Contacts of the helix formed by residues 124 - 133 (chain C) in PDB entry 3CQ6
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 SER 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C TYR* 3.7 18.3 + - - -
122C SER 3.4 4.7 + - - -
123C TYR* 1.3 78.4 - - - +
125C MET* 1.3 63.2 + - - +
127C PRO* 3.4 13.0 - - - +
128C ILE* 3.4 20.7 - - - +
333C ARG* 5.1 3.8 - - - -
402C PO4 2.8 30.4 + - - -
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Residues in contact with MET 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 5.4 0.2 - - + -
256A PRO* 3.8 30.3 - - + -
21C TYR* 3.7 34.3 - - + +
99C ASN* 3.5 22.9 - - - +
123C TYR* 3.1 34.5 - - + +
124C SER* 1.3 81.9 + - - +
126C HIS* 1.3 59.3 + - - +
128C ILE* 3.2 28.8 + - + +
129C LEU* 2.8 56.0 + - + +
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Residues in contact with HIS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 3.8 21.3 - - + +
122C SER* 4.7 2.8 + - - -
123C TYR* 3.3 29.0 + + + +
125C MET* 1.3 77.0 - - - +
127C PRO* 1.4 65.9 - - + +
129C LEU* 3.4 4.2 + - + +
130C ALA* 3.0 28.6 + - - +
137C PHE* 4.3 7.9 - - + -
166C PHE* 3.7 52.2 - + + +
168C THR* 3.2 26.3 + - - -
197C ASP* 2.9 30.4 + - + +
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Residues in contact with PRO 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLN* 4.2 18.4 - - - +
123C TYR 3.3 11.9 - - - +
124C SER* 3.4 10.3 - - - +
126C HIS* 1.4 95.9 - - + +
128C ILE* 1.3 58.4 + - + +
130C ALA* 3.6 0.5 - - - +
131C LYS* 2.9 32.7 + - - +
137C PHE* 3.8 41.5 - - + +
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PRO* 5.8 1.1 - - + -
21C TYR* 3.5 43.7 - - + +
124C SER* 3.4 18.6 - - - +
125C MET* 3.2 26.3 + - + +
127C PRO* 1.3 80.2 - - + +
129C LEU* 1.3 58.7 + - + +
131C LYS* 3.7 6.2 + - - +
132C GLY* 3.0 24.1 + - - -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 3.2 35.9 - - + -
99C ASN* 3.7 35.4 - - - +
102C LEU* 3.9 24.9 - - + -
103C GLN* 4.4 8.5 - - + +
106C LEU* 3.7 16.4 - - + -
125C MET* 2.8 38.6 + - + +
126C HIS* 3.9 3.6 - - - +
128C ILE* 1.3 72.0 - - + +
130C ALA* 1.3 63.8 + - - +
132C GLY* 3.2 2.6 + - - +
133C THR* 2.9 31.0 + - - +
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 3.8 12.0 - - + +
116C ALA* 4.6 5.8 - - + -
126C HIS 3.0 17.5 + - - +
127C PRO 3.6 4.7 - - - +
129C LEU* 1.3 75.8 - - - +
131C LYS* 1.3 61.3 + - - +
133C THR* 2.9 14.0 + - - -
135C THR* 2.8 45.7 + - - +
137C PHE* 4.1 21.3 - - + -
166C PHE* 5.2 0.4 - - + -
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 5.0 10.3 - - - +
15C LEU* 6.0 2.6 - - - +
18C GLU* 2.5 46.0 + - - +
127C PRO 2.9 17.2 + - - +
128C ILE* 3.9 6.1 - - - +
130C ALA* 1.3 75.6 - - - +
132C GLY* 1.3 61.6 + - - +
134C HIS* 3.1 20.2 + - - +
135C THR 3.6 7.3 + - - +
137C PHE* 5.6 0.8 - - + +
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Residues in contact with GLY 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN* 3.9 24.0 + - - +
253A VAL* 6.1 1.6 - - - -
103C GLN* 5.6 1.1 + - - -
128C ILE 3.0 16.9 + - - -
129C LEU* 3.2 5.8 + - - -
130C ALA 3.2 0.4 - - - -
131C LYS* 1.3 76.2 - - - +
133C THR* 1.3 59.9 + - - +
134C HIS* 3.4 8.7 + - - -
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Residues in contact with THR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A HIS* 4.9 3.8 + - - -
103C GLN* 3.7 32.1 - - + +
106C LEU* 3.3 29.8 - - + +
107C GLN* 4.4 11.3 - - + -
111C GLY* 3.4 15.2 - - - -
112C PRO* 4.0 2.3 - - - +
129C LEU* 2.9 18.7 + - + +
130C ALA* 2.9 4.0 + - - -
132C GLY* 1.3 78.6 - - - +
134C HIS* 1.3 73.4 + - - +
135C THR* 2.9 19.9 + - - -
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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