Contacts of the helix formed by residues 144 - 157 (chain A) in PDB entry 1MRA
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 GLY 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LEU 3.6 1.2 + - - -
143A ASP* 1.3 78.3 - - - +
145A VAL* 1.3 59.3 + - - -
146A LYS 3.4 1.3 - - - -
148A ALA* 2.8 34.7 + - - +
169A TYR* 2.9 27.8 + - - -
178A VAL* 4.1 2.2 - - - -
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Residues in contact with VAL 145 (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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144A GLY* 1.3 71.8 - - - +
146A LYS* 1.3 62.4 + - + +
148A ALA* 3.9 0.7 - - - +
149A THR* 2.5 34.0 + - - -
177A ALA* 4.2 13.9 - - + +
178A VAL* 3.9 30.1 - - + +
181A SER* 3.8 26.2 - - - +
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Residues in contact with LYS 146 (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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144A GLY 3.4 0.4 - - - -
145A VAL* 1.3 82.7 - - + +
147A LEU* 1.3 56.9 + - + +
149A THR* 3.1 6.6 + - - -
150A GLU* 2.8 67.7 + - - +
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Residues in contact with LEU 147 (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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20A TYR* 3.9 35.2 - - + +
23A HIS* 4.9 8.7 - - - +
143A ASP* 3.4 31.5 + - + +
144A GLY 3.8 1.0 + - - -
146A LYS* 1.3 81.2 - - + +
148A ALA* 1.3 61.6 + - - +
150A GLU* 3.8 18.8 - - + +
151A ARG* 2.8 57.8 + - + +
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Residues in contact with ALA 148 (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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140A HIS* 4.9 5.0 + - + -
143A ASP* 4.0 15.1 - - + +
144A GLY 2.8 23.6 + - - +
145A VAL 3.9 2.5 - - - +
147A LEU* 1.3 78.8 - - - +
149A THR* 1.3 62.6 + - - +
151A ARG* 3.5 3.5 + - - +
152A ALA* 3.2 23.4 + - - +
165A THR* 4.5 9.9 - - - +
178A VAL* 4.3 10.8 - - + -
182A ILE* 4.0 24.6 - - + +
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Residues in contact with THR 149 (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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145A VAL 2.5 23.6 + - - -
146A LYS* 3.5 4.9 - - - -
148A ALA* 1.3 76.5 - - - +
150A GLU* 1.3 64.8 + - - +
152A ALA* 3.3 2.9 + - - +
153A VAL* 3.3 24.3 + - + +
181A SER* 2.8 35.9 + - - +
182A ILE* 3.9 8.3 + - - +
184A GLN* 4.1 4.3 - - - +
185A ALA* 3.4 28.9 - - + -
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Residues in contact with GLU 150 (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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146A LYS* 2.8 65.0 + - - +
147A LEU* 3.3 22.1 + - + +
148A ALA 3.3 0.2 - - - -
149A THR* 1.3 77.9 - - - +
151A ARG* 1.3 58.4 + - + +
153A VAL* 3.0 23.3 - - + +
154A THR* 2.9 17.0 + - - -
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Residues in contact with ARG 151 (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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20A TYR* 2.8 68.0 - - + +
23A HIS* 4.7 1.2 - - - -
138A ASP* 4.9 0.2 - - - +
139A SER 4.4 1.4 + - - -
140A HIS* 2.8 70.9 + - + +
141A SER* 3.4 7.1 + - - +
143A ASP* 3.3 24.9 + - - -
147A LEU* 2.8 41.7 + - + +
148A ALA* 4.1 3.1 - - - +
150A GLU* 1.3 76.4 - - + +
152A ALA* 1.3 55.9 + - - +
154A THR* 3.5 8.0 + - - -
155A ALA* 3.2 18.9 + - - +
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Residues in contact with ALA 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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140A HIS* 4.1 0.6 - - + -
148A ALA 3.2 16.0 + - - +
149A THR* 3.9 4.0 - - - +
150A GLU 3.2 0.6 - - - -
151A ARG* 1.3 72.2 - - - +
153A VAL* 1.3 67.6 + - - +
154A THR 3.1 1.3 - - - -
155A ALA* 3.1 6.5 + - - +
156A ALA* 3.0 26.0 + - - +
163A VAL* 4.2 18.3 - - + +
182A ILE* 3.8 27.4 - - + -
185A ALA* 5.8 0.2 - - + -
186A VAL* 4.2 11.2 - - + +
190A PHE* 4.8 1.8 - - + -
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Residues in contact with VAL 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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149A THR* 3.3 13.9 - - + +
150A GLU* 3.0 20.6 - - - +
152A ALA* 1.3 75.4 - - - +
154A THR* 1.3 66.9 + - + +
156A ALA* 3.5 3.4 + - - +
157A GLU* 2.8 44.5 + - - +
185A ALA* 3.9 30.5 - - + +
186A VAL* 4.7 5.2 - - + -
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Residues in contact with THR 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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150A GLU 2.9 16.4 + - - +
151A ARG* 3.5 10.7 + - - -
152A ALA 3.1 0.2 - - - -
153A VAL* 1.3 81.3 - - + +
155A ALA* 1.4 48.4 + - - +
157A GLU* 2.7 43.3 + - + +
158A LEU* 2.8 31.6 + - + +
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Residues in contact with ALA 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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138A ASP* 4.2 12.8 - - + +
140A HIS* 4.3 0.2 - - + -
151A ARG 3.2 13.3 + - - +
152A ALA 3.1 6.4 + - - +
154A THR* 1.4 70.3 - - - +
156A ALA* 1.3 55.2 - - - +
158A LEU* 2.7 27.5 + - - -
159A GLY 3.1 0.3 + - - -
160A PHE* 3.0 36.3 + - + -
163A VAL* 3.3 34.1 - - + -
190A PHE* 4.8 0.7 - - + -
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Residues in contact with ALA 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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152A ALA 3.0 11.1 + - - +
153A VAL* 3.8 3.8 - - - +
155A ALA* 1.3 78.6 - - - +
157A GLU* 1.3 57.2 + - - +
159A GLY* 2.9 19.1 + - - -
160A PHE 3.4 14.2 + - - +
186A VAL* 4.8 8.7 - - + -
190A PHE* 3.5 24.7 - - + -
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Residues in contact with GLU 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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153A VAL* 2.8 30.2 + - - +
154A THR* 2.7 32.5 + - + +
156A ALA* 1.3 75.9 - - - +
158A LEU* 1.3 58.1 + - + +
159A GLY 3.1 3.0 + - - -
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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