Contacts of the helix formed by residues 100 - 121 (chain R) in PDB entry 6L49
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 100 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Q GLU* 3.5 48.2 - - + +
95Q LYS* 3.8 36.6 - - + +
96Q LEU* 4.8 8.1 - - + +
98R LEU 3.9 4.5 - - - +
99R LEU* 1.3 88.0 - - + +
101R GLY* 1.3 56.2 + - - +
103R LEU* 3.1 13.9 + - + +
104R ALA* 2.6 34.1 + - - -
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Residues in contact with GLY 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q GLU* 3.4 1.6 + - - -
95Q LYS* 5.7 0.2 - - - +
100R PRO* 1.3 73.3 - - - +
102R GLU* 1.3 56.7 + - - +
104R ALA* 3.5 4.5 + - - +
105R LYS* 2.9 34.6 + - - +
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Residues in contact with GLU 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 4.5 3.9 + - - -
61Q GLU* 5.5 4.0 - - - +
90Q ASP* 5.7 0.3 - - - +
92Q GLU* 2.7 30.7 + - - +
101R GLY* 1.3 69.7 - - - -
103R LEU* 1.3 60.5 + - - +
105R LYS* 3.8 8.5 - - + +
106R HIS* 2.9 68.5 + - + +
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Residues in contact with LEU 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 3.3 35.0 - - + +
58Q LEU* 3.8 26.5 - - + -
61Q GLU* 4.5 10.5 - - + -
90Q ASP* 5.2 1.3 - - - +
92Q GLU* 2.8 32.4 + - + +
93Q LEU* 4.4 11.7 - - + -
96Q LEU* 4.1 7.9 - - + -
99R LEU* 3.8 28.7 - - + -
100R PRO* 3.1 17.2 + - + +
102R GLU* 1.3 76.9 - - - +
104R ALA* 1.3 57.6 + - - +
106R HIS 3.5 0.2 + - - -
107R ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R VAL* 3.6 19.3 - - - +
96R ARG* 4.0 16.2 - - + +
99R LEU* 3.4 25.0 - - + +
100R PRO 2.6 22.0 + - - +
101R GLY* 3.9 4.9 - - - +
103R LEU* 1.3 71.8 - - - +
105R LYS* 1.3 58.0 + - - +
107R ALA 3.7 0.5 - - - -
108R VAL* 2.8 35.1 + - - +
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Residues in contact with LYS 105 (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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96R ARG* 6.0 4.5 - - - +
101R GLY 2.9 21.8 + - - +
102R GLU* 3.8 9.0 - - + +
104R ALA* 1.3 76.0 - - - +
106R HIS* 1.3 65.5 + - + +
108R VAL* 3.3 9.2 + - + +
109R SER* 3.0 29.1 + - - -
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Residues in contact with HIS 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 3.3 34.5 + - + +
61Q GLU* 5.6 0.8 + - - -
102R GLU* 2.9 44.1 + - + +
105R LYS* 1.3 86.6 - - + +
107R ALA* 1.3 58.0 + - - +
109R SER* 2.7 20.4 + - - -
110R GLU* 3.0 22.7 + - + +
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Residues in contact with ALA 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 3.9 3.8 + - - -
54Q VAL* 3.9 20.5 - - + +
57Q TYR* 3.9 18.1 - - + -
95R VAL* 3.7 21.1 - - + -
99R LEU* 3.9 10.1 - - + -
103R LEU 2.9 18.8 + - - +
106R HIS* 1.3 74.1 - - - +
108R VAL* 1.3 60.2 + - - +
110R GLU* 4.1 3.1 - - - +
111R GLY* 2.9 27.2 + - - -
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Residues in contact with VAL 108 (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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50Q TYR* 3.3 19.7 + - - +
92R GLN* 4.1 7.2 - - + +
95R VAL* 4.3 4.0 - - + -
96R ARG* 3.5 54.7 - - + +
104R ALA 2.8 20.5 + - - +
105R LYS* 3.5 10.1 - - + +
106R HIS 3.3 0.2 - - - -
107R ALA* 1.3 76.6 - - - +
109R SER* 1.3 51.8 + - - +
112R THR* 2.5 49.1 + - + +
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Residues in contact with SER 109 (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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105R LYS* 3.0 14.7 + - - -
106R HIS* 2.7 27.5 + - - -
108R VAL* 1.3 78.4 - - - +
110R GLU* 1.3 57.2 + - - +
112R THR* 3.0 17.4 + - - -
113R LYS* 3.0 20.5 + - - +
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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
----------------------------------------------------------
23Q LEU* 5.5 5.7 - - - +
53Q ALA* 3.9 12.3 - - + +
57Q TYR* 4.6 27.0 - - + +
106R HIS* 3.0 20.6 + - + +
107R ALA* 4.1 5.2 - - - +
109R SER* 1.3 77.5 + - - +
111R GLY* 1.3 58.8 + - - +
113R LYS* 3.4 22.5 + - - +
114R ALA* 3.0 28.8 + - - +
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Residues in contact with GLY 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 3.5 25.6 - - - -
53Q ALA* 3.9 16.7 - - - +
54Q VAL* 5.1 0.2 - - - -
107R ALA 2.9 18.5 + - - -
110R GLU* 1.3 77.9 - - - +
112R THR* 1.3 56.9 + - - +
114R ALA* 3.3 1.9 + - - +
115R VAL* 2.9 33.3 + - - +
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Residues in contact with THR 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 3.7 5.4 - - + -
92R GLN* 3.9 27.1 - - - +
108R VAL* 2.5 31.9 + - + +
109R SER* 3.0 15.6 + - - -
111R GLY* 1.3 71.8 - - - +
113R LYS* 1.3 58.6 - - - +
115R VAL* 3.8 6.9 - - + +
116R THR* 2.8 36.4 + - - +
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Residues in contact with LYS 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109R SER 3.0 18.8 + - - +
110R GLU* 3.6 22.3 + - - +
111R GLY 3.3 0.2 - - - -
112R THR* 1.3 77.4 + - - +
114R ALA* 1.3 57.5 + - - +
116R THR* 2.7 19.4 + - - +
117R LYS* 2.9 48.1 + - + +
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Residues in contact with ALA 114 (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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21Q ALA 4.6 1.9 - - - +
23Q LEU* 4.0 15.7 - - + -
49Q VAL* 3.3 26.9 - - + +
53Q ALA* 3.7 20.2 - - + -
110R GLU 3.0 17.1 + - - +
111R GLY 3.8 2.5 - - - +
113R LYS* 1.3 73.6 - - - +
115R VAL* 1.3 59.9 + - - +
117R LYS* 3.3 14.1 + - - +
118R TYR* 2.9 23.6 + - - +
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Residues in contact with VAL 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q GLY* 3.3 31.8 - - - +
49Q VAL* 4.5 3.8 - - + -
50Q TYR* 3.8 11.2 - - + +
88R SER* 3.4 31.0 - - - +
111R GLY 2.9 20.3 + - - +
112R THR* 3.8 8.5 - - + +
113R LYS 3.3 0.2 - - - -
114R ALA* 1.3 77.5 - - - +
116R THR* 1.3 57.3 + - + +
118R TYR* 3.3 3.1 + - - +
119R THR* 2.6 45.3 + - - +
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Residues in contact with THR 116 (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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112R THR* 2.8 18.3 + - - +
113R LYS* 2.7 21.8 + - - +
115R VAL* 1.3 79.0 - - + +
117R LYS* 1.3 53.6 + - - +
119R THR* 4.0 5.3 - - - -
120R SER* 2.6 40.5 + - - -
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Residues in contact with LYS 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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20Q ARG 3.7 4.7 - - - +
21Q ALA 3.4 27.4 + - - +
22Q GLY* 3.8 17.0 + - - -
23Q LEU* 4.9 5.1 - - - +
113R LYS* 2.9 52.1 + - + +
114R ALA* 3.6 12.6 - - - +
115R VAL 3.3 0.2 - - - -
116R THR* 1.3 79.5 - - - +
118R TYR* 1.3 57.0 + - - +
120R SER* 4.1 3.2 - - - -
121R ALA* 3.1 30.0 + - - +
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Residues in contact with TYR 118 (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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17Q ARG* 3.4 41.5 + - + -
20Q ARG* 4.1 49.0 + - + -
21Q ALA* 4.5 5.1 - - + +
27Q VAL* 5.5 0.2 - - + -
45Q ALA* 3.2 46.7 - - + +
46Q GLY* 4.7 1.3 - - - -
49Q VAL* 3.6 24.0 - - + -
114R ALA 2.9 17.0 + - - +
115R VAL* 3.9 3.6 - - - +
117R LYS* 1.3 75.0 - - - +
119R THR* 1.3 63.7 + - - +
121R ALA 3.0 23.5 - - - +
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Residues in contact with THR 119 (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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-133I C 6.0 2.0 - - - +
45Q ALA* 6.0 1.0 - - - +
46Q GLY* 5.7 2.1 - - - -
115R VAL* 2.6 31.8 + - - +
116R THR* 4.0 6.0 - - - -
118R TYR* 1.3 80.4 - - - +
120R SER* 1.3 64.0 + - - +
121R ALA 3.5 4.3 + - - +
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Residues in contact with SER 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 THR* 2.6 25.7 + - - -
117R LYS* 4.3 4.3 - - - -
119R THR* 1.3 76.7 - - - +
121R ALA* 1.3 58.6 + - - +
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Residues in contact with ALA 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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20Q ARG* 4.1 36.7 - - + +
117R LYS 3.1 17.3 + - - +
118R TYR* 3.0 19.9 - - - +
119R THR 3.9 4.3 - - - +
120R SER* 1.3 80.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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