Contacts of the helix formed by residues 151 - 162 (chain A) in PDB entry 3MRR
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A TRP 3.1 5.8 + - - -
148A GLU* 3.2 13.2 + - - +
149A ALA* 3.3 17.9 + - - -
150A ALA* 1.3 78.0 - - - +
152A VAL* 1.3 64.4 + - - +
153A ALA 3.4 2.0 - - - -
154A GLU* 3.3 41.1 + - + +
155A GLN* 3.4 18.9 + - + +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A TRP* 3.8 15.0 - - + -
147A TRP* 3.0 40.1 + - + +
150A ALA* 4.2 12.8 - - + +
151A HIS* 1.3 74.4 - - - +
153A ALA* 1.3 67.4 + - - +
155A GLN* 3.1 16.0 + - - +
156A LEU* 3.0 27.1 + - + +
6P GLY* 3.6 26.9 - - - +
8P VAL* 3.6 27.1 - - + -
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.9 19.9 - - + +
130A LEU 3.6 12.5 - - - +
131A ARG* 3.9 16.4 - - - +
133A TRP* 3.7 29.0 - - - +
151A HIS 3.4 0.4 - - - -
152A VAL* 1.3 79.3 - - - +
154A GLU* 1.3 63.3 + - - +
156A LEU* 3.3 3.6 + - - +
157A ARG* 2.8 32.1 + - - +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 5.2 5.4 - - - +
148A GLU 5.4 0.3 - - - +
151A HIS* 3.3 45.8 + - + +
153A ALA* 1.3 82.9 + - - +
155A GLN* 1.3 61.6 + - + +
157A ARG* 3.5 7.2 + - - +
158A ALA* 3.2 23.4 + - - +
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Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA 4.4 7.2 + - - +
151A HIS* 3.4 13.2 - - + +
152A VAL* 3.1 19.7 + - - +
154A GLU* 1.3 75.6 - - + +
156A LEU* 1.3 63.7 - - - +
158A ALA* 3.4 8.0 + - - +
159A TYR* 3.2 20.1 + - - +
5P ILE* 4.5 36.6 - - + +
6P GLY* 3.6 30.1 + - - +
8P VAL* 5.8 1.6 - - - +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 5.9 0.7 - - + -
114A HIS* 3.6 42.0 - - + +
126A LEU* 4.2 12.8 - - + -
133A TRP* 3.6 32.1 - - + -
152A VAL* 3.0 23.3 + - + +
153A ALA 3.8 3.6 - - - +
155A GLN* 1.3 74.7 - - - +
157A ARG* 1.3 58.5 + - - +
159A TYR* 3.2 8.1 + - + +
160A LEU* 2.8 40.3 + - + +
3P ALA* 5.1 10.3 - - + -
5P ILE 4.2 6.1 - - - +
6P GLY* 3.9 24.7 - - - +
7P THR* 5.5 0.9 - - - +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP 4.4 7.0 + - - -
130A LEU* 3.7 37.7 - - + +
131A ARG* 3.2 42.9 - - - +
153A ALA 2.8 21.9 + - - +
154A GLU* 3.8 7.9 - - - +
156A LEU* 1.3 72.7 - - - +
158A ALA* 1.3 57.9 + - - +
161A GLU* 2.9 73.4 + - - +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU 3.2 13.7 + - - +
155A GLN* 3.5 11.4 - - - +
157A ARG* 1.3 76.9 - - - +
159A TYR* 1.3 61.7 + - - +
161A GLU* 4.6 2.0 - - - +
162A GLY* 3.1 22.7 + - - -
163A THR* 3.8 2.7 + - - -
5P ILE* 6.3 2.0 - - + -
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A MET* 3.9 11.6 - - - +
7A TYR* 3.9 3.6 - - - -
99A TYR* 3.6 26.0 - + - -
100A GLY* 5.5 0.2 - - - -
155A GLN 3.2 9.8 + - - +
156A LEU* 3.2 11.1 + - + +
158A ALA* 1.3 79.8 - - - +
160A LEU* 1.3 83.3 + - + +
163A THR* 3.2 35.8 + - + -
164A CYS* 2.8 49.0 + - + -
1P LEU 2.7 29.1 + - - -
2P LEU 3.7 3.1 - - - -
3P ALA* 3.5 37.5 - - + -
4P GLY 5.0 0.7 - - - -
5P ILE* 5.2 4.9 - - + +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 4.7 3.4 - - + -
100A GLY 3.3 31.2 - - - +
101A CYS* 3.6 13.3 - - - +
109A PHE* 3.6 15.1 - - - -
112A GLY* 4.5 6.3 - - - -
113A TYR 3.7 23.6 - - - +
114A HIS* 4.7 2.2 - - + -
126A LEU* 3.8 28.7 - - + -
130A LEU* 4.1 15.9 - - + -
156A LEU* 2.8 31.8 + - + +
157A ARG 4.1 2.0 - - - +
159A TYR* 1.3 97.4 - - + +
161A GLU* 1.3 60.0 + - - +
164A CYS* 3.7 5.7 - - - +
165A VAL* 3.8 2.6 - - - +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.8 40.0 - - + +
129A ASP 5.3 0.7 - - - +
130A LEU* 3.9 11.4 - - + +
157A ARG* 2.9 60.9 + - - +
158A ALA* 4.6 1.7 - - - +
160A LEU* 1.3 76.2 - - - +
162A GLY* 1.3 56.9 + - - +
165A VAL* 3.1 18.1 - - - +
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ALA 3.1 14.4 + - - -
161A GLU* 1.3 77.9 - - - +
163A THR* 1.3 66.6 + - - +
164A CYS 3.3 0.7 - - - -
165A VAL* 3.0 9.3 - - - +
166A GLU* 3.0 25.0 + - - +
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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