Contacts of the helix formed by residues 110 - 121 (chain C) in PDB entry 2WJZ
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 PRO 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106C ALA 2.9 14.6 - - - +
107C VAL 3.8 7.0 - - - +
108C GLU 3.8 5.2 - - - +
109C ASN* 1.3 83.7 - - - +
111C SER* 1.3 63.8 + - - +
112C LEU 2.8 7.2 + - - -
113C ILE* 2.9 28.3 + - + +
114C THR 3.9 0.2 + - - -
156C TRP* 4.0 20.0 - - + -
159C GLU* 5.0 2.5 - - + +
163C ARG* 3.4 40.3 - - + +
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Residues in contact with SER 111 (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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109C ASN* 3.1 18.4 + - - -
110C PRO* 1.3 78.3 - - - +
112C LEU* 1.3 55.4 + - - +
113C ILE 3.3 0.2 - - - -
114C THR* 3.1 10.7 + - - -
115C GLN* 2.9 32.4 + - - +
163C ARG* 3.6 20.7 + - - +
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Residues in contact with LEU 112 (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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84C HIS 4.1 15.0 - - - +
85C ASP* 3.9 2.9 - - - +
86C PHE* 3.6 35.4 - - + +
102C ILE* 4.2 24.0 - - + -
105C ALA* 3.9 33.4 - - + +
106C ALA* 5.0 0.4 - - - -
109C ASN* 2.9 27.8 + - + +
110C PRO 2.8 0.2 + - - -
111C SER* 1.3 75.2 - - - +
113C ILE* 1.3 66.1 + - - +
115C GLN* 3.2 11.2 + - + +
116C ILE* 3.2 33.4 + - + +
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Residues in contact with ILE 113 (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 ILE* 3.9 23.1 - - + -
106C ALA* 4.2 9.4 - - + -
110C PRO* 2.9 12.6 + - + +
112C LEU* 1.3 78.3 - - - +
114C THR* 1.3 62.0 + - - +
116C ILE 3.6 0.2 + - - -
117C ALA* 3.1 21.0 + - - +
125C VAL* 3.9 11.3 - - + +
127C VAL* 3.9 17.5 - - + -
156C TRP* 4.3 12.1 - - + -
160C VAL* 4.2 17.0 - - + -
163C ARG* 3.7 28.3 - - + -
164C GLY 3.8 0.7 - - - -
165C ALA* 3.3 40.4 - - + +
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C SER* 3.1 12.6 + - - -
113C ILE* 1.3 75.0 - - - +
115C GLN* 1.3 67.4 + - - +
117C ALA* 3.1 4.6 + - + +
118C GLN* 2.9 51.7 + - + +
163C ARG* 2.8 41.3 + - - +
164C GLY* 5.7 0.2 - - - -
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Residues in contact with GLN 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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86C PHE* 3.1 53.8 + - + +
87C GLU* 5.2 3.2 + - - -
109C ASN* 4.8 5.9 - - - +
111C SER* 2.9 15.1 + - - +
112C LEU* 3.5 21.0 - - + +
114C THR* 1.3 77.3 - - - +
116C ILE* 1.3 60.8 + - - +
118C GLN* 4.2 8.8 - - - +
119C THR* 3.5 13.0 + - - -
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Residues in contact with ILE 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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86C PHE* 3.8 15.5 - - + -
89C ALA* 3.6 26.7 - - + -
93C ILE* 4.1 14.8 - - + -
100C VAL* 4.3 12.6 - - + -
102C ILE* 4.5 15.7 - - + -
112C LEU* 3.2 37.5 + - + +
113C ILE 4.0 0.2 - - - +
115C GLN* 1.3 74.1 - - - +
117C ALA* 1.3 59.1 + - - +
119C THR 3.3 0.3 + - - -
120C PHE* 2.8 52.7 + - + +
124C ALA* 4.9 1.1 - - + -
125C VAL* 3.8 20.0 - - + -
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Residues in contact with ALA 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 ILE 3.1 17.6 + - - +
114C THR* 3.1 10.2 + - + +
116C ILE* 1.3 78.2 - - - +
118C GLN* 1.3 58.5 + - + +
121C GLY* 2.7 40.0 + - - -
122C SER* 3.6 12.1 + - - +
125C VAL* 3.7 4.0 - - + +
164C GLY* 3.5 25.8 - - - +
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Residues in contact with GLN 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 THR* 2.9 39.9 + - + +
115C GLN* 4.2 7.4 + - - +
117C ALA* 1.3 79.4 - - + +
119C THR* 1.3 63.8 + - - +
121C GLY 4.5 0.9 + - - -
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Residues in contact with THR 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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86C PHE* 3.2 33.6 - - + -
115C GLN 3.5 3.7 + - - -
116C ILE 3.3 1.4 + - - -
118C GLN* 1.3 80.7 - - - +
120C PHE* 1.3 89.1 + - + +
121C GLY 3.5 0.6 + - - -
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Residues in contact with PHE 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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86C PHE* 3.9 6.5 - + - -
90C SER* 3.3 49.8 - - - -
93C ILE* 3.5 36.6 - - + -
94C LEU* 3.7 21.5 - - + -
116C ILE* 2.8 24.8 + - + +
119C THR* 1.3 96.8 - - + +
121C GLY* 1.3 62.6 + - - +
123C GLN* 3.8 12.5 + - - +
124C ALA* 3.8 24.0 - - + +
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Residues in contact with GLY 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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116C ILE 4.2 0.2 - - - +
117C ALA* 2.7 31.9 + - - -
118C GLN 4.4 1.0 + - - -
119C THR 3.5 1.8 + - - -
120C PHE* 1.3 74.9 - - - +
122C SER* 1.3 66.0 + - - -
123C GLN* 3.1 15.9 - - - -
124C ALA* 3.1 14.9 + - - +
125C VAL* 4.0 2.3 - - - +
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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