Contacts of the helix formed by residues 103 - 123 (chain R) in PDB entry 6M44
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 103 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92Q GLU* 3.3 48.0 - - + +
95Q LYS* 4.1 32.7 - - + +
96Q LEU* 4.4 12.6 - - + +
101R LEU 4.1 4.5 - - - +
102R LEU* 1.4 86.7 - - + +
104R GLY* 1.3 69.6 + - - +
105R GLU 3.6 0.7 - - - -
106R LEU* 3.0 18.7 + - + +
107R ALA* 2.9 15.7 + - - -
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Residues in contact with GLY 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q GLU* 3.8 3.3 + - - -
102R LEU 3.9 1.0 + - - -
103R PRO* 1.3 68.3 - - - +
105R GLU* 1.3 55.1 + - - +
107R ALA* 2.8 28.9 + - - +
108R LYS* 3.1 13.0 + - - +
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Residues in contact with GLU 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q GLU* 3.3 18.7 + - + +
104R GLY* 1.3 71.3 - - - +
106R LEU* 1.3 62.2 + - + +
108R LYS* 3.0 33.2 + - - +
109R HIS* 2.9 60.1 + - + +
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Residues in contact with LEU 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 3.7 11.9 - - + +
58Q LEU* 4.1 20.9 - - + -
61Q GLU* 4.2 28.5 - - + +
90Q ASP* 5.6 2.2 - - - +
92Q GLU* 2.8 27.2 + - + +
93Q LEU* 4.0 35.4 - - + +
96Q LEU* 4.5 9.4 - - + -
102R LEU* 4.0 5.5 - - + +
103R PRO* 3.0 25.1 + - + +
105R GLU* 1.3 70.7 - - + +
107R ALA* 1.3 60.9 + - - +
109R HIS* 4.7 2.5 - - - -
110R ALA* 3.1 28.0 + - - +
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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
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98R VAL* 4.5 9.0 - - + +
99R ARG* 4.6 13.9 - - + +
102R LEU* 4.0 24.1 - - + +
103R PRO 2.9 10.0 + - - +
104R GLY* 2.8 13.2 + - - +
106R LEU* 1.3 72.5 - - - +
108R LYS* 1.3 59.1 + - - +
110R ALA* 2.7 7.1 + - - -
111R VAL* 2.5 41.8 + - + -
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Residues in contact with LYS 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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99R ARG* 6.1 1.6 - - - +
104R GLY 3.1 7.3 + - - +
105R GLU* 3.0 42.4 + - - +
107R ALA* 1.3 75.2 - - - +
109R HIS* 1.3 60.4 + - + +
111R VAL* 3.4 9.6 + - - +
112R SER* 2.8 37.6 + - - -
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Residues in contact with HIS 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 3.0 40.9 + - + +
105R GLU* 2.9 54.0 + - + +
106R LEU 3.9 0.4 - - - +
107R ALA 3.1 0.6 - - - -
108R LYS* 1.3 85.7 - - + +
110R ALA* 1.3 53.2 + - - +
112R SER* 3.4 6.5 + - - -
113R GLU* 2.9 38.5 + - + +
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Residues in contact with ALA 110 (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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54Q VAL* 3.9 21.6 - - + +
57Q TYR* 3.9 17.2 - - + -
98R VAL* 3.9 9.2 - - + -
102R LEU* 3.7 22.7 - - + -
106R LEU 3.1 19.6 + - - +
107R ALA 2.7 9.1 + - - +
109R HIS* 1.3 67.6 - - - +
111R VAL* 1.3 63.7 + - - +
113R GLU* 3.4 3.4 + - - +
114R GLY* 2.9 22.2 + - - -
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Residues in contact with VAL 111 (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* 3.1 22.0 + - - +
95R GLN* 4.1 15.9 - - + +
98R VAL* 4.5 10.3 - - + +
99R ARG* 4.1 45.5 - - + +
107R ALA* 2.5 30.4 + - + +
108R LYS* 3.5 8.5 - - - +
110R ALA* 1.3 70.7 - - - +
112R SER* 1.3 52.5 + - - +
115R THR* 2.9 43.1 + - - +
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Residues in contact with SER 112 (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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108R LYS* 2.8 20.4 + - - -
109R HIS* 3.4 7.9 - - - -
110R ALA 3.2 0.2 - - - -
111R VAL* 1.3 73.3 - - - +
113R GLU* 1.3 53.4 + - - +
114R GLY 2.9 6.8 + - - -
115R THR* 3.0 7.1 + - - -
116R LYS* 2.8 37.5 + - - +
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Residues in contact with GLU 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q LEU* 5.2 6.4 - - - +
53Q ALA* 3.3 27.2 - - - +
56Q GLU* 5.4 5.5 - - - +
57Q TYR* 4.2 35.3 - - + +
109R HIS* 2.9 21.8 + - + +
110R ALA 4.0 3.8 - - - +
112R SER* 1.3 71.2 + - - +
114R GLY* 1.3 57.3 + - - +
116R LYS* 4.0 30.1 + - - +
117R ALA* 3.6 11.3 + - - +
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Residues in contact with GLY 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 3.4 43.3 - - - -
53Q ALA* 4.2 2.0 - - - -
54Q VAL* 4.9 0.2 - - - -
110R ALA 2.9 15.7 + - - -
111R VAL 3.7 1.3 - - - -
112R SER 2.9 0.8 + - - -
113R GLU* 1.3 74.5 - - - +
115R THR* 1.3 62.9 + - - +
116R LYS 3.2 0.7 - - - -
117R ALA* 3.3 4.3 + - - +
118R VAL* 3.1 19.6 + - - +
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Residues in contact with THR 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 3.3 7.4 - - - -
95R GLN* 3.4 18.7 + - - -
111R VAL* 2.9 30.2 + - - +
112R SER* 3.6 5.6 - - - -
114R GLY* 1.3 69.2 - - - +
116R LYS* 1.3 63.6 + - - +
118R VAL* 3.4 6.2 + - - +
119R THR* 3.1 34.8 + - - +
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Residues in contact with LYS 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112R SER* 2.8 18.7 + - - +
113R GLU* 4.0 30.8 + - + +
115R THR* 1.3 77.0 - - - +
117R ALA* 1.3 58.6 + - - +
119R THR* 3.4 6.3 + - - +
120R LYS* 3.0 45.0 + - + +
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Residues in contact with ALA 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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21Q ALA* 3.6 14.9 - - - +
23Q LEU* 4.0 17.3 - - + -
49Q VAL* 3.3 16.3 - - + +
53Q ALA* 3.7 17.0 - - + -
113R GLU 3.6 16.1 + - - +
114R GLY 3.3 6.1 + - - +
116R LYS* 1.3 77.2 - - + +
118R VAL* 1.3 60.4 + - - +
120R LYS* 3.7 1.0 + - - +
121R TYR* 3.1 30.0 + - - +
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Residues in contact with VAL 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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46Q GLY* 3.8 27.8 - - - +
49Q VAL* 3.9 5.8 - - + -
50Q TYR* 3.8 22.9 - - + +
91R SER* 4.2 14.4 - - - +
114R GLY 3.1 16.1 + - - +
115R THR* 3.7 10.3 - - - +
116R LYS 3.3 0.2 - - - -
117R ALA* 1.3 71.3 - - - +
119R THR* 1.3 62.2 + - - +
121R TYR* 3.0 6.4 + - + +
122R THR* 2.7 44.5 + - + +
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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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115R THR* 3.1 23.2 + - - +
116R LYS* 3.6 6.3 - - - -
118R VAL* 1.3 77.5 - - - +
120R LYS* 1.3 56.5 + - - +
122R THR* 2.6 20.5 + - - -
123R SER* 3.1 29.2 + - - +
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Residues in contact with LYS 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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19Q SER 5.9 0.2 - - - -
20Q ARG 3.3 16.6 + - - +
21Q ALA 3.7 19.3 - - - +
22Q GLY* 4.0 15.3 - - - +
116R LYS* 3.0 33.3 + - + +
117R ALA 3.9 4.5 - - - +
118R VAL 3.2 0.2 - - - -
119R THR* 1.3 76.7 - - - +
121R TYR* 1.3 57.4 + - - +
123R SER* 4.0 6.2 - - - -
124R ALA* 3.4 17.3 + - - +
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Residues in contact with TYR 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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17Q ARG* 3.1 66.6 + - + +
20Q ARG* 3.9 28.9 + - + +
21Q ALA* 3.8 8.7 - - + -
45Q ALA* 4.5 17.8 + - + +
46Q GLY* 5.6 3.1 - - - -
49Q VAL* 3.8 28.0 - - + -
117R ALA 3.1 18.4 + - - +
118R VAL* 3.0 6.5 + - + +
120R LYS* 1.3 74.1 - - - +
122R THR* 1.3 76.4 + - + +
123R SER 3.2 1.8 - - - -
124R ALA* 3.2 15.4 + - - +
125R LYS* 3.6 12.6 + - - +
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Residues in contact with THR 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R VAL* 2.7 24.7 + - + +
119R THR* 2.6 26.3 + - - -
121R TYR* 1.3 85.7 - - + +
123R SER* 1.3 56.5 + - - +
125R LYS* 3.6 18.5 + - - +
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Residues in contact with SER 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119R THR* 3.1 23.1 + - - +
120R LYS* 4.0 6.1 - - - -
121R TYR 3.2 0.2 - - - -
122R THR* 1.3 73.6 + - - +
124R ALA* 1.3 60.7 + - - +
125R LYS* 3.3 9.1 + - - +
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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
------------------------------------------------------------
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