Contacts of the helix formed by residues 149 - 167 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ASN* 1.3 107.3 + - + +
150F GLY* 1.3 60.0 + - - +
151F LEU* 3.4 2.7 - - - -
152F TYR* 3.3 20.9 + + + +
153F LEU* 3.2 39.8 + - + +
1008F FE 2.3 30.4 - - - -
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Residues in contact with GLY 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ILE* 3.2 20.1 - - - +
145F GLY 3.3 22.0 - - - -
147F GLU 2.7 20.1 + - - -
148F ASN* 3.5 1.6 - - - +
149F HIS* 1.3 69.5 - - - +
151F LEU* 1.3 60.1 + - - +
153F LEU* 3.3 4.8 + - - -
154F ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005A HIS* 4.0 29.8 - - + +
36F LEU* 4.1 19.6 - - + +
83F LEU* 3.7 40.6 - - + +
141F ILE* 6.1 0.7 - - + -
145F GLY 4.0 2.4 + - - -
146F ASN* 4.1 26.2 + - + +
148F ASN 5.2 1.5 + - - +
149F HIS* 3.4 1.0 - - - +
150F GLY* 1.3 74.6 - - - +
152F TYR* 1.3 58.4 + - - +
154F ALA* 3.8 3.7 - - + +
155F ASP* 2.9 31.2 + - - +
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Residues in contact with TYR 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 5.7 0.9 - - - -
149F HIS* 3.3 24.0 + + + +
150F GLY 3.3 0.6 - - - -
151F LEU* 1.3 78.3 - - - +
153F LEU* 1.3 75.7 + - + +
155F ASP* 3.2 6.7 + - + +
156F GLN* 2.9 66.6 + - + +
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Residues in contact with LEU 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ILE* 4.1 19.4 - - + +
149F HIS* 3.2 31.2 + - + +
150F GLY* 3.6 9.0 - - - +
152F TYR* 1.3 97.7 - - + +
154F ALA* 1.3 61.4 + - - +
156F GLN* 3.3 6.4 + - + +
157F TYR* 3.0 23.7 + - - +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F LEU* 4.0 19.7 - - + -
141F ILE* 4.4 16.8 - - + +
144F ILE* 3.6 24.1 - - + +
145F GLY 5.4 0.9 - - - +
150F GLY 2.9 17.6 + - - +
151F LEU* 3.8 5.6 - - + +
153F LEU* 1.3 76.4 - - - +
155F ASP* 1.3 62.3 + - - +
157F TYR* 3.3 4.5 + - - +
158F VAL* 3.1 29.1 + - - +
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Residues in contact with ASP 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F SER 4.2 2.8 - - - +
36F LEU* 3.3 32.0 - - + +
37F ASP* 3.5 12.3 + - - +
38F GLY* 3.1 20.5 + - - -
39F ALA* 2.9 27.6 + - - +
83F LEU* 4.8 4.4 - - + +
151F LEU 2.9 19.4 + - - +
152F TYR* 3.2 7.7 + - + +
154F ALA* 1.3 76.3 - - - +
156F GLN* 1.3 66.4 + - - +
158F VAL* 3.6 4.4 + - - +
159F LYS* 3.0 26.3 + - - +
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Residues in contact with GLN 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ASP* 4.8 0.2 + - - -
152F TYR* 2.9 59.6 + - + +
153F LEU* 3.8 7.0 - - + +
155F ASP* 1.3 81.0 + - - +
157F TYR* 1.3 60.4 + - - +
159F LYS* 3.2 44.7 + - - +
160F GLY* 3.0 24.6 + - - -
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Residues in contact with TYR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ASP* 5.0 6.5 + - - +
137F ILE* 4.8 8.5 - - + -
140F LYS* 3.5 53.7 - - + -
141F ILE* 6.3 0.4 - - + -
144F ILE* 4.8 5.2 - - + -
153F LEU 3.0 13.9 + - - +
154F ALA* 3.4 11.4 - - - +
155F ASP 3.3 0.2 - - - -
156F GLN* 1.3 75.9 - - - +
158F VAL* 1.3 71.0 + - + +
160F GLY* 3.2 3.7 + - - -
161F ILE* 3.1 51.5 + - + +
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Residues in contact with VAL 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F GLY 4.2 0.7 - - - -
39F ALA* 3.6 23.8 - - + +
42F PHE* 3.4 35.4 - - + +
83F LEU* 5.7 1.6 - - + -
87F PHE* 4.5 6.5 - - + -
137F ILE* 3.8 29.8 - - + -
141F ILE* 5.0 6.5 - - + -
154F ALA 3.1 17.1 + - - +
155F ASP* 3.9 6.1 - - - +
157F TYR* 1.3 79.5 - - + +
159F LYS* 1.3 63.3 + - - +
161F ILE* 3.2 8.2 + - - +
162F ALA* 3.0 22.0 + - - +
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Residues in contact with LYS 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ASP* 2.8 36.2 + - - -
38F GLY* 3.6 23.5 - - - +
41F LEU* 5.1 7.9 - - + -
155F ASP 3.0 12.8 + - - +
156F GLN* 3.2 42.5 + - - +
157F TYR 3.3 0.4 - - - -
158F VAL* 1.3 75.4 - - - +
160F GLY* 1.3 62.6 + - - +
162F ALA* 3.3 4.9 + - - +
163F LYS* 3.0 47.0 + - + +
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Residues in contact with GLY 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F GLN 3.0 14.1 + - - -
157F TYR 3.2 4.2 + - - -
159F LYS* 1.3 75.6 - - - +
161F ILE* 1.3 61.5 + - - +
163F LYS* 4.1 6.4 - - - +
164F SER* 3.1 26.2 + - - -
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Residues in contact with ILE 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE* 3.9 11.9 - - + -
133F LEU* 3.9 19.7 - - + -
136F ASP* 6.3 1.1 - - + -
137F ILE* 3.9 19.5 - - + -
157F TYR* 3.1 50.5 + - + +
158F VAL* 3.2 8.7 + - - +
160F GLY* 1.3 75.6 - - - +
162F ALA* 1.3 62.0 + - - +
164F SER* 2.8 22.1 + - - +
165F ARG* 3.2 30.8 + - + +
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Residues in contact with ALA 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 4.0 17.0 - - + -
42F PHE* 3.7 37.2 - - + +
45F ASP* 4.3 5.9 - - - +
158F VAL 3.0 13.4 + - - +
159F LYS* 3.6 9.6 - - - +
161F ILE* 1.3 77.5 - - - +
163F LYS* 1.3 60.4 + - - +
165F ARG* 3.5 5.9 + - - +
166F LYS* 3.3 27.8 + - - +
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Residues in contact with LYS 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 4.6 15.0 - - + -
159F LYS* 3.0 37.6 + - + +
160F GLY* 4.1 5.6 - - - +
162F ALA* 1.3 76.8 - - - +
164F SER* 1.3 62.0 + - - +
165F ARG 3.5 0.2 + - - -
166F LYS* 3.6 19.8 + - + +
167F SER* 3.3 15.9 + - - +
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Residues in contact with SER 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F GLY 3.1 15.6 + - - -
161F ILE* 2.8 23.9 + - - +
163F LYS* 1.3 77.6 - - - +
165F ARG* 1.3 61.7 + - - +
166F LYS 3.5 0.2 - - - -
167F SER* 3.3 22.7 - - - +
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Residues in contact with ARG 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE* 4.7 5.5 - - - -
49F GLU* 6.3 0.4 - - - +
129F GLU* 4.0 30.9 + - - +
130F GLU* 5.1 10.9 + - - +
133F LEU* 3.6 30.2 - - - +
161F ILE* 3.2 34.6 + - + +
162F ALA* 4.0 4.9 - - - +
163F LYS 3.2 0.2 - - - -
164F SER* 1.3 83.3 - - - +
166F LYS* 1.3 64.0 + - - +
167F SER* 3.4 1.1 - - - -
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Residues in contact with LYS 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 3.8 28.8 - - - +
45F ASP* 2.9 37.9 + - - +
162F ALA 3.3 13.8 + - - +
163F LYS* 3.8 15.0 - - + +
165F ARG* 1.3 77.9 - - - +
167F SER* 1.3 63.1 + - - +
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Residues in contact with SER 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F LYS 3.3 12.8 - - - +
164F SER* 3.3 19.6 - - - +
165F ARG 4.4 0.9 - - - -
166F LYS* 1.3 83.6 - - - +
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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