Contacts of the helix formed by residues 131 - 139 (chain G) in PDB entry 3P1M
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 THR 131 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110G LEU* 4.8 2.9 - - - +
129G ALA 3.5 7.4 + - - +
130G ILE* 1.3 77.9 - - - +
132G ASP* 1.3 66.2 + - - +
133G GLU* 3.5 10.6 + - - +
134G GLU* 3.1 24.4 + - - +
135G ASN* 3.0 22.2 + - - +
153G GLN* 5.6 1.5 + - - +
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Residues in contact with ASP 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ILE 4.0 0.2 + - - -
131G THR* 1.3 73.6 - - - +
133G GLU* 1.3 63.1 + - - +
135G ASN* 3.1 8.7 + - - +
136G ASP* 2.9 31.8 + - - +
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Residues in contact with GLU 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G THR 4.8 2.4 - - - +
110G LEU* 3.8 33.4 - - + +
131G THR* 3.2 10.2 + - - +
132G ASP* 1.3 80.7 - - - +
134G GLU* 1.3 64.1 + - - +
136G ASP* 3.3 20.0 + - - +
137G MET* 3.5 10.9 + - - +
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Residues in contact with GLU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G LEU* 3.7 17.8 - - + +
130G ILE* 3.8 12.3 - - + +
131G THR* 3.1 18.2 + - - +
133G GLU* 1.3 78.5 - - - +
135G ASN* 1.3 60.5 + - - +
137G MET* 3.0 5.9 + - - +
138G LEU* 2.8 26.7 + - + +
149G ARG* 2.7 48.6 + - - +
150G LEU* 3.1 36.9 + - + +
153G GLN* 3.4 25.0 - - + +
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Residues in contact with ASN 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ILE* 3.6 27.8 - - + +
131G THR 3.0 14.5 + - - +
132G ASP* 3.1 13.4 + - - +
134G GLU* 1.3 77.1 - - - +
136G ASP* 1.3 64.4 + - - +
138G LEU* 4.1 7.2 - - - +
139G ASP* 2.9 40.5 + - - +
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Residues in contact with ASP 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G ASP* 2.9 21.5 + - - +
133G GLU* 3.5 13.0 - - - +
134G GLU 3.2 0.2 - - - -
135G ASN* 1.3 81.1 + - - +
137G MET* 1.3 77.7 + - + +
139G ASP* 3.6 16.4 + - - +
140G LEU* 3.9 9.5 - - - +
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Residues in contact with MET 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLY* 5.7 4.7 - - - +
105A ALA* 4.2 15.5 - - + -
114A THR* 5.6 1.6 - - + -
110G LEU* 3.2 34.5 - - + +
111G ALA* 3.8 21.3 - - - +
112G CYS 3.6 15.9 - - - +
113G SER* 2.8 24.7 + - - -
133G GLU 4.0 8.7 - - - +
134G GLU 3.0 4.0 + - - +
136G ASP* 1.3 91.3 - - + +
138G LEU* 1.3 65.2 + - - +
140G LEU* 3.1 24.1 + - + +
141G ALA 3.5 0.7 + - - -
150G LEU* 3.6 14.8 - - + -
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G HIS* 4.5 1.1 - - + -
130G ILE* 3.5 26.9 - - + -
134G GLU* 2.8 17.3 + - - +
135G ASN* 3.8 10.3 - - - +
137G MET* 1.3 73.7 - - - +
139G ASP* 1.3 66.3 + - - +
141G ALA* 2.9 24.9 + - + +
144G LEU* 3.5 32.8 - - + +
148G SER* 3.8 21.8 - - - +
149G ARG* 4.1 18.2 - - - +
150G LEU* 3.7 29.5 - - + +
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Residues in contact with ASP 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.8 2.9 - - - +
172A ALA* 3.9 16.8 - - + +
175A ARG* 2.7 41.8 + - - +
135G ASN* 2.9 34.7 + - - +
136G ASP* 3.7 12.3 - - - +
138G LEU* 1.3 77.6 - - - +
140G LEU* 1.3 58.3 + - + +
141G ALA 3.3 0.4 - - - -
144G LEU* 4.3 8.3 - - - +
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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