Contacts of the helix formed by residues 108 - 121 (chain R) in PDB entry 3D29
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 ASN 108 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106R ASP 3.8 4.9 + - - -
107R ILE* 1.3 78.4 - - - +
109R VAL* 1.3 66.7 + - - +
110R GLU* 4.3 7.2 - - + +
111R SER* 3.0 27.8 + - - +
112R LEU* 3.0 11.6 + - - +
142R ASP* 3.7 24.4 - - - +
143R ALA 5.3 0.4 - - - +
144R ASP* 3.4 31.7 + - - +
70Z HIS* 4.5 17.6 - - + +
72Z LYS* 4.1 18.7 - - - +
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Residues in contact with VAL 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R HIS* 4.8 0.2 - - + -
74R ILE* 4.0 19.7 - - + -
107R ILE 3.5 0.8 + - - -
108R ASN* 1.3 71.1 - - - +
110R GLU* 1.3 60.7 + - - +
112R LEU* 3.4 2.1 + - - +
113R THR* 2.9 28.5 + - - -
138R ILE* 4.3 17.3 - - + +
140R GLY* 3.7 17.3 - - - +
141R HIS 3.5 34.5 - - - +
142R ASP* 3.1 18.1 + - + +
147R GLN* 3.9 13.7 - - + +
149R PHE* 3.6 22.9 - - + -
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Residues in contact with GLU 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R ASN* 3.1 5.3 - - + +
109R VAL* 1.3 79.6 - - - +
111R SER* 1.3 63.7 + - - +
113R THR* 3.2 4.8 + - - -
114R GLN* 2.9 32.7 + - - +
147R GLN* 4.4 9.2 - - - +
149R PHE* 3.9 31.5 - - + -
157R PHE* 4.3 15.9 - - + -
65S LYS* 6.0 0.3 + - - -
69Z ASP 4.8 6.4 - - - +
70Z ASN* 4.9 12.1 - - - +
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Residues in contact with SER 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R ILE* 4.1 15.5 - - - -
108R ASN* 3.0 14.0 + - - +
110R GLU* 1.3 80.5 + - - +
112R LEU* 1.3 58.0 + - - +
114R GLN* 3.0 8.4 + - - +
115R SER* 2.8 34.8 + - - -
69Z ASP 3.7 11.9 + - - -
70Z HIS* 3.3 32.5 - - - -
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Residues in contact with LEU 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R ILE* 4.0 12.3 - - + -
74R ILE* 3.9 23.1 - - + -
92R ALA* 3.2 40.4 - - + +
95R ALA* 4.4 6.7 - - + -
96R ALA* 4.4 2.9 - - + +
107R ILE* 3.8 21.0 - - + +
108R ASN 3.0 11.2 + - - +
109R VAL 3.6 7.0 - - - +
111R SER* 1.3 75.9 - - - +
113R THR* 1.3 64.2 + - - +
115R SER* 3.3 6.0 + - - -
116R VAL* 3.1 24.7 + - + +
138R ILE* 3.8 32.8 - - + -
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Residues in contact with THR 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109R VAL 2.9 14.7 + - - -
110R GLU* 3.4 9.4 - - - -
111R SER 3.1 0.2 - - - -
112R LEU* 1.3 74.9 - - - +
114R GLN* 1.3 65.3 + - - +
116R VAL* 3.1 5.0 + - - +
117R CYS* 3.0 21.1 + - - +
138R ILE* 3.7 29.7 - - + +
149R PHE* 3.5 27.8 - - + -
151R ALA* 4.5 6.3 - - + -
157R PHE* 3.6 37.9 - - + -
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Residues in contact with GLN 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110R GLU* 2.9 18.7 + - - +
111R SER* 3.4 11.7 - - - +
113R THR* 1.3 77.1 - - - +
115R SER* 1.3 63.4 + - - +
117R CYS* 3.3 7.3 + - - +
118R ASP* 3.1 22.0 + - - +
155R GLY 4.9 2.6 - - - +
157R PHE* 3.5 31.7 - - + -
65S LYS* 4.4 15.0 - - - +
86S ARG* 3.3 51.9 + - - +
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Residues in contact with SER 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R HIS* 2.8 33.8 + - - -
95R ALA* 3.8 17.4 - - - +
107R ILE* 5.7 1.3 - - - -
111R SER 2.8 13.0 + - - -
112R LEU* 3.3 14.8 - - - +
113R THR 3.1 0.2 - - - -
114R GLN* 1.3 77.4 - - - +
116R VAL* 1.3 62.6 + - - +
118R ASP* 3.2 22.6 + - - +
119R LEU 3.9 2.3 + - - -
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Residues in contact with VAL 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R MET* 3.5 40.8 - - + +
91R HIS* 4.3 7.6 - - + -
92R ALA* 3.7 31.4 - - + -
112R LEU* 3.1 20.8 + - + +
113R THR 3.1 7.7 + - - +
115R SER* 1.3 76.2 - - - +
117R CYS* 1.3 63.5 + - - +
119R LEU* 3.2 21.2 + - + +
120R ALA* 3.8 2.8 + - - +
136R LEU* 4.1 13.7 - - + -
138R ILE* 4.2 11.2 - - + -
151R ALA* 5.0 6.3 - - + -
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Residues in contact with CYS 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113R THR 3.0 11.3 + - - +
114R GLN* 3.7 15.5 - - - +
115R SER 3.3 0.2 - - - -
116R VAL* 1.3 78.7 - - - +
118R ASP* 1.3 57.4 + - - +
119R LEU 3.1 0.2 - - - -
120R ALA* 2.9 30.9 - - - +
121R LEU 4.4 0.7 + - - -
151R ALA* 3.8 16.4 - - - -
152R GLU 4.8 2.7 - - - -
155R GLY* 3.2 21.7 - - - +
156R THR 3.6 13.0 - - - -
157R PHE* 3.5 37.5 - - + -
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Residues in contact with ASP 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R GLN* 3.1 22.0 + - - +
115R SER* 3.4 12.9 - - - +
116R VAL 3.2 0.6 - - - -
117R CYS* 1.3 77.4 - - - +
119R LEU* 1.3 63.0 + - + +
121R LEU* 4.5 3.3 + - - +
122R ARG* 3.3 34.9 + - - +
86S ARG* 2.9 45.0 + - - -
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Residues in contact with LEU 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R SER* 4.7 2.5 - - - +
88R MET* 4.6 11.0 - - + -
91R HIS* 3.6 56.3 - - + +
115R SER 4.1 1.3 - - - +
116R VAL* 3.6 13.2 - - - +
117R CYS 3.1 0.6 - - - -
118R ASP* 1.3 78.4 - - + +
120R ALA* 1.3 70.2 + - - +
122R ARG* 2.9 40.6 + - + +
128R MET* 4.1 7.6 - - - +
132R PHE* 4.0 23.3 - - + -
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Residues in contact with ALA 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116R VAL 3.8 2.2 + - - +
117R CYS* 2.9 22.8 + - - +
119R LEU* 1.3 80.1 - - - +
121R LEU* 1.3 59.3 + - - +
122R ARG 3.1 2.6 + - - -
123R PHE* 3.2 16.4 - - - -
128R MET* 3.6 8.7 - - - +
131R PRO* 4.7 1.9 - - - +
132R PHE* 4.4 14.2 - - + -
152R GLU 4.3 3.1 - - - +
153R PRO* 3.8 16.1 - - + +
155R GLY* 3.3 27.6 - - - +
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Residues in contact with LEU 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R LEU* 4.3 10.1 - - + -
24R VAL* 4.2 13.0 - - + -
117R CYS 4.4 1.2 + - - -
118R ASP 4.5 2.9 + - - +
119R LEU 3.5 0.8 - - - -
120R ALA* 1.3 75.9 - - + +
122R ARG* 1.3 50.8 + - - +
123R PHE* 2.7 54.3 + - + +
126R ARG* 3.7 21.7 + - - +
153R PRO 4.5 1.1 - - - +
154R SER 3.5 22.7 - - - +
155R GLY* 5.0 0.4 - - - -
81S LEU* 5.5 3.8 - - + -
83S PRO* 3.7 28.5 - - + -
84S ASP* 4.0 3.6 - - - +
130S ARG* 3.3 26.5 - - - +
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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