Contacts of the helix formed by residues 106 - 121 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B VAL* 3.6 4.8 - - - +
105B LEU* 1.3 99.5 - - + +
107B PRO* 1.3 74.0 - - + +
108B GLU* 4.1 11.4 - - + +
109B GLU* 3.0 40.4 + - + +
110B ILE* 3.3 8.7 + - - +
286B ILE* 3.9 4.3 - - - -
290B ALA* 4.0 20.6 - - + -
293B ARG* 3.3 42.8 - - + -
294B THR* 6.1 4.0 - - + -
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Residues in contact with PRO 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TRP* 1.3 89.8 - - + +
108B GLU* 1.3 62.3 + - - +
110B ILE* 3.2 14.6 + - + +
111B ALA* 3.0 22.0 + - - +
283B ALA 6.1 0.7 - - - +
286B ILE* 4.0 3.8 - - + -
287B ARG* 3.9 35.7 - - + +
290B ALA* 3.7 20.4 - - + -
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B TRP* 3.2 7.5 - - + +
107B PRO* 1.3 78.8 - - + +
109B GLU* 1.3 58.2 + - + +
111B ALA* 3.3 7.8 + - - +
112B ARG* 3.0 55.9 + - - +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B HIS 5.1 3.8 - - - +
84B TYR* 3.5 55.3 - - + +
85B PRO* 5.3 0.2 - - - +
104B VAL* 3.4 10.1 - - + +
105B LEU* 3.0 31.4 + - - +
106B TRP* 3.0 32.6 + - + +
108B GLU* 1.3 76.8 - - + +
110B ILE* 1.3 63.8 + - - +
112B ARG* 3.3 1.6 + - - +
113B LEU* 3.0 29.4 + - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.4 8.1 - - + -
104B VAL* 3.6 24.5 - - + -
106B TRP 3.3 5.8 + - - +
107B PRO* 3.2 13.4 + - + +
109B GLU* 1.3 76.2 - - - +
111B ALA* 1.3 65.5 - - - +
113B LEU* 3.2 4.0 + - - +
114B LYS* 3.0 27.3 + - + +
279B LEU* 3.8 40.0 - - + +
283B ALA* 3.9 26.9 - - + +
286B ILE* 3.8 22.2 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PRO 3.0 12.7 + - - +
108B GLU* 3.7 10.5 - - - +
109B GLU 3.3 0.4 - - - -
110B ILE* 1.3 79.8 - - + +
112B ARG* 1.3 64.8 + - + +
114B LYS* 3.3 16.8 + - - +
115B GLU* 3.3 18.8 + - - +
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 3.1 30.4 + - - +
88B ARG* 4.8 1.6 - - - +
108B GLU* 3.0 43.0 + - - +
109B GLU* 3.8 3.4 - - - +
110B ILE 3.3 0.2 - - - -
111B ALA* 1.3 78.6 - - + +
113B LEU* 1.3 57.3 + - - +
115B GLU* 3.3 15.3 + - - +
116B LEU* 2.9 38.0 + - + +
63C ASP* 2.9 32.3 + - - +
67C ARG* 5.3 8.3 - - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B TYR* 3.8 20.0 - - + -
87B ILE* 3.8 36.8 - - + -
88B ARG* 3.8 17.5 - - + +
91B LEU* 4.6 8.5 - - + +
103B LEU* 5.3 0.2 - - + -
104B VAL* 3.8 28.5 - - + -
109B GLU 3.0 19.0 + - - +
110B ILE 3.2 4.5 + - - +
112B ARG* 1.3 75.3 - - - +
114B LYS* 1.3 65.0 + - - +
116B LEU* 3.7 4.3 - - + +
117B GLU* 2.9 28.2 + - - +
124B VAL* 4.4 3.4 - - + -
279B LEU* 3.7 27.6 - - + -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE* 3.0 25.0 + - + +
111B ALA* 3.3 10.7 + - - +
113B LEU* 1.3 77.0 - - - +
115B GLU* 1.3 65.8 + - + +
117B GLU* 3.5 18.7 + - - +
118B ALA* 3.5 11.8 + - - +
279B LEU* 3.6 30.9 - - + +
280B ASP* 3.0 33.3 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 3.3 13.4 + - - +
112B ARG* 3.3 17.6 + - - +
114B LYS* 1.3 80.6 - - + +
116B LEU* 1.3 66.2 + - + +
118B ALA* 3.1 9.7 + - - +
119B ARG* 2.8 45.3 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ARG* 3.5 48.0 - - + +
91B LEU* 4.2 14.6 - - + -
112B ARG* 2.9 28.3 + - + +
113B LEU* 3.3 6.9 + - + +
115B GLU* 1.3 78.2 - - + +
117B GLU* 1.3 57.6 + - - +
119B ARG* 3.1 19.0 + - + +
120B THR* 2.8 34.9 + - + +
62C GLU* 6.1 1.8 - - - +
66C ASP* 5.1 10.8 - - - +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.1 3.5 - - + +
113B LEU 2.9 20.6 + - - +
114B LYS* 3.6 20.3 + - - +
116B LEU* 1.3 73.0 - - - +
118B ALA* 1.3 59.0 - - - +
120B THR* 3.6 3.8 - - - -
121B GLY* 3.0 28.1 + - - -
122B ARG 3.4 21.2 - - - +
123B ARG* 3.0 28.3 + - - -
124B VAL* 2.9 37.3 + - + +
279B LEU* 3.4 26.3 - - + +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS 3.5 7.8 + - - +
115B GLU* 3.1 12.5 + - - +
117B GLU* 1.3 81.1 - - - +
119B ARG* 1.3 71.8 + - - +
120B THR 3.5 0.2 - - - -
121B GLY* 4.6 1.7 + - - -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 2.8 56.7 + - - +
116B LEU* 3.1 16.1 + - + +
117B GLU 3.0 0.4 - - - -
118B ALA* 1.3 94.3 - - - +
120B THR* 1.3 64.7 + - + +
121B GLY 3.9 0.2 - - - -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.5 44.5 - - + +
92B ARG* 4.2 9.0 - - + +
94B GLY* 5.3 1.6 - - - -
116B LEU* 2.8 27.7 + - + +
117B GLU* 3.6 7.1 + - - -
119B ARG* 1.3 88.1 - - + +
121B GLY* 1.3 61.8 + - - +
122B ARG* 3.1 18.1 + - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU 3.0 10.3 + - - -
118B ALA 4.6 2.2 + - - -
119B ARG 3.9 0.8 - - - -
120B THR* 1.3 76.2 - - - +
122B ARG* 1.4 79.1 + - - +
123B ARG* 5.6 1.6 - - - +
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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