Contacts of the helix formed by residues 149 - 165 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ASN 5.3 0.2 + - - -
148C ASN* 1.3 102.5 + - - +
150C GLY* 1.3 62.3 + - - +
151C LEU* 3.3 3.6 - - - +
152C TYR* 3.2 22.1 + + + +
153C LEU* 3.0 46.1 + - + +
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Residues in contact with GLY 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE* 3.2 22.0 - - - +
145C GLY 3.4 20.2 - - - -
147C GLU 3.0 18.0 + - - -
148C ASN 3.1 1.7 + - - -
149C HIS* 1.3 77.2 - - - +
151C LEU* 1.3 56.6 + - - +
153C LEU* 3.3 5.0 + - - -
154C ALA* 3.0 26.9 + - - +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.3 20.4 - - + +
83C LEU* 3.9 39.4 - - + +
141C ILE* 6.2 0.7 - - + -
145C GLY 3.8 3.8 + - - +
146C ASN* 4.4 31.6 + - + +
149C HIS* 3.3 1.5 - - - -
150C GLY* 1.3 71.8 - - - +
152C TYR* 1.3 65.5 + - - +
154C ALA* 3.4 4.9 + - + +
155C ASP* 3.0 25.5 + - - +
1005D HIS* 3.7 32.3 - - + +
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Residues in contact with TYR 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 5.9 0.9 - - - -
149C HIS* 3.2 25.9 + + + +
151C LEU* 1.3 76.3 - - - +
153C LEU* 1.3 78.0 + - + +
155C ASP* 3.2 7.3 + - + +
156C GLN* 2.9 66.3 + - + +
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ILE* 4.1 20.3 - - + +
149C HIS* 3.0 35.0 + - + +
150C GLY* 3.6 7.9 - - - +
152C TYR* 1.3 96.6 - - + +
154C ALA* 1.3 58.0 + - - +
156C GLN* 3.5 5.7 + - + +
157C TYR* 3.1 27.0 + - - +
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.3 17.9 - - + -
141C ILE* 4.3 16.8 - - + +
144C ILE* 3.6 23.5 - - + +
145C GLY 5.5 1.3 - - - +
150C GLY 3.0 16.6 + - - +
151C LEU* 3.8 6.7 - - + +
153C LEU* 1.3 73.8 - - - +
155C ASP* 1.3 60.6 + - - +
157C TYR* 3.4 4.2 + - - +
158C VAL* 3.0 35.1 + - - +
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER 4.1 2.6 - - - +
36C LEU* 3.4 31.0 - - + +
37C ASP* 3.2 15.2 + - - +
38C GLY* 3.1 19.4 + - - -
39C ALA* 2.9 25.5 + - - +
83C LEU* 4.9 4.5 - - + +
151C LEU 3.0 17.7 + - - +
152C TYR* 3.2 7.8 + - + +
154C ALA* 1.3 73.8 - - - +
156C GLN* 1.3 66.5 + - - +
158C VAL* 3.3 4.5 + - - -
159C LYS* 2.9 29.3 + - - +
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Residues in contact with GLN 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP* 4.6 0.4 + - - -
152C TYR* 2.9 60.0 + - + +
153C LEU* 3.8 7.9 - - + +
155C ASP* 1.3 83.3 + - - +
157C TYR* 1.3 57.2 + - - +
159C LYS* 3.2 40.4 + - - +
160C GLY* 3.0 25.5 + - - -
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ASP* 5.3 4.9 - - + +
137C ILE* 5.0 6.3 - - + -
140C LYS* 3.6 50.7 - - + +
144C ILE* 4.7 5.4 - - + -
153C LEU 3.1 14.3 + - - +
154C ALA* 3.4 12.3 - - - +
155C ASP 3.2 0.2 - - - -
156C GLN* 1.3 77.4 - - - +
158C VAL* 1.3 70.0 + - + +
160C GLY* 3.2 3.5 + - - -
161C ILE* 3.2 49.8 + - + +
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLY 4.1 0.7 - - - -
39C ALA* 3.8 21.1 - - + +
42C PHE* 3.4 37.2 - - + -
83C LEU* 5.6 1.3 - - + -
87C PHE* 4.4 7.4 - - + -
137C ILE* 3.8 28.0 - - + -
141C ILE* 5.0 8.3 - - + -
154C ALA 3.0 18.1 + - - +
155C ASP* 3.9 4.7 - - - +
157C TYR* 1.3 81.0 - - + +
159C LYS* 1.3 62.6 + - - +
161C ILE* 3.3 8.3 + - - +
162C ALA* 3.0 21.8 + - - +
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP* 3.0 43.4 + - - -
38C GLY* 3.6 20.1 + - - -
41C LEU* 4.8 7.6 - - + -
155C ASP 2.9 16.5 + - - +
156C GLN* 3.2 36.1 + - - +
158C VAL* 1.3 76.0 - - - +
160C GLY* 1.3 62.1 + - - +
162C ALA* 3.3 5.0 + - - +
163C LYS* 3.0 46.8 + - + +
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Residues in contact with GLY 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLN 3.0 14.7 + - - -
157C TYR 3.2 4.0 + - - -
159C LYS* 1.3 77.0 - - - +
161C ILE* 1.3 60.4 + - - +
163C LYS* 3.4 7.4 + - - +
164C SER* 3.0 25.7 + - - -
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Residues in contact with ILE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.8 23.3 - - + -
133C LEU* 4.0 14.6 - - + -
136C ASP* 6.2 1.1 - - + -
137C ILE* 3.8 22.4 - - + -
157C TYR* 3.2 47.9 + - + +
158C VAL* 3.3 8.3 + - - +
160C GLY* 1.3 73.2 - - - +
162C ALA* 1.3 65.5 + - - +
164C SER* 3.0 19.9 + - - -
165C ARG* 3.2 24.2 + - + +
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.0 16.2 - - + -
42C PHE* 3.8 38.8 - - - +
45C ASP* 4.4 6.3 - - + +
158C VAL 3.0 12.7 + - - +
159C LYS* 3.5 9.4 - - - +
161C ILE* 1.3 77.2 - - - +
163C LYS* 1.3 62.8 + - - +
165C ARG* 3.4 13.7 + - - +
166C LYS* 3.6 18.7 + - - +
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Residues in contact with LYS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.3 17.5 - - + -
159C LYS* 3.0 37.2 + - + +
160C GLY* 3.8 6.7 - - - +
162C ALA* 1.3 78.3 - - - +
164C SER* 1.3 61.0 + - - +
166C LYS* 3.3 29.5 + - + +
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Residues in contact with SER 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C GLY 3.0 14.4 + - - -
161C ILE* 3.0 18.9 + - - +
163C LYS* 1.3 76.7 - - - +
165C ARG* 1.3 62.1 + - - +
166C LYS 3.3 5.0 + - - -
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Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 4.6 5.3 - - - -
129C GLU* 3.8 34.6 + - - +
130C GLU* 5.1 9.5 - - - +
133C LEU* 3.5 31.4 - - - +
161C ILE* 3.2 35.1 + - + +
162C ALA* 3.4 7.2 + - - +
163C LYS 3.2 0.6 - - - -
164C SER* 1.3 78.2 - - - +
166C LYS* 1.3 65.0 + - - +
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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