Contacts of the helix formed by residues 113 - 126 (chain C) in PDB entry 6AH0
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 VAL 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C THR* 1.3 77.4 - - - +
114C TYR* 1.3 55.8 + - - +
116C MET* 3.0 3.9 + - - +
117C ASP* 3.0 25.6 + - - -
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Residues in contact with TYR 114 (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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112C THR 3.4 0.6 - - - -
113C VAL* 1.3 72.9 - - - +
115C GLU* 1.3 62.1 + - - +
117C ASP* 3.2 3.7 + - - +
118C PHE* 3.0 18.7 + - - -
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Residues in contact with GLU 115 (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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112C THR* 3.4 7.8 + - - +
113C VAL 3.2 0.4 - - - -
114C TYR* 1.3 76.7 - - - +
116C MET* 1.3 54.4 + - - +
118C PHE* 3.2 2.8 + - - +
119C LEU* 2.9 27.7 + - - -
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Residues in contact with MET 116 (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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112C THR 3.1 10.7 + - - -
113C VAL* 3.0 9.3 + - - +
115C GLU* 1.3 75.7 - - - +
117C ASP* 1.3 61.9 + - - +
119C LEU* 3.2 2.2 + - - +
120C ALA* 2.9 21.0 + - - -
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Residues in contact with ASP 117 (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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113C VAL 3.0 13.1 + - - -
114C TYR* 3.2 4.2 + - - +
116C MET* 1.3 75.0 - - - +
118C PHE* 1.3 63.6 + - - +
120C ALA* 3.2 2.9 + - - +
121C ASP* 3.0 18.7 + - - -
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Residues in contact with PHE 118 (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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114C TYR 3.0 14.0 + - - -
115C GLU* 3.2 3.3 + - - +
117C ASP* 1.3 76.0 - - - +
119C LEU* 1.3 61.6 + - - +
121C ASP* 3.2 3.3 + - - +
122C LEU* 3.0 19.9 + - - -
76e MET* 5.6 9.4 - - - +
77e LEU* 6.1 2.5 - - - +
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Residues in contact with LEU 119 (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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115C GLU 2.9 15.0 + - - -
116C MET* 3.7 3.6 - - - +
118C PHE* 1.3 76.7 - - - +
120C ALA* 1.3 60.5 + - - +
122C LEU* 3.2 2.3 + - - +
123C MET* 2.9 21.7 + - - -
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Residues in contact with ALA 120 (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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116C MET 2.9 15.5 + - - -
117C ASP* 3.7 3.6 - - - +
119C LEU* 1.3 73.1 - - - +
121C ASP* 1.3 64.5 + - - +
123C MET* 3.2 2.9 + - - +
124C ASP* 2.9 20.6 + - - -
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Residues in contact with ASP 121 (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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117C ASP 3.0 14.2 + - - -
118C PHE* 3.2 3.5 + - - +
120C ALA* 1.3 76.9 - - - +
122C LEU* 1.3 61.7 + - - +
124C ASP* 3.2 3.5 + - - +
125C ASN* 3.0 19.6 + - - -
76e MET* 5.4 8.5 - - - +
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Residues in contact with LEU 122 (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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118C PHE 3.0 14.8 + - - -
119C LEU* 3.7 3.4 - - - +
121C ASP* 1.3 76.6 - - - +
123C MET* 1.3 61.0 + - - +
125C ASN* 3.2 10.8 + - - +
126C SER* 3.7 7.1 + - - -
128C LEU* 5.4 2.4 + - - -
129C ILE* 5.1 8.4 + - - -
199C LEU* 6.1 7.6 - - - +
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Residues in contact with MET 123 (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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119C LEU 2.9 14.3 + - - -
120C ALA* 3.2 3.8 + - - +
122C LEU* 1.3 74.6 - - - +
124C ASP* 1.3 60.6 + - - +
126C SER* 3.4 13.9 + - - -
545C PRO* 5.5 8.1 - - - +
546C ALA 5.4 3.6 - - - +
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Residues in contact with ASP 124 (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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120C ALA 2.9 13.7 + - - -
121C ASP* 3.2 5.3 + - - +
123C MET* 1.3 77.2 - - - +
125C ASN* 1.3 62.2 + - - +
126C SER* 3.3 0.9 + - - -
545C PRO* 6.4 0.9 - - - -
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Residues in contact with ASN 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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121C ASP 3.0 13.8 + - - -
122C LEU* 3.2 6.0 + - - +
124C ASP* 1.3 77.4 - - - +
126C SER* 1.3 56.0 + - - +
127C GLU* 3.1 12.5 + - - -
128C LEU 5.5 1.1 - - - +
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Residues in contact with SER 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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122C LEU 3.7 7.3 + - - -
123C MET 3.4 12.1 + - - -
124C ASP 3.3 3.7 - - - -
125C ASN* 1.3 73.9 - - - +
127C GLU* 1.3 56.0 + - - +
128C LEU 3.7 1.1 - - - +
129C ILE* 4.5 9.3 - - - +
441C PRO* 4.2 21.0 - - - +
442C LYS 4.3 4.9 + - - -
546C ALA 5.7 4.5 - - - -
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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