Contacts of the helix formed by residues 106 - 121 (chain C) in PDB entry 3O9Z
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 TRP 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C VAL* 3.6 4.2 - - - +
105C LEU* 1.3 97.9 - - + +
107C PRO* 1.4 71.3 - - + +
108C GLU* 3.6 23.1 - - + +
109C GLU* 2.9 39.6 + - + +
110C ILE* 3.3 8.3 + - - +
286C ILE* 3.9 4.9 - - - -
290C ALA* 3.9 21.3 - - + -
293C ARG* 3.3 42.4 - - + -
294C THR* 5.8 6.3 - - + -
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Residues in contact with PRO 107 (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 TRP* 1.4 83.8 - - + +
108C GLU* 1.3 78.6 + - - +
110C ILE* 3.1 14.0 + - + +
111C ALA* 3.0 21.8 + - - +
283C ALA 6.1 0.2 - - - +
286C ILE* 4.3 4.9 - - + -
287C ARG* 3.9 35.7 - - + +
290C ALA* 3.7 21.1 - - + -
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Residues in contact with GLU 108 (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 TRP* 3.2 18.5 - - + +
107C PRO* 1.3 95.2 - - - +
109C GLU* 1.3 55.9 + - - +
111C ALA* 3.3 8.8 + - - +
112C ARG* 3.1 48.9 + - - +
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Residues in contact with GLU 109 (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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81C HIS 5.1 3.3 - - - +
84C TYR* 3.5 53.5 - - + +
85C PRO* 5.3 0.2 - - - +
104C VAL* 3.4 8.3 - - + +
105C LEU* 3.0 31.2 + - - +
106C TRP* 2.9 33.7 + - + +
108C GLU* 1.3 76.9 - - - +
110C ILE* 1.4 66.3 + - - +
112C ARG* 3.3 11.2 + - - +
113C LEU* 3.0 29.6 + - - +
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Residues in contact with ILE 110 (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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103C LEU* 4.3 6.5 - - + -
104C VAL* 3.6 23.8 - - + +
106C TRP 3.3 5.1 + - - +
107C PRO* 3.1 11.8 + - + +
109C GLU* 1.4 76.4 - - - +
111C ALA* 1.3 63.5 - - - +
113C LEU* 3.2 6.7 + - - +
114C LYS* 3.0 42.7 + - - +
279C LEU* 3.7 33.2 - - + +
283C ALA* 4.0 23.8 - - + +
286C ILE* 3.9 25.4 - - + -
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Residues in contact with ALA 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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107C PRO 3.0 12.2 + - - +
108C GLU* 3.6 11.7 - - - +
110C ILE* 1.3 78.9 - - - +
112C ARG* 1.3 63.0 + - + +
114C LYS* 3.3 25.4 + - - +
115C GLU* 3.4 23.3 + - - +
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Residues in contact with ARG 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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63B ASP* 3.3 26.1 + - - -
84C TYR* 2.9 42.1 + - + +
88C ARG* 4.7 2.0 - - - +
108C GLU* 3.1 33.8 + - - +
109C GLU* 3.8 18.6 - - - +
110C ILE 3.3 0.2 - - - -
111C ALA* 1.3 77.9 - - + +
113C LEU* 1.3 63.8 + - - +
115C GLU* 3.2 19.1 + - - +
116C LEU* 3.0 30.7 + - + +
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Residues in contact with LEU 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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84C TYR* 3.8 19.5 - - + -
87C ILE* 3.7 34.1 - - + -
88C ARG* 4.0 15.3 - - + -
91C LEU* 4.3 10.1 - - + +
103C LEU* 4.0 12.8 - - + -
104C VAL* 3.8 29.2 - - + -
109C GLU 3.0 19.3 + - - +
110C ILE* 3.6 4.5 - - - +
112C ARG* 1.3 74.6 - - - +
114C LYS* 1.3 60.2 + - - +
116C LEU* 3.9 4.3 - - + +
117C GLU* 2.9 32.6 + - - +
124C VAL* 4.4 2.5 - - + -
279C LEU* 3.7 17.3 - - + -
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Residues in contact with LYS 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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110C ILE* 3.0 25.0 + - - +
111C ALA* 3.5 20.3 - - - +
112C ARG 3.2 0.2 - - - -
113C LEU* 1.3 76.6 - - - +
115C GLU* 1.3 63.2 + - + +
117C GLU* 3.4 10.5 + - - +
118C ALA* 3.3 20.1 + - - +
279C LEU* 3.6 33.8 - - + +
280C ASP* 3.8 20.0 - - - +
283C ALA* 6.0 1.1 - - - -
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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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111C ALA* 3.4 19.2 + - - +
112C ARG* 3.2 18.0 + - - +
113C LEU 3.2 0.4 - - - -
114C LYS* 1.3 79.8 - - + +
116C LEU* 1.3 64.4 + - + +
118C ALA* 3.3 8.6 + - - +
119C ARG* 3.2 22.2 + - - +
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Residues in contact with LEU 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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62B GLU* 5.8 3.1 - - - +
66B ASP* 5.4 3.6 - - - +
88C ARG* 3.7 46.9 - - + +
91C LEU* 3.7 21.1 - - + -
112C ARG* 3.0 24.8 + - + +
113C LEU* 3.2 4.7 + - + +
115C GLU* 1.3 77.7 - - + +
117C GLU* 1.3 65.0 + - - +
119C ARG* 3.3 30.6 + - + +
120C THR* 2.9 32.7 + - + +
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Residues in contact with GLU 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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91C LEU* 4.1 3.1 - - + +
113C LEU 2.9 17.2 + - - +
114C LYS* 3.6 13.8 - - - +
115C GLU 3.3 0.2 - - - -
116C LEU* 1.3 75.7 - - - +
118C ALA* 1.3 58.3 + - - +
120C THR* 3.4 2.4 + - - -
121C GLY* 2.9 32.4 + - - -
122C ARG 3.4 18.0 - - - +
123C ARG* 3.0 29.6 + - - -
124C VAL* 2.9 39.3 + - + +
279C LEU* 3.5 24.5 - - - +
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Residues in contact with ALA 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 LYS 3.3 8.1 + - - +
115C GLU* 3.3 11.8 + - - +
116C LEU 3.2 0.4 - - - -
117C GLU* 1.3 80.6 - - - +
119C ARG* 1.3 63.7 + - - +
120C THR 3.5 0.3 + - - -
121C GLY* 3.9 4.3 + - - -
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Residues in contact with ARG 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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62B GLU* 5.3 3.6 + - - -
66B ASP* 4.2 28.9 + - - +
115C GLU 3.2 10.7 + - - +
116C LEU* 3.5 36.1 - - + +
118C ALA* 1.3 81.2 - - - +
120C THR* 1.3 65.9 + - + +
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Residues in contact with THR 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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91C LEU* 3.6 34.8 - - + +
92C ARG* 4.9 3.1 - - - +
94C GLY* 5.8 1.0 - - - -
116C LEU* 2.9 21.7 + - + +
117C GLU* 3.4 3.6 + - - -
119C ARG* 1.3 87.5 - - + +
121C GLY* 1.3 62.5 + - - +
122C ARG* 3.3 32.2 + - - +
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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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117C GLU 2.9 11.1 + - - -
118C ALA 3.9 3.9 + - - -
119C ARG 3.6 2.0 + - - -
120C THR* 1.3 78.5 - - - +
122C ARG* 1.3 76.0 + - - +
123C ARG* 5.3 2.8 - - - +
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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