Contacts of the helix formed by residues 186 - 196 (chain A) in PDB entry 3BSH
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A THR* 3.2 28.5 + - - +
185A TYR* 1.3 79.8 - - - +
187A PRO* 1.3 66.7 - - - +
188A GLU* 3.1 33.3 - - - +
189A MET* 2.8 29.6 + - - +
190A ALA 3.3 7.3 + - - -
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Residues in contact with PRO 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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185A TYR 3.5 0.8 - - - +
186A SER* 1.3 83.3 - - - +
188A GLU* 1.3 76.7 + - - +
190A ALA* 2.9 5.3 + - + +
191A LYS* 2.9 25.5 + - - +
232A TRP* 3.6 57.0 - - + +
235A LYS* 3.5 35.7 - - + +
236A VAL* 4.1 4.0 - - + +
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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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186A SER* 3.1 17.4 - - - +
187A PRO* 1.3 95.5 - - - +
189A MET* 1.3 75.7 + - + +
191A LYS* 3.4 20.0 - - - +
192A VAL* 3.5 7.3 + - - +
235A LYS* 3.6 35.0 + - - +
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Residues in contact with MET 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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140A THR* 3.9 18.8 - - + +
152A HIS* 3.6 23.8 - - + +
153A LEU* 4.0 18.8 - - + -
158A GLN* 3.3 26.5 - - - +
185A TYR* 4.2 15.0 - - + -
186A SER* 2.8 19.6 + - - +
188A GLU* 1.3 97.2 - - + +
190A ALA* 1.3 66.2 + - - +
191A LYS 3.1 1.3 - - - -
192A VAL* 3.1 27.3 + - + +
193A TYR* 3.2 20.6 - - + -
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Residues in contact with ALA 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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179A LEU* 4.2 7.4 - - + -
185A TYR* 4.0 21.8 - - + -
186A SER 3.3 3.4 + - - -
187A PRO* 2.9 9.9 + - + +
189A MET* 1.3 76.3 - - - +
191A LYS* 1.3 54.0 + - - +
193A TYR* 2.9 10.6 + - - +
194A ILE* 2.8 48.1 + - + +
232A TRP* 3.8 28.0 - - + -
236A VAL* 4.6 0.4 - - + -
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Residues in contact with LYS 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 PRO 2.9 11.5 + - - +
188A GLU* 3.4 14.4 - - - +
190A ALA* 1.3 77.0 - - - +
192A VAL* 1.3 66.1 + - - +
194A ILE* 4.3 3.8 - - - -
195A ASP* 3.1 44.3 + - - +
235A LYS 4.2 8.3 - - - +
236A VAL* 3.4 40.8 + - + +
237A GLY* 3.6 14.5 - - - +
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Residues in contact with VAL 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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158A GLN* 3.9 28.7 - - + +
162A LYS* 3.5 31.2 + - + +
188A GLU 3.8 3.4 - - - +
189A MET* 3.1 40.1 + - + +
191A LYS* 1.3 80.7 - - - +
193A TYR* 1.3 70.2 + - + +
195A ASP* 4.2 2.3 - - - +
196A GLY* 3.3 15.4 + - - -
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Residues in contact with TYR 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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91A ILE* 4.1 15.5 - - + -
152A HIS* 3.1 40.2 + + + -
157A VAL* 3.8 1.0 - - - +
158A GLN* 3.2 42.3 + - + +
161A LEU* 3.5 33.7 - - + +
162A LYS* 4.0 15.0 - - + +
165A LEU* 4.1 20.9 - - + -
177A TRP* 5.8 0.9 - - + -
179A LEU* 6.2 3.8 - - + -
185A TYR* 5.5 3.4 - + - -
189A MET* 3.2 26.5 - - + -
190A ALA* 2.9 9.8 + - - +
192A VAL* 1.3 79.7 - - + +
194A ILE* 1.3 60.6 + - + +
196A GLY 3.4 5.4 + - - -
197A THR* 2.4 30.9 + - - +
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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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177A TRP* 5.1 3.8 - - + -
179A LEU* 4.2 17.5 - - + -
190A ALA* 2.8 32.2 + - + +
191A LYS* 4.0 3.4 - - - +
193A TYR* 1.3 73.4 - - + +
195A ASP* 1.3 65.7 - - - +
197A THR* 3.3 3.5 + - - -
198A SER* 2.9 28.6 + - - -
199A PRO* 3.6 5.0 - - + +
202A ALA* 4.2 15.5 - - + -
232A TRP* 4.6 3.1 - - + -
236A VAL* 3.6 30.1 - - + -
241A SER* 4.2 4.0 - - - +
242A ALA* 3.9 28.3 - - + +
243A GLY* 4.1 19.1 - - - +
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Residues in contact with ASP 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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191A LYS* 3.1 47.6 + - - +
192A VAL* 4.2 2.2 - - - +
194A ILE* 1.3 86.0 - - - +
196A GLY* 1.3 57.6 + - - +
197A THR 3.1 4.4 + - - -
198A SER* 3.7 13.2 + - - +
236A VAL 4.9 0.7 - - - +
241A SER* 4.8 8.3 + - - -
242A ALA 5.6 0.3 + - - -
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Residues in contact with GLY 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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162A LYS* 4.0 22.5 - - - +
166A LEU* 3.5 16.8 - - - +
192A VAL 3.3 9.5 + - - -
193A TYR 3.4 0.8 + - - -
194A ILE 3.4 0.2 + - - -
195A ASP* 1.3 76.2 - - - +
197A THR* 1.3 69.6 + - - +
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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