Contacts of the helix formed by residues 132 - 139 (chain M) in PDB entry 6CNB
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 ASN 132 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30I PRO* 5.2 0.2 - - - +
31I TYR 4.8 1.1 - - - +
32I GLU* 3.1 38.7 + - + +
127M GLU* 5.3 0.2 + - - -
130M PHE 3.7 1.8 - - - -
131M TYR* 1.3 86.2 - - - +
133M LYS* 1.3 66.4 + - - +
134M ASP* 3.0 29.9 + - - +
135M LYS* 3.1 40.4 + - + +
136M ALA 3.5 5.7 + - - -
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Residues in contact with LYS 133 (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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127M GLU* 3.2 27.0 + - - +
131M TYR* 3.3 20.1 - - + -
132M ASN* 1.3 72.5 - - - +
134M ASP* 1.3 61.7 + - - +
135M LYS 3.3 0.2 - - - -
136M ALA* 3.0 5.1 + - + -
137M GLU* 2.5 48.4 + - + +
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Residues in contact with ASP 134 (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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18I ASP* 5.3 5.0 - - - +
132M ASN* 3.0 21.1 - - - +
133M LYS* 1.3 86.0 - - - +
135M LYS* 1.3 50.5 + - - +
137M GLU* 3.0 8.0 + - - +
138M SER* 2.4 39.0 + - - -
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Residues in contact with LYS 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I CYS 4.7 1.7 + - - +
27I ARG* 5.0 4.4 - - - +
28I SER* 3.6 14.1 - - - +
29I CYS* 3.4 22.6 + - - +
30I PRO* 3.2 46.2 - - + -
31I TYR 5.0 0.9 - - - +
32I GLU* 6.0 0.4 - - - +
132M ASN* 3.1 28.4 + - + +
134M ASP* 1.3 77.6 - - - +
136M ALA* 1.3 61.5 + - - +
138M SER* 2.4 29.6 + - - +
140M TRP* 3.0 56.6 + - + +
183M PHE* 5.4 0.9 - - - -
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Residues in contact with ALA 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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30I PRO* 6.0 0.6 - - - +
131M TYR* 3.0 34.1 - - + +
132M ASN 3.5 2.6 + - - -
133M LYS* 3.0 9.9 + - + +
135M LYS* 1.3 78.9 - - - +
137M GLU* 1.3 65.3 + - - +
140M TRP* 2.8 20.9 - - - +
141M ASN* 2.8 21.0 - - + +
142M GLY* 3.3 15.5 - - - +
143M VAL* 3.8 6.7 - - + +
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Residues in contact with GLU 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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133M LYS* 2.5 36.0 + - + +
134M ASP* 3.0 8.7 - - - +
136M ALA* 1.3 80.1 - - + +
138M SER* 1.3 66.1 + - - +
139M GLU 5.3 0.4 - - - -
141M ASN* 4.7 9.8 - - - +
143M VAL* 5.7 4.7 - - - +
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Residues in contact with SER 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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134M ASP 2.4 23.6 + - - -
135M LYS* 2.4 29.7 + - - -
137M GLU* 1.3 75.9 - - - +
139M GLU* 1.3 71.9 + - - +
140M TRP* 4.0 16.1 - - - -
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Residues in contact with GLU 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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135M LYS 3.8 0.2 + - - -
136M ALA 4.7 0.4 - - - -
138M SER* 1.3 90.5 + - - +
140M TRP* 1.3 84.4 + - + +
141M ASN* 3.8 10.2 + - - +
188M ASP* 3.2 31.5 - - + +
189M ALA* 5.4 2.2 - - - +
192M THR* 4.3 22.7 - - + +
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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