Contacts of the helix formed by residues 132 - 141 (chain G) in PDB entry 3CJQ
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 GLY 132 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129G THR* 2.7 28.7 + - - -
130G GLY 3.0 1.8 - - - -
131G SER* 1.3 79.5 - - - +
133G VAL* 1.3 64.0 + - - +
134G LEU 2.9 4.0 + - - -
135G ALA* 3.1 5.6 + - - +
136G ILE* 2.8 29.2 + - - +
158G ALA* 4.0 11.2 - - - -
171G PHE* 4.3 5.2 - - - -
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Residues in contact with VAL 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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77G VAL* 4.7 6.1 - - + -
91G LEU* 4.1 12.5 - - + +
93G ILE* 4.0 26.5 - - + -
100G GLY* 3.5 17.3 - - - +
102G GLY 5.6 0.2 - - - +
107G THR* 3.8 22.7 - - + -
111G LEU* 4.1 23.1 - - + -
131G SER* 3.2 19.5 + - - +
132G GLY* 1.3 76.2 - - - +
134G LEU* 1.3 63.6 + - + +
136G ILE* 3.3 5.2 + - - +
137G ALA* 2.8 26.3 + - - +
303G SAH 4.1 8.5 - - - +
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Residues in contact with LEU 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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107G THR* 4.0 7.0 - - + +
110G ALA* 3.6 34.1 - - + -
111G LEU* 4.0 22.7 - - + +
114G LEU* 3.8 12.2 - - + +
124G VAL* 6.4 0.2 - - - -
126G ASP* 3.6 25.7 + - - +
129G THR 5.3 0.2 + - - -
132G GLY 2.9 3.0 + - - -
133G VAL* 1.3 78.6 - - + +
135G ALA* 1.3 58.1 + - - +
137G ALA* 3.1 5.4 + - - +
138G ALA* 2.8 34.3 + - - +
189G VAL* 3.7 18.7 - - + +
191G ASN* 4.4 8.5 - - + +
303G SAH 3.5 33.0 - - - +
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Residues in contact with ALA 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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126G ASP* 3.1 28.9 + - + +
129G THR* 3.9 8.1 - - - +
132G GLY 3.6 4.9 - - - +
134G LEU* 1.3 74.5 - - - +
136G ILE* 1.3 63.2 + - - +
138G ALA* 3.4 1.8 + - - -
139G GLU* 3.1 26.3 + - - +
145G ALA* 3.6 22.5 - - + +
147G GLY* 4.5 4.9 - - - -
169G PRO* 4.1 7.9 - - + -
171G PHE* 4.0 15.3 - - + -
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Residues in contact with ILE 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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91G LEU* 4.5 14.6 - - + -
93G ILE* 4.1 7.9 - - + -
131G SER 4.5 0.7 - - - +
132G GLY* 2.8 26.6 + - - +
133G VAL* 3.5 6.7 - - - +
135G ALA* 1.3 76.5 - - - +
137G ALA* 1.3 61.8 + - - +
139G GLU* 3.1 6.0 + - - +
140G LYS* 3.0 22.6 + - + +
158G ALA 4.6 0.9 - - - +
161G ASN* 3.7 33.7 - - + +
162G ALA* 3.7 26.5 - - + +
165G ASN* 3.9 22.7 - - + +
167G VAL* 3.8 19.7 - - + -
169G PRO* 4.7 4.3 - - + -
171G PHE* 5.0 1.1 - - + -
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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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75G PHE* 3.8 21.5 - - + -
91G LEU* 3.9 7.0 - - + -
111G LEU* 3.6 26.5 - - + -
114G LEU* 4.1 6.3 - - + -
133G VAL 2.8 20.5 + - - +
134G LEU 3.1 6.0 + - - +
136G ILE* 1.3 73.1 - - - +
138G ALA* 1.3 56.4 + - - +
140G LYS* 3.1 6.7 + - - +
141G LEU* 2.9 34.4 + - - +
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Residues in contact with ALA 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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114G LEU* 4.4 4.3 - - + +
118G LEU* 3.7 26.2 - - + -
124G VAL* 4.0 17.9 - - + -
134G LEU 2.8 19.5 + - - +
135G ALA* 3.6 5.8 - - - +
137G ALA* 1.3 72.9 - - - +
139G GLU* 1.3 61.9 + - - +
141G LEU* 3.2 3.0 + - - +
142G GLY 3.0 4.9 + - - -
143G GLY* 2.7 26.9 + - - -
145G ALA* 3.9 16.4 - - + -
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Residues in contact with GLU 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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119A ARG* 2.8 33.5 + - - -
135G ALA 3.1 18.8 + - - +
136G ILE 3.1 6.5 + - - +
138G ALA* 1.3 75.2 - - - +
140G LYS* 1.3 60.3 + - - +
142G GLY* 2.8 21.5 + - - -
143G GLY 3.2 11.2 - - - +
145G ALA* 2.8 30.6 + - + +
167G VAL* 3.6 21.3 - - + +
168G ARG 4.1 8.5 + - - -
169G PRO* 3.7 26.1 - - + +
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Residues in contact with LYS 140 (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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75G PHE* 4.4 4.5 - - + -
89G ILE* 4.0 28.8 - - + +
90G PRO* 4.0 19.3 + - - +
91G LEU* 4.0 15.0 - - + -
136G ILE* 3.0 17.8 + - - +
137G ALA 3.1 7.6 + - - +
139G GLU* 1.3 78.8 - - - +
141G LEU* 1.3 59.8 + - - +
142G GLY 3.4 0.3 + - - -
165G ASN* 2.9 42.2 + - - +
167G VAL* 4.0 11.8 - - + +
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Residues in contact with LEU 141 (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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74G PRO* 4.9 4.9 - - + -
75G PHE* 3.6 26.7 - - + -
89G ILE* 4.3 16.8 - - + -
114G LEU* 3.8 38.8 - - + +
115G ALA* 3.8 11.4 - - + +
118G LEU* 3.7 25.1 - - + +
120G PRO* 4.3 12.8 - - - +
137G ALA 2.9 16.5 + - - +
138G ALA 3.8 4.5 - - - +
139G GLU 3.1 0.4 - - - -
140G LYS* 1.3 74.2 - - - +
142G GLY* 1.3 60.3 + - - +
143G GLY 3.4 0.9 - - - -
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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