 + - + +
150B MET* 5.5 1.0 - - - +
188B GLY 2.9 19.5 + - - +
189B ASP* 3.8 5.6 + - - +
191B ALA* 1.3 78.1 - - - +
193B ALA* 1.3 56.8 + - - +
195B LYS* 3.4 3.4 + - - +
196B LEU* 2.9 28.2 + - - +
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Residues in contact with ALA 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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38B TRP* 3.9 11.0 - - + -
42B THR* 3.7 26.9 - - + -
44B VAL* 5.5 2.0 - - + -
99B VAL* 5.7 0.7 - - + -
101B PHE* 3.6 19.7 - - + -
189B ASP 3.0 18.3 + - - +
190B ILE 3.7 0.4 - - - +
192B GLN* 1.3 76.0 - - - +
194B ARG* 1.3 59.0 + - - +
196B LEU* 3.3 2.2 + - - -
197B TYR* 2.9 40.9 + - + +
199B CYS* 4.7 1.6 - - - -
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Residues in contact with ARG 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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40B LYS 5.6 0.2 + - - -
41B HIS* 2.9 36.6 + - - +
42B THR* 4.6 5.1 - - - +
190B ILE* 3.0 35.0 + - - +
191B ALA* 3.7 6.7 - - - +
193B ALA* 1.3 76.4 - - - +
195B LYS* 1.3 58.6 + - + +
198B LYS* 3.0 7.4 + - - -
199B CYS* 2.9 55.3 + - + +
200B PRO 5.7 4.6 + - - -
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Residues in contact with LYS 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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140B LEU* 2.8 51.4 + - + +
141B GLY* 4.2 8.3 + - - -
142B GLU* 2.9 24.5 + - + +
191B ALA* 3.0 23.3 + - - +
192B GLN 3.8 3.4 - - - +
194B ARG* 1.3 75.3 - - + +
196B LEU* 1.3 65.6 + - - +
198B LYS* 3.3 18.0 + - - +
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Residues in contact with LEU 196 (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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2B ALA* 3.9 22.9 - - + -
3B THR* 4.0 21.1 - - + +
9B VAL* 4.0 27.6 - - + +
99B VAL 3.7 12.1 - - - +
100B GLY* 4.5 4.5 - - - +
101B PHE* 4.1 13.9 - - + -
138B GLU* 4.8 8.7 - - + -
140B LEU* 4.3 13.2 - - + +
192B GLN 2.9 18.3 + - - +
193B ALA* 3.8 3.8 - - - +
195B LYS* 1.3 78.4 - - - +
197B TYR* 1.3 83.6 + - + +
198B LYS* 3.4 8.7 + - - +
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Residues in contact with TYR 197 (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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9B VAL* 3.5 18.7 - - + -
10B TRP* 3.2 48.0 + - + -
12B ASP 6.0 1.0 - - - -
13B GLY* 3.5 28.0 + - - -
15B ILE* 5.4 1.1 - - + -
43B CYS* 3.8 11.8 - - - -
44B VAL* 4.1 17.3 - - + -
99B VAL* 2.6 42.3 + - + -
193B ALA* 2.9 23.5 + - + +
196B LEU* 1.3 89.2 - - + +
198B LYS* 1.3 71.3 + - - +
199B CYS* 3.2 15.9 + - - -
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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