Contacts of the helix formed by residues 132 - 136 (chain M) in PDB entry 2W4G
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 132 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16M TYR* 4.4 16.4 - - + -
113M TRP* 4.4 19.5 - - + +
115M ILE* 4.4 28.9 - - + -
128M PRO* 3.6 25.8 - - + -
130M LYS* 3.7 16.1 + - + +
131M TRP* 1.3 120.4 + - - +
133M PRO* 1.3 70.0 - - + +
134M VAL* 2.8 32.4 + - + +
135M TYR* 4.0 14.0 + - + +
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Residues in contact with PRO 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M GLU* 3.9 14.1 - - + +
13M ALA* 3.5 17.4 - - - +
16M TYR* 3.2 42.2 - - + +
131M TRP* 3.5 17.4 - - + +
132M LEU* 1.3 85.8 - - + +
134M VAL* 1.3 56.4 + - - -
135M TYR 3.4 1.6 - - - -
136M ASN* 2.8 44.9 - - - +
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Residues in contact with VAL 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M ALA* 4.6 5.8 - - + -
16M TYR* 4.2 18.2 - - + +
17M LEU* 4.3 13.2 - - + -
115M ILE* 5.1 1.8 - - + -
116M TYR* 3.9 11.7 - - + -
132M LEU* 2.8 29.9 + - + -
133M PRO* 1.3 76.5 - - + +
135M TYR* 1.3 80.1 + - + +
136M ASN 2.8 8.6 + - - -
139M VAL* 3.7 9.2 - - + +
154M HIS* 3.0 44.5 - - + +
156M PHE* 3.6 3.8 - - - -
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Residues in contact with TYR 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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115M ILE* 4.3 11.2 - - + +
116M TYR* 2.7 29.2 + - - -
125M THR* 5.7 1.2 - - - +
128M PRO* 5.6 4.6 - - + +
131M TRP* 6.3 2.0 - - + +
132M LEU* 4.0 12.6 + - + +
133M PRO 3.4 0.6 - - - -
134M VAL* 1.3 97.6 - - + +
136M ASN* 1.3 64.1 - - - +
137M PRO* 3.5 4.2 - - - +
140M VAL* 4.4 8.5 - - - +
154M HIS* 4.9 1.6 - - - -
155M ILE* 6.1 1.1 - - + -
156M PHE* 4.3 14.9 - + + -
187M VAL* 5.1 7.9 - - + +
188M ASN* 3.9 14.0 + - - -
191M ARG* 3.1 50.3 - - + -
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Residues in contact with ASN 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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12M GLU* 5.2 3.8 - - - +
13M ALA* 5.1 0.8 - - + +
131M TRP* 3.9 16.4 - - - -
133M PRO* 2.8 43.3 + - - +
134M VAL 2.8 2.2 - - - -
135M TYR* 1.3 78.8 - - - +
137M PRO* 1.3 73.1 - - + +
138M LYS* 2.5 30.2 + - + +
139M VAL* 2.5 46.4 + - + +
140M VAL* 3.3 4.1 + - - -
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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