Contacts of the helix formed by residues 154 - 168 (chain A) in PDB entry 2MGX
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 SER 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A LYS 3.6 1.9 + - - -
153A LEU* 1.3 75.6 - - - +
155A ILE* 1.3 66.8 + - - +
156A PRO* 3.9 4.3 - - - +
157A VAL* 3.1 18.2 + - - +
158A LYS* 3.5 4.9 + - - +
187A HIS* 3.0 24.1 + - - -
190A GLU* 2.6 36.4 + - - -
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Residues in contact with ILE 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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107A SER* 3.2 33.4 - - - +
108A GLU* 6.4 0.4 - - + -
153A LEU 3.7 1.9 + - - +
154A SER* 1.3 68.4 - - - +
156A PRO* 1.4 73.2 - - + +
158A LYS* 3.0 20.7 + - - +
159A LYS* 3.1 24.0 + - + +
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Residues in contact with PRO 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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154A SER* 3.5 12.8 - - - +
155A ILE* 1.4 96.7 - - + +
157A VAL* 1.3 57.9 + - + +
159A LYS* 3.4 17.6 + - + +
160A ARG* 3.0 51.5 + - + +
186A ASP* 6.6 0.2 - - + -
187A HIS* 4.0 20.6 - - + +
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Residues in contact with VAL 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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148A TRP* 6.5 0.2 - - + -
153A LEU* 4.5 18.6 - - + -
154A SER* 3.1 16.3 + - - +
155A ILE 3.1 0.2 + - - -
156A PRO* 1.3 77.9 - - + +
158A LYS* 1.3 64.4 + - + +
160A ARG* 4.0 1.0 - - - +
161A MET* 3.0 26.4 + - + +
183A LEU* 4.3 19.1 - - + +
187A HIS* 3.7 19.5 - - + +
190A GLU* 3.3 28.0 - - - +
191A VAL* 3.6 25.8 - - + -
194A TRP* 4.6 2.9 - - + -
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Residues in contact with LYS 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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108A GLU* 4.9 18.6 + - + +
109A ALA* 4.2 12.5 + - - +
148A TRP* 2.8 84.6 + - + +
152A LYS* 4.8 2.8 - - - +
153A LEU* 3.3 36.2 - - + +
154A SER 3.5 10.7 + - - +
155A ILE* 3.0 9.5 + - - +
157A VAL* 1.3 74.1 - - + +
159A LYS* 1.3 61.7 + - + +
161A MET 3.5 0.3 + - - -
162A ALA* 3.0 29.6 + - - +
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Residues in contact with LYS 159 (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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106A GLY 2.8 42.4 + - - +
107A SER* 4.0 12.9 - - - +
108A GLU* 4.6 2.2 - - - +
109A ALA* 5.6 2.2 - - - +
155A ILE* 3.1 40.7 + - + +
156A PRO* 3.6 14.6 - - - +
157A VAL 3.3 0.2 - - - -
158A LYS* 1.3 76.2 - - - +
160A ARG* 1.3 66.5 + - + +
162A ALA* 3.1 21.9 + - - +
163A LEU* 3.3 6.2 + - - +
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Residues in contact with ARG 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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156A PRO* 3.0 29.1 + - - +
157A VAL 4.3 0.2 - - - +
159A LYS* 1.3 83.2 - - + +
161A MET* 1.3 61.8 + - - +
163A LEU* 3.2 24.3 + - + +
164A LEU 3.5 4.2 + - - -
179A ILE* 3.6 18.2 - - + +
182A SER* 3.2 29.8 + - - -
183A LEU* 3.5 27.4 - - + +
186A ASP* 2.6 44.5 + - - +
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Residues in contact with MET 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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114A VAL* 3.4 35.0 - - + -
118A LEU* 3.9 26.5 - - + -
144A LEU* 4.4 19.7 - - + -
148A TRP* 4.1 10.5 - - + -
157A VAL* 3.0 24.0 + - + +
158A LYS* 3.9 5.6 - - - +
160A ARG* 1.3 74.8 - - - +
162A ALA* 1.3 62.8 + - - +
163A LEU 3.1 0.4 - - - -
164A LEU* 2.9 41.6 + - + +
165A VAL* 3.2 9.5 + - + -
179A ILE* 5.7 3.6 - - + -
183A LEU* 5.4 6.2 - - + +
194A TRP* 5.9 4.0 - - - +
198A VAL* 6.3 2.5 - - + -
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Residues in contact with ALA 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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106A GLY 6.0 3.1 - - - +
109A ALA* 3.7 23.8 - - + -
114A VAL* 5.1 2.5 - - + -
158A LYS 3.0 14.5 + - - +
159A LYS* 3.1 13.9 + - - +
161A MET* 1.3 78.4 - - - +
163A LEU* 1.3 59.6 + - - +
165A VAL* 3.2 23.9 + - + +
166A GLN* 3.2 19.2 + - - +
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Residues in contact with LEU 163 (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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159A LYS 3.3 5.3 + - - +
160A ARG* 3.2 17.7 + - + +
161A MET 3.1 0.4 - - - -
162A ALA* 1.3 76.7 - - - +
164A LEU* 1.3 66.5 + - - +
166A GLN* 3.0 27.6 + - + +
167A GLU* 3.3 19.9 + - + +
175A ALA 5.7 2.9 - - - +
178A ASP* 6.0 0.7 - - - +
179A ILE* 4.0 18.4 - - + -
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Residues in contact with LEU 164 (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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118A LEU* 4.6 3.8 - - + -
160A ARG 3.5 2.8 + - - -
161A MET* 2.9 37.6 + - + +
163A LEU* 1.3 81.9 - - - +
165A VAL* 1.3 53.6 + - - +
167A GLU* 3.1 7.2 + - - +
168A LEU* 2.7 65.5 + - + +
176A ALA* 4.5 19.7 - - + +
179A ILE* 3.5 38.6 - - + -
198A VAL* 4.1 23.6 - - + -
202A ILE* 6.0 0.2 - - + -
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Residues in contact with VAL 165 (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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113A ASP* 3.8 14.8 - - - +
114A VAL* 3.8 33.2 - - + +
117A PRO* 3.6 32.8 - - + +
118A LEU* 6.0 0.2 - - + -
161A MET* 3.5 21.1 - - + +
162A ALA* 3.2 15.9 + - - +
163A LEU 3.1 0.6 - - - -
164A LEU* 1.3 78.5 - - + +
166A GLN* 1.3 68.5 + - - +
168A LEU* 3.6 19.3 + - + +
169A SER* 3.9 8.8 + - - -
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Residues in contact with GLN 166 (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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113A ASP* 4.9 7.5 + - - -
162A ALA* 3.2 21.1 + - - +
163A LEU* 3.0 17.0 + - + +
165A VAL* 1.3 92.2 + - - +
167A GLU* 1.3 66.8 + - + +
169A SER* 2.9 20.0 + - - -
170A SER* 4.9 1.4 + - - -
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Residues in contact with GLU 167 (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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163A LEU* 3.3 24.7 + - + +
164A LEU* 3.1 8.4 + - - +
166A GLN* 1.3 81.4 - - + +
168A LEU* 1.3 57.7 + - - +
169A SER 3.1 5.2 - - - -
170A SER* 3.0 28.8 + - - +
172A ARG* 3.6 36.4 + - + +
175A ALA* 3.7 25.4 - - + +
176A ALA* 5.3 4.5 - - + +
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Residues in contact with LEU 168 (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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117A PRO* 3.3 44.2 - - + +
118A LEU* 3.7 21.1 - - + +
121A ALA* 3.8 20.9 - - + +
164A LEU* 2.7 34.5 + - + +
165A VAL* 3.7 12.1 - - + +
166A GLN 3.3 0.4 - - - -
167A GLU* 1.3 73.9 - - - +
169A SER* 1.3 58.6 + - - +
170A SER 3.1 13.2 + - - +
172A ARG 6.3 0.2 - - - -
173A TRP* 4.3 23.5 - - + -
201A LEU* 4.9 6.3 - - + -
202A ILE* 6.1 2.5 - - + -
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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