Contacts of the helix formed by residues 149 - 165 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU 5.0 1.6 - - - -
144A ILE* 3.6 31.3 + - + +
147A GLU* 4.6 1.8 + - - +
148A ASN* 3.2 36.4 + - - -
149A HIS* 3.3 7.4 + + - -
150A GLY* 4.3 10.3 - - - -
153A LEU* 3.2 25.3 - - + +
1008A FE 2.5 30.6 - - - -
149B HIS* 3.4 15.1 + + - -
148D ASN* 1.3 83.3 - - - +
150D GLY* 1.3 63.5 + - - +
151D LEU* 3.4 3.1 - - - +
152D TYR* 3.4 9.4 + - + +
153D LEU* 3.1 28.3 + - + +
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Residues in contact with GLY 150 (chain D).
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* 4.1 9.2 - - - -
144D ILE* 3.2 19.1 - - - +
145D GLY 3.5 18.8 - - - -
147D GLU 2.7 21.7 + - - -
148D ASN* 3.4 1.6 - - - +
149D HIS* 1.3 69.0 - - - +
151D LEU* 1.3 59.1 + - - +
153D LEU* 3.2 2.3 + - - -
154D ALA* 2.9 27.1 + - - +
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.0 28.3 - - + +
1005C HIS* 4.1 18.2 - - + +
36D LEU* 4.3 12.3 - - + +
83D LEU* 3.6 41.5 - - + +
141D ILE* 6.1 1.6 - - + -
145D GLY 3.9 4.5 + - - +
146D ASN* 4.7 17.6 - - + +
147D GLU 4.7 0.4 + - - -
148D ASN 5.0 2.6 + - - +
149D HIS* 5.2 0.4 - - - -
150D GLY* 1.3 75.9 - - - +
152D TYR* 1.3 55.9 + - - +
154D ALA* 3.3 5.1 + - + +
155D ASP* 2.9 30.9 + - - +
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Residues in contact with TYR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 3.7 29.2 - - + -
143A LEU* 3.9 19.4 + - + +
144A ILE* 3.6 39.3 - - + -
153A LEU* 4.1 23.6 + - + -
157A TYR* 3.4 26.1 - + - +
149D HIS* 3.4 14.8 + - + +
150D GLY 3.3 0.6 - - - -
151D LEU* 1.3 75.8 - - - +
153D LEU* 1.3 84.3 + - + +
155D ASP* 3.3 2.9 + - + +
156D GLN* 3.0 54.1 + - + +
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.5 14.8 - - + -
149B HIS* 3.5 44.9 - - + +
152B TYR* 4.1 28.2 + - + -
153B LEU* 4.8 9.4 - - + -
144D ILE* 4.1 8.5 - - + -
149D HIS* 3.1 16.2 + - + +
150D GLY 3.2 6.9 + - - +
152D TYR* 1.3 95.2 - - + +
154D ALA* 1.3 56.9 + - - +
156D GLN* 3.4 6.0 + - + +
157D TYR* 3.0 28.4 + - - +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D LEU* 4.2 17.5 - - + -
141D ILE* 4.3 17.5 - - + +
144D ILE* 3.7 25.0 - - + +
145D GLY 5.5 0.9 - - - +
150D GLY 2.9 16.2 + - - +
151D LEU* 3.6 7.0 - - + +
153D LEU* 1.3 77.4 - - - +
155D ASP* 1.3 60.7 + - - +
157D TYR* 3.3 4.9 + - - +
158D VAL* 3.1 28.8 + - - +
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Residues in contact with ASP 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 3.5 9.7 + - - +
143A LEU* 5.1 2.0 - - + -
36D LEU* 3.2 31.7 - - + +
37D ASP* 3.2 12.1 - - - +
38D GLY* 2.9 22.9 + - - -
39D ALA* 2.8 27.9 + - - +
83D LEU* 4.7 5.0 - - + +
151D LEU 2.9 20.9 + - - +
152D TYR* 3.8 7.2 - - + +
154D ALA* 1.3 72.3 - - - +
156D GLN* 1.3 61.8 + - - +
158D VAL* 3.5 5.3 + - - +
159D LYS* 3.0 26.9 + - - +
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Residues in contact with GLN 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 4.5 3.2 - - - +
157A TYR* 3.9 18.8 - - - -
152D TYR* 3.0 53.1 + - + +
153D LEU* 3.7 7.9 - - + +
154D ALA 3.2 0.2 - - - -
155D ASP* 1.3 82.2 + - - +
157D TYR* 1.3 64.7 + - - +
159D LYS* 3.2 42.8 + - - +
160D GLY* 3.1 19.4 + - - -
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Residues in contact with TYR 157 (chain D).
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* 4.3 4.5 + - - -
152B TYR* 3.7 24.9 + + + +
156B GLN* 4.0 23.3 - - - -
159B LYS* 3.5 17.8 + - - -
136D ASP* 5.0 9.2 + - - +
137D ILE* 5.0 4.3 - - + -
140D LYS* 3.5 39.6 - - + +
141D ILE* 6.4 0.9 - - + -
144D ILE* 4.8 2.2 - - + -
153D LEU 3.0 13.9 + - - +
154D ALA* 3.3 11.2 + - - +
156D GLN* 1.3 76.0 - - - +
158D VAL* 1.3 71.1 + - + +
160D GLY* 3.2 4.0 + - - -
161D ILE* 3.2 50.2 + - + +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA* 3.7 22.2 - - + +
42D PHE* 3.5 35.4 - - + +
83D LEU* 5.8 1.8 - - + -
87D PHE* 4.6 6.7 - - + -
137D ILE* 3.7 29.4 - - + -
141D ILE* 4.9 7.6 - - + -
154D ALA 3.1 17.8 + - - +
155D ASP* 3.9 5.4 - - - +
156D GLN 3.4 0.2 - - - -
157D TYR* 1.3 82.0 - - + +
159D LYS* 1.3 56.4 + - - +
161D ILE* 3.3 8.0 + - - +
162D ALA* 2.9 28.2 + - - +
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Residues in contact with LYS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 4.4 0.2 - - - +
157A TYR* 3.3 20.0 + - + -
37D ASP* 3.1 37.4 + - - -
38D GLY* 3.7 21.7 + - - -
41D LEU* 4.9 8.1 - - + -
155D ASP 3.0 15.5 + - - +
156D GLN* 3.2 38.9 - - - +
157D TYR 3.2 0.4 - - - -
158D VAL* 1.3 76.8 - - - +
160D GLY* 1.3 56.7 + - - +
162D ALA* 3.4 3.8 + - - +
163D LYS* 3.0 55.5 + - + +
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Residues in contact with GLY 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D GLN 3.1 13.4 + - - -
157D TYR* 3.2 4.6 + - - -
159D LYS* 1.3 73.5 - - - +
161D ILE* 1.3 59.9 + - - +
163D LYS* 3.6 6.8 + - - +
164D SER* 3.0 31.2 + - - -
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.9 17.0 - - + -
133D LEU* 3.8 27.4 - - + -
136D ASP* 6.2 1.8 - - + -
137D ILE* 4.0 20.6 - - + -
157D TYR* 3.2 49.1 + - + +
158D VAL* 3.3 8.3 + - - +
160D GLY* 1.3 73.2 - - - +
162D ALA* 1.3 65.5 + - - +
164D SER* 3.1 9.2 + - - +
165D ARG* 3.0 32.3 + - + +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLY 4.5 0.2 - - - +
41D LEU* 4.0 18.2 - - + -
42D PHE* 3.7 38.4 - - - +
45D ASP* 4.3 9.5 - - + +
158D VAL 2.9 17.4 + - - +
159D LYS* 3.7 7.0 - - - +
161D ILE* 1.3 77.8 - - - +
163D LYS* 1.3 62.2 + - - +
165D ARG* 3.6 10.6 + - - +
166D LYS 3.7 13.9 + - - +
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 4.3 16.6 - - + -
159D LYS* 3.0 45.5 + - + +
160D GLY* 4.0 6.1 - - - +
162D ALA* 1.3 76.5 - - - +
164D SER* 1.3 59.0 + - - +
166D LYS* 3.0 23.5 + - - +
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D GLY 3.0 16.5 + - - -
161D ILE* 3.1 16.3 + - - +
163D LYS* 1.3 72.0 - - - +
165D ARG* 1.3 60.1 + - - +
166D LYS* 3.0 9.2 + - - +
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Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 4.4 7.4 - - - -
129D GLU* 2.8 36.3 + - - +
130D GLU* 5.1 9.7 - - - +
133D LEU* 3.4 41.8 - - - +
161D ILE* 3.0 29.2 + - + +
162D ALA* 4.0 5.8 - - - +
163D LYS 3.2 0.4 - - - -
164D SER* 1.3 77.4 - - - +
166D LYS* 1.3 66.7 + - - +
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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