Contacts of the helix formed by residues 151 - 162 (chain P) in PDB entry 3HAE
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 151 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147P TRP 3.3 1.2 + - - -
148P GLU 3.0 20.9 + - - -
149P ALA* 3.1 25.7 - - - -
150P ALA* 1.3 77.9 - - - +
152P VAL* 1.3 64.2 + - - +
153P ALA* 3.2 4.5 + - - -
154P GLU* 3.0 45.2 + - + +
155P GLN* 3.8 4.0 + - - +
65T LYS* 4.3 25.6 - - + +
66T GLY* 6.3 2.9 - - - -
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Residues in contact with VAL 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P TRP* 4.4 14.1 - - + -
147P TRP* 3.0 37.8 + - + +
150P ALA* 3.9 19.7 - - + +
151P HIS* 1.3 77.0 - - - +
153P ALA* 1.3 63.0 + - - +
155P GLN* 3.1 19.0 + - + +
156P LEU* 3.1 24.6 + - + +
7R THR* 3.5 37.0 - - + +
96S SER* 5.7 2.0 - - - -
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Residues in contact with ALA 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P LEU* 4.3 9.3 - - + +
130P LEU 4.2 11.8 - - - +
131P ARG* 4.0 21.3 - - - +
133P TRP* 3.9 24.6 - - - +
147P TRP 4.5 1.6 + - - -
151P HIS 3.2 1.2 + - - -
152P VAL* 1.3 76.2 - - - +
154P GLU* 1.3 66.8 + - - +
156P LEU* 3.0 4.2 + - - +
157P ARG* 2.7 38.2 + - - +
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Residues in contact with GLU 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P LEU 5.5 0.2 - - - +
131P ARG* 5.0 4.5 - - - +
151P HIS* 3.0 45.5 + - + +
153P ALA* 1.3 85.6 + - - +
155P GLN* 1.3 61.7 + - - +
157P ARG* 3.4 11.4 + - - +
158P ALA* 3.1 24.1 + - - +
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Residues in contact with GLN 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P HIS 3.8 3.3 + - - +
152P VAL* 3.1 21.3 + - + +
153P ALA 3.1 0.4 - - - -
154P GLU* 1.3 77.1 - - - +
156P LEU* 1.3 67.1 - - - +
158P ALA* 3.2 14.4 + - - +
159P TYR* 3.2 12.4 + - - +
3R LEU* 5.4 5.1 - - + +
5R TRP* 3.8 36.7 + - + +
7R THR* 4.4 13.9 + - - -
96S SER* 4.3 11.1 - - - +
56T GLY 5.3 4.7 - - - +
57T GLY 4.7 1.3 - - - +
58T THR* 3.3 28.1 - - - +
59T ALA* 4.0 15.6 - - - +
65T LYS* 5.5 4.9 + - - -
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Residues in contact with LEU 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P HIS* 3.6 38.1 - - + +
126P LEU* 3.9 10.8 - - + -
133P TRP* 3.8 26.0 - - + -
152P VAL* 3.1 12.4 + - + +
153P ALA* 3.0 9.1 + - - +
155P GLN* 1.3 78.3 - - - +
157P ARG* 1.3 52.3 - - - +
159P TYR* 3.0 8.4 + - + +
160P LEU* 2.8 55.0 + - + +
3R LEU* 3.4 35.0 - - + +
5R TRP 5.7 0.7 - - - +
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Residues in contact with ARG 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P ASP 4.7 3.9 + - - -
130P LEU* 3.7 34.2 + - + +
131P ARG* 3.7 29.5 - - - +
153P ALA 2.7 21.1 + - - +
154P GLU* 3.5 10.3 - - - +
156P LEU* 1.3 72.0 - - - +
158P ALA* 1.3 59.3 + - + +
159P TYR 3.2 0.2 + - - -
160P LEU* 3.2 4.1 + - - +
161P GLU* 2.7 74.0 + - - +
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Residues in contact with ALA 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154P GLU 3.1 12.9 + - - +
155P GLN* 3.2 9.8 + - - +
157P ARG* 1.3 77.7 - - - +
159P TYR* 1.3 63.4 + - - +
161P GLU* 4.6 2.9 - - - +
162P GLY* 3.1 22.1 + - - +
163P THR* 3.6 3.5 + - - -
56T GLY* 4.9 19.8 - - - +
58T THR* 5.6 3.4 - - - +
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Residues in contact with TYR 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P MET* 4.6 5.4 - - - +
7P TYR* 4.4 4.5 - - - -
99P TYR* 3.5 30.0 - + - -
155P GLN 3.2 8.8 + - - +
156P LEU* 3.0 9.5 + - - +
158P ALA* 1.3 76.9 - - - +
160P LEU* 1.3 78.0 + - + +
163P THR* 2.9 35.1 + - + -
164P CYS* 2.8 47.2 + - + -
1R SER 2.4 30.9 + - - -
2R LEU* 3.7 2.6 - - - -
3R LEU* 3.5 50.8 + - + -
4R MET 5.3 0.2 - - - -
56T GLY* 5.7 1.5 - - - -
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P TYR* 4.4 5.2 - - + -
100P GLY 3.5 25.6 - - - +
101P CYS* 3.8 2.4 - - - +
109P PHE* 3.7 6.2 - - - -
112P GLY* 4.4 11.7 - - - -
113P TYR 3.6 29.4 - - - +
126P LEU* 3.8 26.9 - - + -
130P LEU* 4.0 10.5 - - + -
156P LEU* 2.8 32.5 + - + +
157P ARG* 4.0 2.9 - - - +
159P TYR* 1.3 98.2 - - + +
161P GLU* 1.3 59.4 + - - +
164P CYS* 3.5 16.1 - - - +
165P VAL* 3.5 12.1 - - - +
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Residues in contact with GLU 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLN* 5.2 12.4 + - - +
109P PHE* 3.8 30.2 - - + +
130P LEU* 4.0 22.7 - - + +
157P ARG* 2.7 67.6 + - - +
158P ALA* 4.6 2.5 - - - +
160P LEU* 1.3 71.7 - - - +
162P GLY* 1.3 59.3 + - - +
165P VAL* 3.3 17.6 - - - +
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Residues in contact with GLY 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158P ALA 3.1 13.1 + - - -
161P GLU* 1.3 81.4 - - - +
163P THR* 1.3 65.4 + - - +
164P CYS 3.2 1.1 - - - -
165P VAL* 3.0 10.5 + - - +
166P GLU* 2.9 35.3 + - - +
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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