Contacts of the helix formed by residues 149 - 162 (chain A) in PDB entry 1MUG
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.8 29.9 - - + +
39A LYS* 3.5 43.5 - - + +
40A VAL* 3.6 29.6 - - + -
43A GLN* 4.1 6.3 - - - +
148A SER* 1.3 73.0 - - - +
150A GLU* 1.3 56.8 + - - +
152A LEU* 3.3 4.5 + - - +
153A VAL* 2.9 44.2 + - + +
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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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148A SER* 3.1 11.0 + - - +
149A LEU* 1.3 79.9 - - - +
151A LYS* 1.3 67.0 + - + +
153A VAL* 3.3 6.9 + - - +
154A GLU* 3.0 43.5 + - + +
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Residues in contact with LYS 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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139A PRO* 4.9 1.4 - - - +
147A VAL* 3.6 24.0 - - + +
148A SER* 3.1 19.6 + - - +
150A GLU* 1.3 82.8 - - + +
152A LEU* 1.3 62.9 + - - +
154A GLU* 3.4 18.1 + - - +
155A ALA* 3.0 25.6 + - - +
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Residues in contact with LEU 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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36A ARG* 3.5 43.5 - - + +
40A VAL* 3.8 29.4 - - + -
139A PRO* 3.7 22.7 - - + +
140A ASN 4.1 7.0 - - - +
141A PRO* 4.0 11.0 - - + -
147A VAL* 3.4 33.2 - - + -
148A SER 3.1 8.0 + - - +
149A LEU* 3.4 9.2 - - - +
151A LYS* 1.3 77.0 - - - +
153A VAL* 1.3 62.8 + - - +
155A ALA* 3.2 2.4 + - - +
156A TYR* 3.0 36.3 + - + -
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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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40A VAL* 4.2 17.0 - - - -
43A GLN* 3.9 50.0 - - + +
44A ALA* 4.0 3.1 - - - +
149A LEU* 2.9 39.1 + - + +
150A GLU* 3.8 5.8 - - - +
152A LEU* 1.3 72.8 - - - +
154A GLU* 1.3 57.5 + - + +
157A ARG* 2.9 55.4 + - - +
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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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150A GLU* 3.0 38.5 + - + +
151A LYS* 3.6 19.3 - - - +
153A VAL* 1.3 77.3 - - - +
155A ALA* 1.3 62.2 + - - +
157A ARG* 3.4 30.2 + - - +
158A GLU* 3.1 22.2 + - - +
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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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136A TRP* 5.2 0.5 - - - -
138A LEU* 3.7 16.0 - - + +
139A PRO* 3.8 29.8 - - + -
151A LYS 3.0 16.9 + - - +
152A LEU 3.7 2.9 - - - +
154A GLU* 1.3 76.9 - - - +
156A TYR* 1.3 62.9 + - + +
158A GLU* 3.4 22.6 + - - +
159A LEU 3.7 2.8 + - - -
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Residues in contact with TYR 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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14A PHE* 4.1 18.2 - + - -
37A PHE* 4.6 7.0 - + - -
40A VAL* 3.6 22.2 - - + -
41A ILE* 4.1 13.9 - - + -
44A ALA* 3.7 18.4 - - + -
46A PHE* 3.4 8.9 - + + -
107A LEU* 3.4 18.8 - - + +
138A LEU* 3.8 31.4 - - + -
139A PRO* 2.8 34.7 + - + -
141A PRO* 3.4 23.3 - - + +
152A LEU* 3.0 34.0 + - + +
155A ALA* 1.3 77.1 - - + +
157A ARG* 1.3 65.2 + - - +
159A LEU* 3.1 15.6 + - - +
160A ASP 3.1 9.9 + - - -
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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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43A GLN 4.8 9.2 + - - -
44A ALA* 3.5 27.0 - - + +
153A VAL* 2.9 41.4 + - - +
154A GLU* 3.5 34.5 + - - +
155A ALA 3.3 0.2 - - - -
156A TYR* 1.3 73.5 - - - +
158A GLU* 1.3 65.3 + - - +
160A ASP* 3.7 0.4 - - - +
161A GLN* 2.9 56.5 + - + +
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Residues in contact with GLU 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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124A GLY* 5.0 7.9 - - - -
125A LYS* 5.0 4.2 + - - +
136A TRP* 3.5 25.6 - - + -
154A GLU 3.1 13.5 + - - +
155A ALA* 3.5 16.1 - - - +
156A TYR 3.2 0.2 - - - -
157A ARG* 1.3 76.7 - - - +
159A LEU* 1.3 58.3 + - - +
161A GLN* 3.5 11.3 + - - +
162A ALA* 3.1 27.0 + - - +
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Residues in contact with LEU 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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12A VAL* 4.0 15.7 - - + -
14A PHE* 4.7 0.4 - - + -
46A PHE* 3.9 15.9 - - + -
103A ALA* 4.2 6.1 - - + -
105A ALA* 3.9 27.4 - - + -
136A TRP* 3.6 52.4 - - + +
138A LEU* 4.1 10.5 - - + -
155A ALA 3.7 3.9 + - - +
156A TYR* 3.1 11.7 + - - +
158A GLU* 1.3 77.3 - - - +
160A ASP* 1.3 67.3 + - - +
162A ALA* 3.0 9.7 + - - +
163A LEU* 3.2 31.3 + - + +
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Residues in contact with ASP 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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11A ARG* 2.9 51.4 + - - +
44A ALA 3.2 28.7 - - - +
45A GLY* 3.5 22.6 - - - +
46A PHE* 3.5 23.2 + - + -
156A TYR 3.1 6.4 + - - +
157A ARG 3.7 4.5 - - - +
159A LEU* 1.3 75.0 - - - +
161A GLN* 1.3 68.6 + - - +
163A LEU 3.4 6.4 - - - +
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Residues in contact with GLN 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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157A ARG* 2.9 50.5 + - + +
158A GLU* 4.0 7.4 - - - +
160A ASP* 1.3 79.7 - - - +
162A ALA* 1.3 63.0 + - - +
163A LEU 3.3 0.6 + - - -
164A VAL* 4.2 14.7 + - - +
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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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134A GLN* 5.2 5.0 + - - +
136A TRP* 3.6 27.6 - - + -
158A GLU 3.1 16.7 + - - +
159A LEU 3.0 6.6 + - - +
161A GLN* 1.3 78.8 - - - +
163A LEU* 1.3 64.5 + - + +
164A VAL* 3.5 10.3 + - - +
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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