Contacts of the helix formed by residues 172 - 186 (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 LEU 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ALA* 1.3 71.5 - - - +
173A ASP* 1.3 62.5 + - - +
175A ASP* 3.2 9.0 + - + -
176A LEU* 3.1 35.8 + - + +
196A TYR* 4.5 0.7 - - - +
207A LYS* 4.5 22.0 - - + +
208A ARG* 3.4 59.1 - - + +
211A ALA* 3.9 26.7 - - + -
212A LEU* 5.1 1.1 - - + -
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Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 2.9 10.1 + - + +
172A LEU* 1.3 81.0 - - - +
174A GLN* 1.3 59.2 + - + +
176A LEU* 3.5 17.3 + - - +
177A ALA* 3.0 25.5 + - - +
180A ARG* 5.4 2.3 + - - -
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Residues in contact with GLN 174 (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* 5.3 0.2 - - - +
169A TYR* 3.3 32.8 - - + +
170A PRO* 3.5 19.3 - - - +
171A ALA* 2.7 43.7 + - + +
173A ASP* 1.3 76.2 - - + +
175A ASP* 1.3 67.6 + - - +
177A ALA* 3.1 7.3 + - - +
178A VAL* 3.0 28.5 + - + +
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.4 12.0 - - + +
168A GLY 2.8 11.7 + - - -
169A TYR* 2.8 31.5 + - - -
171A ALA 3.4 0.6 + - - -
172A LEU* 3.2 13.4 + - + +
174A GLN* 1.3 78.0 - - - +
176A LEU* 1.3 62.1 + - - +
178A VAL* 3.5 4.7 + - - +
179A VAL* 3.1 23.8 + - - +
196A TYR* 2.6 29.1 + - - +
208A ARG* 2.4 32.4 + - - -
212A LEU* 4.8 6.3 - - + -
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Residues in contact with LEU 176 (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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172A LEU* 3.1 29.5 + - + +
173A ASP* 3.7 18.2 - - - +
175A ASP* 1.3 78.5 - - - +
177A ALA* 1.3 54.0 + - - +
179A VAL* 3.0 3.9 + - - +
180A ARG* 2.8 69.9 + - - +
211A ALA* 4.3 19.1 - - + -
212A LEU* 3.5 26.2 - - + +
215A GLU* 3.7 23.1 - - + +
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Residues in contact with ALA 177 (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* 4.2 17.9 - - + +
173A ASP 3.0 16.7 + - - +
174A GLN* 3.1 12.5 + - - +
176A LEU* 1.3 76.1 - - - +
178A VAL* 1.3 65.2 + - - +
180A ARG* 3.7 7.8 - - - +
181A SER* 3.0 24.1 + - - -
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Residues in contact with VAL 178 (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 4.1 0.2 - - - -
145A VAL* 3.9 30.9 - - + +
148A ALA* 4.3 9.0 - - + -
149A THR* 4.9 0.3 + - - -
165A THR* 4.3 19.3 - - + +
167A ILE* 4.7 6.1 - - + -
169A TYR* 3.4 38.1 - - + +
174A GLN* 3.0 6.0 + - + +
175A ASP 3.5 9.0 - - - +
177A ALA* 1.3 81.9 - - - +
179A VAL* 1.3 65.7 + - + +
180A ARG 3.4 0.2 + - - -
181A SER* 3.5 2.2 + - - -
182A ILE* 3.3 36.7 + - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A THR* 4.7 2.2 - - + -
167A ILE* 4.6 8.7 - - + -
175A ASP 3.1 13.3 + - - +
176A LEU* 3.0 9.3 + - - +
178A VAL* 1.3 86.9 - - + +
180A ARG* 1.3 60.9 + - - +
182A ILE* 3.6 5.9 + - - +
183A ARG* 3.2 21.4 + - + +
192A ILE* 4.1 18.0 - - + +
194A VAL* 3.9 28.0 - - + -
212A LEU* 4.7 7.2 - - + -
215A GLU* 4.1 27.6 - - + +
217A VAL* 4.2 15.0 - - + -
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Residues in contact with ARG 180 (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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173A ASP* 5.4 2.8 + - - -
176A LEU* 2.8 55.2 + - - +
177A ALA* 3.8 5.8 - - - +
179A VAL* 1.3 71.4 - - - +
181A SER* 1.3 60.9 - - - +
183A ARG* 3.2 6.9 + - - +
184A GLN* 2.9 30.0 + - - +
215A GLU* 2.3 52.3 + - + +
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Residues in contact with SER 181 (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* 3.8 20.8 - - - +
149A THR* 2.8 28.3 + - - +
177A ALA 3.0 15.2 + - - -
178A VAL 4.1 2.2 - - - -
179A VAL 3.4 0.2 - - - -
180A ARG* 1.3 77.4 - - - +
182A ILE* 1.3 62.3 + - - +
184A GLN* 2.9 40.9 + - - +
185A ALA* 3.1 5.5 + - - +
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Residues in contact with ILE 182 (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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148A ALA* 4.0 28.5 - - + +
149A THR* 4.0 13.0 - - - +
152A ALA* 3.8 23.3 - - + -
163A VAL* 4.5 12.1 - - + -
165A THR* 3.9 30.5 - - + -
178A VAL* 3.3 17.6 + - + +
179A VAL* 3.9 6.5 - - - +
180A ARG 3.2 0.2 - - - -
181A SER* 1.3 76.9 - - - +
183A ARG* 1.3 58.8 + - - +
185A ALA* 3.1 7.3 + - - +
186A VAL* 2.8 34.3 + - + +
192A ILE* 4.0 22.2 - - + -
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Residues in contact with ARG 183 (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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179A VAL* 3.2 14.9 + - + +
180A ARG* 3.2 8.6 + - - +
182A ILE* 1.3 80.6 - - - +
184A GLN* 1.3 56.2 + - - +
186A VAL* 4.4 2.7 - - - +
187A GLY* 2.6 59.6 + - - -
188A ASP* 3.6 33.4 + - - +
190A PHE* 2.7 28.5 + - - +
192A ILE* 3.2 38.8 - - + +
215A GLU 4.6 11.4 + - - +
216A GLY* 3.3 24.5 + - - -
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Residues in contact with GLN 184 (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* 4.1 6.7 - - - +
180A ARG 2.9 13.1 + - - +
181A SER* 2.9 36.3 + - - +
183A ARG* 1.3 78.2 - - - +
185A ALA* 1.3 86.9 + - - +
186A VAL 3.2 0.7 + - - -
187A GLY* 3.8 4.2 + - - -
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Residues in contact with ALA 185 (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* 3.4 18.8 - - + +
152A ALA* 5.8 0.2 - - + -
153A VAL* 3.9 22.0 - - + +
181A SER 3.1 9.4 + - - +
182A ILE* 3.1 6.3 + - - +
184A GLN* 1.3 101.9 - - - +
186A VAL* 1.3 63.4 + - + +
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Residues in contact with VAL 186 (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* 4.2 32.3 - - + +
153A VAL* 4.5 4.5 - - - +
156A ALA* 4.8 8.1 - - + -
182A ILE* 2.8 27.8 + - + +
183A ARG* 4.3 3.8 - - - +
184A GLN 4.4 0.2 - - - -
185A ALA* 1.3 88.1 - - + +
187A GLY* 1.3 63.7 + - - +
189A ASP 5.2 1.7 + - - +
190A PHE* 3.4 48.6 - - + +
192A ILE* 5.1 0.9 - - + -
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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