Contacts of the helix formed by residues 149 - 165 (chain B) in PDB entry 3BVI
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 HIS 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008A FE 2.5 29.4 - - - -
148B ASN* 1.3 95.8 + - - +
150B GLY* 1.3 61.9 + - - +
151B LEU 3.3 2.5 - - - +
152B TYR* 3.4 9.2 + - + +
153B LEU* 3.1 28.8 + - + +
143D LEU 4.9 2.7 - - - -
144D ILE* 3.6 30.2 + - + +
147D GLU* 4.6 2.2 + - - +
148D ASN* 3.0 31.7 + - - -
149D HIS* 3.4 14.6 + + - -
150D GLY* 4.1 13.0 - - - -
153D LEU* 3.5 22.4 - - + +
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Residues in contact with GLY 150 (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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144B ILE* 3.2 20.7 - - - +
145B GLY 3.5 20.6 - - - -
147B GLU 2.8 19.3 + - - -
148B ASN* 3.4 1.2 + - - -
149B HIS* 1.3 69.8 - - - +
151B LEU* 1.3 60.2 + - - +
153B LEU* 3.2 5.5 + - - -
154B ALA* 2.8 27.9 + - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.3 11.1 - - + +
83B LEU* 3.9 39.2 - - + +
141B ILE* 6.3 0.9 - - + -
145B GLY 4.1 2.2 + - - -
146B ASN* 4.2 36.5 + - - +
148B ASN 4.5 4.5 + - - +
149B HIS* 3.3 0.6 - - - +
150B GLY* 1.3 73.1 - - - +
152B TYR* 1.3 59.8 + - - +
154B ALA* 3.4 4.6 + - + +
155B ASP* 2.9 30.9 + - - +
143D LEU* 4.1 17.3 - - + +
1005E HIS* 4.3 25.4 - - + +
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Residues in contact with TYR 152 (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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149B HIS* 3.4 15.0 + - + +
150B GLY 3.3 0.2 - - - -
151B LEU* 1.3 78.1 - - - +
153B LEU* 1.3 75.8 + - + +
155B ASP* 3.2 3.2 + - + +
156B GLN* 3.0 63.3 + - + +
140D LYS* 4.3 16.2 - - + -
143D LEU* 3.9 18.3 + - + +
144D ILE* 3.6 44.0 - - + -
153D LEU* 4.1 27.2 + - + -
157D TYR* 3.7 29.0 + + - +
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Residues in contact with LEU 153 (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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149A HIS* 6.0 3.8 - - - +
144B ILE* 4.1 20.1 - - + +
149B HIS* 3.1 28.5 + - + +
150B GLY* 3.2 9.6 + - - +
152B TYR* 1.3 97.8 - - + +
154B ALA* 1.3 61.7 + - - +
156B GLN* 3.5 6.4 + - + +
157B TYR* 3.1 23.4 + - - +
153D LEU* 4.8 9.9 - - + -
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Residues in contact with ALA 154 (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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83B LEU* 4.0 18.6 - - + -
141B ILE* 4.4 17.3 - - + +
144B ILE* 3.6 22.8 - - + +
145B GLY 5.6 1.1 - - - +
150B GLY 2.8 19.7 + - - +
151B LEU* 3.7 7.4 - - + +
153B LEU* 1.3 71.4 - - - +
155B ASP* 1.3 63.2 + - - +
157B TYR* 3.3 4.0 + - - +
158B VAL* 3.1 29.0 + - - +
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Residues in contact with ASP 155 (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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36B LEU* 3.2 33.2 - - + +
37B ASP* 3.6 0.2 - - - +
38B GLY* 3.0 17.3 + - - -
39B ALA* 3.0 26.7 + - - +
83B LEU* 4.8 4.6 - - + +
151B LEU 2.9 17.9 + - - +
152B TYR* 3.6 6.7 - - - +
154B ALA* 1.3 76.2 - - - +
156B GLN* 1.3 59.3 + - - +
158B VAL* 3.5 5.3 + - - +
159B LYS* 2.9 26.5 + - - +
140D LYS* 2.9 28.7 + - - +
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Residues in contact with GLN 156 (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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152B TYR* 3.0 50.8 + - + +
153B LEU* 3.9 7.0 - - + +
155B ASP* 1.3 75.5 + - - +
157B TYR* 1.3 58.8 + - - +
159B LYS* 3.1 44.9 + - - +
160B GLY* 2.9 25.6 + - - -
140D LYS* 3.6 19.6 - - - +
157D TYR* 4.0 10.6 - - - -
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Residues in contact with TYR 157 (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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136B ASP* 5.2 5.7 + - - +
137B ILE* 4.9 7.2 - - + -
140B LYS* 3.6 51.8 - - + -
141B ILE* 6.6 0.2 - - + -
144B ILE* 4.7 5.2 - - + -
153B LEU 3.1 14.5 + - - +
154B ALA* 3.5 11.4 - - - +
156B GLN* 1.3 76.4 - - - +
158B VAL* 1.3 70.4 + - + +
160B GLY* 3.3 3.6 + - - +
161B ILE* 3.1 50.0 + - + +
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Residues in contact with VAL 158 (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 GLY 4.2 0.2 - - - -
39B ALA* 3.7 22.9 - - + +
42B PHE* 3.4 36.3 - - + +
83B LEU* 5.7 1.6 - - + -
87B PHE* 4.5 7.0 - - + -
137B ILE* 3.7 29.8 - - + -
141B ILE* 4.9 8.1 - - + -
154B ALA 3.1 18.6 + - - +
155B ASP* 3.8 4.5 - - - +
157B TYR* 1.3 78.5 - - + +
159B LYS* 1.3 65.9 + - - +
161B ILE* 3.1 7.8 + - - +
162B ALA* 3.0 21.5 + - - +
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Residues in contact with LYS 159 (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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37B ASP* 2.9 32.0 + - - -
38B GLY* 3.6 28.0 + - - +
41B LEU* 4.8 8.1 - - + -
155B ASP 2.9 13.0 + - - +
156B GLN* 3.1 44.1 + - - +
158B VAL* 1.3 73.9 - - - +
160B GLY* 1.3 63.9 + - - +
162B ALA* 3.2 5.4 + - - +
163B LYS* 3.0 52.5 + - + +
157D TYR* 3.5 18.0 + - - -
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Residues in contact with GLY 160 (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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156B GLN 2.9 14.0 + - - -
157B TYR* 3.6 4.9 - - - -
158B VAL 3.2 0.4 - - - -
159B LYS* 1.3 76.9 - - - +
161B ILE* 1.3 60.3 + - - +
163B LYS* 3.5 7.5 + - - +
164B SER* 3.1 23.7 + - - -
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Residues in contact with ILE 161 (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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42B PHE* 3.8 24.2 - - + -
133B LEU* 4.0 14.4 - - + -
136B ASP* 6.1 2.0 - - + -
137B ILE* 3.8 20.9 - - + -
157B TYR* 3.1 46.0 + - + +
158B VAL* 3.1 10.5 + - - +
160B GLY* 1.3 72.2 - - - +
162B ALA* 1.3 68.0 + - - +
164B SER* 2.8 22.8 + - - +
165B ARG* 3.1 24.4 + - + +
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Residues in contact with ALA 162 (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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41B LEU* 3.9 20.4 - - + -
42B PHE* 3.8 35.6 - - + +
45B ASP* 4.5 6.5 - - - +
158B VAL 3.0 12.1 + - - +
159B LYS* 3.5 9.9 - - - +
161B ILE* 1.3 77.9 - - - +
163B LYS* 1.3 62.7 + - - +
165B ARG* 3.3 13.8 + - - +
166B LYS* 3.4 18.2 + - - +
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Residues in contact with LYS 163 (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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41B LEU* 4.4 14.6 - - + -
159B LYS* 3.0 45.0 + - + +
160B GLY* 4.0 6.1 - - - +
162B ALA* 1.3 77.3 - - - +
164B SER* 1.3 62.4 + - - +
166B LYS* 3.3 29.3 + - + +
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Residues in contact with SER 164 (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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160B GLY 3.1 13.9 + - - -
161B ILE* 2.8 23.4 + - - +
163B LYS* 1.3 77.1 - - - +
165B ARG* 1.3 63.9 + - - +
166B LYS 3.5 5.0 + - - -
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Residues in contact with ARG 165 (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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42B PHE* 4.6 5.1 - - - -
129B GLU* 2.8 43.0 + - - +
130B GLU* 5.0 8.9 - - - +
133B LEU* 3.5 38.7 - - - +
161B ILE* 3.1 30.3 + - + +
162B ALA* 3.7 6.5 - - - +
163B LYS 3.3 0.4 - - - -
164B SER* 1.3 77.2 - - - +
166B LYS* 1.3 62.2 + - - +
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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