Contacts of the helix formed by residues 106 - 121 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D VAL* 3.5 5.0 - - - +
105D LEU* 1.3 99.5 - - + +
107D PRO* 1.4 74.1 - - + +
108D GLU* 4.1 14.8 - - + +
109D GLU* 3.0 41.8 + - + +
110D ILE* 3.3 8.5 + - - +
172D GLU* 5.9 0.2 - - - -
286D ILE* 3.9 4.5 - - - -
290D ALA* 3.8 17.5 - - + -
293D ARG* 3.5 40.2 - - - -
294D THR* 3.9 21.8 - - + -
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Residues in contact with PRO 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TRP* 1.4 87.6 - - + +
108D GLU* 1.3 61.8 - - - +
110D ILE* 3.2 14.7 + - + +
111D ALA* 3.1 21.2 + - - +
283D ALA 5.7 0.7 - - - +
286D ILE* 4.0 4.7 - - + -
287D ARG* 3.8 36.6 - - + +
290D ALA* 3.8 20.2 - - + -
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TRP* 3.2 11.3 - - + +
107D PRO* 1.3 79.3 - - - +
109D GLU* 1.3 61.2 + - + +
111D ALA* 3.3 9.2 + - - +
112D ARG* 3.1 26.5 + - - +
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D HIS 5.7 0.7 - - - +
84D TYR* 3.6 54.7 - - + +
104D VAL* 3.4 8.4 - - + +
105D LEU* 3.0 31.9 + - - +
106D TRP* 3.0 33.3 + - + +
108D GLU* 1.3 78.1 - - + +
110D ILE* 1.3 64.5 + - - +
112D ARG 3.2 0.9 + - - -
113D LEU* 3.0 29.2 + - - +
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Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 4.4 7.0 - - + -
104D VAL* 3.5 25.1 - - + -
106D TRP 3.3 5.6 + - - +
107D PRO* 3.2 11.1 + - + +
109D GLU* 1.3 76.3 - - - +
111D ALA* 1.3 64.7 + - - +
113D LEU* 3.3 4.4 + - - +
114D LYS* 3.0 33.8 + - + +
279D LEU* 3.9 30.7 - - + +
283D ALA* 4.2 29.6 - - + +
286D ILE* 3.7 26.0 - - + -
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PRO 3.1 12.2 + - - +
108D GLU* 3.6 11.9 - - - +
109D GLU 3.2 0.2 - - - -
110D ILE* 1.3 79.3 - - - +
112D ARG* 1.3 63.6 + - - +
114D LYS* 3.3 17.1 + - - +
115D GLU* 3.3 18.3 + - - +
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 2.9 31.8 + - - +
66A ASP* 2.8 36.4 + - - +
84D TYR* 3.1 27.1 - - + +
88D ARG* 3.7 7.5 - - - +
108D GLU 3.1 16.7 + - - +
109D GLU* 3.2 2.9 + - - +
111D ALA* 1.3 76.8 - - - +
113D LEU* 1.3 62.2 + - - +
115D GLU* 3.2 35.0 + - - +
116D LEU* 3.0 62.7 + - + +
119D ARG* 4.3 2.4 - - - +
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.7 19.3 - - + -
87D ILE* 3.6 36.8 - - + -
88D ARG* 4.0 16.4 - - + -
91D LEU* 4.2 10.5 - - + +
103D LEU* 5.3 0.2 - - + -
104D VAL* 3.9 27.8 - - + -
109D GLU 3.0 19.0 + - - +
110D ILE* 3.3 4.5 + - - +
112D ARG* 1.3 74.2 - - - +
114D LYS* 1.3 59.8 + - - +
116D LEU* 3.2 2.4 + - - +
117D GLU* 2.8 33.3 + - - +
124D VAL* 4.3 4.3 - - + -
279D LEU* 3.8 28.5 - - + -
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ILE* 3.0 23.7 + - + +
111D ALA* 3.5 10.5 - - - +
112D ARG 3.3 0.2 - - - -
113D LEU* 1.3 72.6 - - - +
115D GLU* 1.3 66.1 + - - +
117D GLU* 3.4 19.6 + - - +
118D ALA* 3.3 19.9 + - - +
123D ARG* 6.1 0.6 - - - +
279D LEU* 3.6 21.7 - - + +
280D ASP* 2.8 35.8 + - - +
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 3.3 14.4 + - - +
112D ARG* 3.2 42.0 + - - +
114D LYS* 1.3 77.6 - - - +
116D LEU* 1.3 66.5 + - + +
118D ALA* 3.2 9.2 + - - +
119D ARG* 3.2 20.3 + - - +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 5.4 2.5 - - - +
66A ASP* 4.7 0.4 - - - +
88D ARG* 3.4 40.6 - - - +
91D LEU* 3.7 21.5 - - + -
112D ARG* 3.0 49.3 + - + +
113D LEU* 3.9 1.6 - - + +
114D LYS 3.2 0.2 - - - -
115D GLU* 1.3 81.0 - - + +
117D GLU* 1.3 65.2 + - - +
119D ARG* 3.3 32.5 + - + +
120D THR* 2.9 33.1 + - + +
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU* 4.3 3.0 - - + +
113D LEU 2.8 16.6 + - - +
114D LYS* 3.5 21.4 + - - +
116D LEU* 1.3 75.3 - - - +
118D ALA* 1.3 62.3 + - - +
120D THR* 3.5 2.4 + - - -
121D GLY* 2.9 27.2 + - - -
122D ARG 3.4 17.9 + - - +
123D ARG* 3.1 29.5 + - - -
124D VAL* 2.9 39.3 + - + +
279D LEU* 3.5 25.3 - - - +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS 3.3 8.5 + - - +
115D GLU* 3.2 11.9 + - - +
117D GLU* 1.3 80.9 - - - +
119D ARG* 1.3 63.1 + - - +
120D THR 3.5 0.3 + - - -
121D GLY* 3.9 4.2 + - - -
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Residues in contact with ARG 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 5.8 0.6 - - - +
65A ARG* 4.3 6.8 - - - +
66A ASP* 2.7 40.8 + - - +
112D ARG* 4.3 2.1 - - - +
115D GLU 3.2 13.2 + - - +
116D LEU* 3.6 32.0 - - + +
117D GLU 3.2 0.4 - - - -
118D ALA* 1.3 79.2 - - - +
120D THR* 1.3 65.7 + - + +
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU* 3.7 34.9 - - + +
92D ARG* 5.4 1.3 - - - -
94D GLY* 5.8 1.7 - - - -
116D LEU* 2.9 22.1 + - + +
117D GLU* 3.5 3.3 + - - -
119D ARG* 1.3 86.0 - - + +
121D GLY* 1.3 62.0 + - - +
122D ARG* 3.3 33.8 + - - +
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Residues in contact with GLY 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLU 2.9 10.5 + - - -
118D ALA* 3.9 4.4 + - - -
119D ARG 3.6 2.0 + - - -
120D THR* 1.3 78.0 - - - +
122D ARG* 1.3 78.3 + - - +
123D ARG* 5.2 3.8 - - - +
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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