Contacts of the helix formed by residues 128 - 137 (chain G) in PDB entry 3WTV
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 ASP 128 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100G PRO* 4.5 3.3 - - - +
107G CYS* 3.0 26.5 + - + +
108G VAL 4.1 1.6 - - - +
109G ILE* 3.1 42.3 - - + +
126G GLU 3.0 6.2 + - - -
127G PHE* 1.3 66.2 - - - +
129G GLU* 1.3 63.9 + - - +
130G GLU* 3.2 12.8 + - - +
131G ARG* 3.2 40.4 + - + +
132G ALA* 3.1 23.1 + - - +
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Residues in contact with GLU 129 (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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9G ARG* 2.8 39.8 + - - +
127G PHE* 2.9 28.5 + - - +
128G ASP* 1.3 71.6 + - - +
130G GLU* 1.3 71.6 + - + +
132G ALA* 3.2 2.4 + - - +
133G GLN* 2.9 49.3 + - - +
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Residues in contact with GLU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G ASP* 3.2 10.0 + - - +
129G GLU* 1.3 85.6 - - + +
131G ARG* 1.3 65.3 + - + +
133G GLN* 2.9 13.8 + - - +
134G GLN* 3.0 29.3 + - - +
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Residues in contact with ARG 131 (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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156F PRO* 3.4 29.7 - - - +
3G ARG* 4.0 5.3 - - - +
71G ALA* 3.0 32.8 - - + +
100G PRO* 4.7 8.5 - - - -
101G MET 5.1 3.3 + - - +
102G ILE* 4.0 10.1 - - - +
107G CYS* 3.0 33.8 - - + +
108G VAL 6.0 0.4 - - - -
128G ASP* 3.2 24.4 + - - +
130G GLU* 1.3 79.6 - - + +
132G ALA* 1.3 56.7 + - - +
134G GLN* 3.3 22.1 + - - +
135G GLU* 2.7 58.5 + - - +
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Residues in contact with ALA 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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8G GLN* 3.5 25.8 - - + +
107G CYS* 3.8 1.5 - - + +
127G PHE* 3.4 31.2 - - + -
128G ASP 3.1 21.3 + - - +
129G GLU* 3.2 6.7 - - - +
130G GLU 3.1 0.2 + - - -
131G ARG* 1.3 76.9 - - - +
133G GLN* 1.3 68.5 + - - +
136G ASP* 3.2 23.7 + - - +
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Residues in contact with GLN 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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129G GLU* 2.9 45.9 + - - +
130G GLU* 2.9 9.6 + - - +
132G ALA* 1.3 81.3 + - - +
134G GLN* 1.3 67.1 + - + +
136G ASP* 3.3 7.1 + - - +
137G ALA* 2.9 26.0 + - - +
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Residues in contact with GLN 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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71G ALA 6.3 1.8 - - - -
130G GLU* 3.0 23.4 + - - +
131G ARG* 3.3 39.4 + - + +
133G GLN* 1.3 77.8 - - + +
135G GLU* 1.3 62.5 + - - +
137G ALA* 3.3 12.4 + - - +
138G LEU* 3.1 21.6 - - + +
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Residues in contact with GLU 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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3G ARG* 2.6 52.8 + - + +
4G VAL* 3.6 36.2 - - + +
8G GLN* 4.3 0.2 - - - +
102G ILE* 4.3 1.3 - - - -
107G CYS* 4.1 8.1 - - - -
131G ARG* 2.7 42.1 + - - +
132G ALA 4.1 1.1 - - - +
134G GLN* 1.3 69.5 - - - +
136G ASP* 1.3 56.4 + - - +
137G ALA 3.0 1.3 - - - -
138G LEU* 2.6 53.1 + - - +
139G ALA* 3.9 1.4 + - - +
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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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4G VAL* 4.6 5.6 - - - -
5G VAL 4.1 3.2 - - - +
6G PRO* 3.2 25.8 - - - +
8G GLN* 3.5 17.4 + - - +
132G ALA 3.2 16.8 + - - +
133G GLN* 3.7 7.4 - - - +
135G GLU* 1.3 77.9 - - - +
137G ALA* 1.3 57.1 + - - +
138G LEU 2.8 5.9 + - - -
139G ALA* 3.1 24.2 + - - +
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Residues in contact with ALA 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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133G GLN 2.9 18.0 + - - +
134G GLN* 3.4 9.2 - - - +
135G GLU 3.0 0.6 + - - -
136G ASP* 1.3 74.1 - - - +
138G LEU* 1.3 70.4 + - + +
139G ALA 3.6 1.1 - - - -
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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