Contacts of the helix formed by residues 134 - 142 (chain M) in PDB entry 6O81
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 ALA 134 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7M PHE 5.8 1.1 - - - +
107M VAL* 5.6 3.8 - - + -
111M LEU* 4.5 15.0 - - + -
130M PHE* 3.0 14.4 + - + +
133M THR* 1.3 73.4 - - - +
135M TRP* 1.3 72.7 + - + +
136M VAL 3.3 1.8 - - - -
137M PHE* 3.3 5.1 + - - +
138M ASP* 3.0 26.4 + - - +
148M ALA* 3.8 25.5 - - + +
152M PHE* 4.5 10.1 - - + -
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Residues in contact with TRP 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M CYS* 4.0 5.6 - - - -
6M ARG* 3.8 47.8 - - + -
7M PHE 3.3 19.5 + - - -
8M TYR* 3.2 24.7 - + - -
9M GLN* 3.6 36.8 - - + +
127M GLU* 4.1 13.9 - - + -
130M PHE* 3.2 28.0 + + + -
131M GLN* 3.6 36.1 - - + +
134M ALA* 1.3 80.9 - - + +
136M VAL* 1.3 60.3 + - - +
138M ASP* 3.7 8.5 - - + +
139M ASP* 2.9 31.0 + - - +
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Residues in contact with VAL 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M GLN 3.6 18.0 + - - +
132M ARG* 4.6 12.3 - - - +
133M THR 5.0 2.2 - - - +
134M ALA 3.3 0.8 - - - +
135M TRP* 1.3 77.8 - - - +
137M PHE* 1.3 59.6 + - + +
139M ASP* 3.4 5.7 + - - +
140M LYS* 2.9 29.7 + - - +
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Residues in contact with PHE 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132M ARG 6.0 0.9 - - - -
133M THR* 3.3 22.0 - - - +
134M ALA 3.3 8.0 + - - +
136M VAL* 1.3 79.9 - - + +
138M ASP* 1.3 58.7 + - - +
140M LYS* 4.3 6.5 - - + -
141M TYR* 2.9 53.9 + + - +
147M GLY 4.4 7.6 - - - +
148M ALA* 4.4 4.0 - - - -
151M ALA* 3.7 31.9 - - + -
152M PHE* 5.4 7.0 - + - -
161M ILE* 3.7 37.7 - - + -
162M LEU* 5.9 0.9 - - - -
164M SER* 5.6 4.5 - - - -
165M LEU* 6.1 4.9 - - + -
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Residues in contact with ASP 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M TYR* 6.0 2.2 - - + -
9M GLN* 4.3 12.1 - - - +
134M ALA 3.0 16.6 + - - +
135M TRP* 3.7 12.3 - - + +
136M VAL 3.3 0.2 - - - -
137M PHE* 1.3 78.6 - - - +
139M ASP* 1.3 56.2 + - - +
142M LYS* 3.1 20.6 + - - -
143M ARG 3.2 28.8 + - - +
144M PRO* 4.2 11.4 - - + -
145M GLY 4.8 3.4 - - - +
148M ALA* 4.8 7.8 - - + +
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Residues in contact with ASP 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M GLN* 5.2 9.1 + - + +
135M TRP 2.9 17.4 + - - +
136M VAL* 3.9 5.2 - - - +
138M ASP* 1.3 74.4 - - - +
140M LYS* 1.3 64.4 + - - +
142M LYS* 3.8 9.3 + - - +
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Residues in contact with LYS 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M VAL 2.9 17.7 + - - +
137M PHE* 3.3 11.4 + - + +
139M ASP* 1.3 80.5 - - - +
141M TYR* 1.3 72.0 + - + +
142M LYS* 5.0 0.9 - - - +
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Residues in contact with TYR 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137M PHE* 2.9 44.8 + + - +
140M LYS* 1.3 86.2 - - + +
142M LYS* 1.3 69.5 + - - +
143M ARG* 3.3 8.3 + - + +
147M GLY* 3.8 32.5 - - - -
150M ASP* 5.5 4.3 - - + -
151M ALA* 4.4 9.2 - - + -
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Residues in contact with LYS 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M ASP 3.1 11.1 + - - -
139M ASP* 3.8 7.9 + - - +
140M LYS 3.3 4.3 - - - +
141M TYR* 1.3 79.7 - - - +
143M ARG* 1.3 57.6 + - - +
144M PRO 4.3 0.4 - - - -
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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