Contacts of the helix formed by residues 81 - 101 (chain Q) in PDB entry 1JJ2
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 81 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20500 G 3.7 0.6 - - - +
20510 G 3.7 13.5 - - - +
27Q HIS* 3.7 30.1 - - + +
31Q ILE* 4.1 9.9 - - + -
50Q VAL* 4.1 1.6 - - + -
57Q VAL* 4.0 19.1 - - + -
59Q PHE* 3.4 31.9 - - + -
79Q ARG* 3.3 9.4 - - + +
80Q TYR* 1.3 82.9 - - - +
82Q GLU* 1.3 59.6 + - - +
83Q LYS 3.4 2.2 - - - -
84Q ALA* 4.6 1.6 - - + -
85Q SER* 2.7 32.2 + - - -
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Residues in contact with GLU 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20500 G 3.2 37.0 + - - +
20510 G 3.3 9.1 + - - +
51Q ILE* 4.3 29.6 - - + +
80Q TYR 2.7 12.3 + - - +
81Q PRO* 1.3 69.7 - - - +
83Q LYS* 1.3 69.2 + - - +
85Q SER* 3.5 5.8 - - - -
86Q LYS* 2.8 63.4 + - - +
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Residues in contact with LYS 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14330 G 4.5 10.3 + - - -
20510 G 3.1 36.0 + - - +
20520 U 2.7 37.0 + - - +
22Q GLN* 3.5 22.8 + - - +
23Q MET* 4.5 10.5 - - + -
24Q SER 5.6 0.7 - - - +
27Q HIS* 6.2 0.2 - - - +
82Q GLU* 1.3 81.2 - - - +
84Q ALA* 1.3 67.4 - - - +
86Q LYS* 2.9 18.6 + - - +
87Q ALA* 3.0 12.6 + - + +
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Residues in contact with ALA 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20510 G 4.6 0.8 + - - -
23Q MET* 3.8 18.8 - - + +
24Q SER 4.6 2.5 - - - +
27Q HIS* 4.0 23.0 + - + +
28Q SER* 4.1 16.4 - - - +
31Q ILE* 3.4 20.6 - - + -
81Q PRO* 3.9 3.4 + - + +
82Q GLU 3.5 0.2 - - - -
83Q LYS* 1.3 78.3 - - - +
85Q SER* 1.3 57.8 + - - +
87Q ALA* 3.1 2.3 + - - +
88Q PHE* 2.9 33.6 + - + -
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Residues in contact with SER 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q ILE* 3.5 16.1 - - - +
47Q LEU* 3.7 19.3 - - - +
50Q VAL* 3.7 15.5 - - - +
51Q ILE* 3.9 19.5 - - - -
81Q PRO 2.7 23.0 + - - -
82Q GLU 3.5 4.7 - - - -
83Q LYS 3.1 0.6 - - - -
84Q ALA* 1.3 78.2 - - - +
86Q LYS* 1.3 57.6 + - - +
88Q PHE* 3.2 6.8 + - - +
89Q LEU* 2.9 31.0 + - - +
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Residues in contact with LYS 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q ILE* 3.6 28.7 - - + -
82Q GLU* 2.8 50.9 + - - +
83Q LYS* 2.9 9.6 + - - +
85Q SER* 1.3 76.5 - - - +
87Q ALA* 1.3 63.8 + - - +
89Q LEU* 3.1 10.6 + - + +
90Q ASP* 3.1 26.9 + - - +
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Residues in contact with ALA 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q LEU* 3.2 17.9 - - + +
21Q ARG* 3.2 31.9 - - - +
23Q MET* 3.5 29.4 - - + -
83Q LYS 3.0 10.0 + - - +
84Q ALA 3.5 3.1 - - - +
86Q LYS* 1.3 76.9 - - - +
88Q PHE* 1.3 57.3 + - - +
90Q ASP* 3.2 8.4 + - - +
91Q LEU 3.0 19.8 + - - -
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Residues in contact with PHE 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q LEU* 4.5 2.5 - - + -
23Q MET* 4.1 11.0 - - + -
28Q SER* 3.7 45.3 - - - -
31Q ILE* 3.7 22.4 - - + -
32Q ALA* 4.1 16.6 - - + -
35Q ILE* 4.0 13.9 - - + -
47Q LEU* 3.6 15.0 - - + -
84Q ALA 2.9 29.5 + - - +
85Q SER* 3.6 7.9 - - - +
86Q LYS 3.2 0.2 - - - -
87Q ALA* 1.3 75.8 - - - +
89Q LEU* 1.3 60.9 + - - +
91Q LEU* 3.0 18.1 + - + +
92Q LEU* 2.8 34.2 + - + +
114Q VAL* 4.2 13.0 - - + -
116Q ALA* 5.0 0.7 - - + -
143Q VAL* 4.2 19.1 - - + -
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Residues in contact with LEU 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q VAL* 3.8 45.0 - - + +
47Q LEU* 3.9 17.7 - - + -
48Q GLU* 4.2 17.0 - - + +
51Q ILE* 3.6 30.5 - - + -
85Q SER 2.9 13.4 + - - +
86Q LYS* 3.1 11.2 + - + +
88Q PHE* 1.3 76.9 - - - +
90Q ASP* 1.3 60.2 + - - +
92Q LEU* 3.3 3.9 + - + +
93Q GLU* 2.8 30.8 + - - +
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Residues in contact with ASP 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4960 G 5.1 6.6 - - - +
18Q LEU* 4.6 3.4 - - + -
21Q ARG* 3.3 25.9 + - - +
86Q LYS* 3.1 16.5 + - - +
87Q ALA* 3.3 10.1 - - - +
88Q PHE 3.1 0.2 - - - -
89Q LEU* 1.3 80.5 - - - +
91Q LEU* 1.3 61.2 + - - +
93Q GLU* 3.4 16.3 + - - +
94Q ASN* 3.1 23.6 + - - +
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Residues in contact with LEU 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q ALA* 3.7 8.1 - - + +
17Q MET* 3.5 45.5 - - - +
18Q LEU* 3.7 13.0 - - + +
87Q ALA 3.0 13.4 + - - +
88Q PHE* 3.0 20.8 + - + +
90Q ASP* 1.3 78.4 - - - +
92Q LEU* 1.3 58.1 + - + +
94Q ASN* 3.4 7.0 + - + +
95Q ALA* 3.0 26.5 + - - +
114Q VAL* 5.0 2.2 - - + -
143Q VAL* 3.7 33.9 - - + +
145Q LEU* 3.9 25.4 - - + -
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Residues in contact with LEU 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q ILE* 4.5 7.9 - - + -
40Q ALA* 4.3 17.3 - - + +
43Q ALA* 3.8 24.0 - - + -
44Q VAL* 4.3 20.4 - - + +
47Q LEU* 4.0 19.5 - - + -
88Q PHE* 2.8 20.7 + - + +
89Q LEU* 3.9 4.9 - - + +
91Q LEU* 1.3 73.8 - - + +
93Q GLU* 1.3 61.1 + - - +
94Q ASN 3.1 1.3 - - - -
95Q ALA* 4.3 3.1 - - + -
96Q VAL* 2.8 39.5 + - + +
111Q ILE* 4.0 19.7 - - + -
145Q LEU* 3.5 24.5 - - + -
147Q LEU* 4.9 1.8 - - + -
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Residues in contact with GLU 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4930 U 4.6 3.8 + - - +
4940 C 3.7 41.1 + - - +
4950 A 5.5 1.6 + - - -
44Q VAL* 5.8 0.6 - - - +
89Q LEU 2.8 18.7 + - - +
90Q ASP* 3.7 16.4 - - - +
92Q LEU* 1.3 75.6 - - - +
94Q ASN* 1.3 58.2 + - - +
96Q VAL* 4.0 4.0 - - - +
97Q GLY* 3.1 24.1 + - - -
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Residues in contact with ASN 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4930 U 4.0 13.6 + - - +
4990 G 3.4 20.8 + - - +
5000 G 2.7 55.5 + - - +
16Q ALA* 3.6 9.3 - - + +
17Q MET 4.7 1.8 + - - +
90Q ASP 3.1 13.1 + - - +
91Q LEU* 3.5 10.7 - - + +
93Q GLU* 1.3 75.1 - - - +
95Q ALA* 1.3 58.0 + - - +
97Q GLY* 3.0 1.9 + - - -
98Q ASN* 2.8 51.2 + - - -
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Residues in contact with ALA 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q ALA* 4.4 1.8 - - - +
15Q LYS 4.2 5.6 - - - +
16Q ALA* 3.5 20.2 - - + -
91Q LEU 3.0 17.6 + - - +
92Q LEU* 3.8 3.6 - - - +
94Q ASN* 1.3 77.0 - - - +
96Q VAL* 1.3 57.4 + - - +
98Q ASN* 3.0 8.1 + - - +
99Q ALA* 2.8 29.6 + - - +
145Q LEU* 4.1 14.6 - - + -
147Q LEU* 3.5 22.9 - - + +
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Residues in contact with VAL 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Q ALA* 3.6 32.1 - - + -
44Q VAL* 5.7 3.6 - - + -
92Q LEU* 2.8 28.6 + - + +
93Q GLU* 4.2 4.5 - - - +
95Q ALA* 1.3 72.2 - - - +
97Q GLY* 1.3 57.0 + - - +
99Q ALA* 3.4 8.2 - - - +
100Q ASP* 3.0 39.5 + - - +
106Q GLY* 3.8 4.0 - - - -
107Q GLU* 3.8 28.9 - - + +
147Q LEU* 4.1 5.2 - - + -
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Residues in contact with GLY 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4920 C 4.9 2.3 + - - -
4930 U 5.4 15.5 - - - +
93Q GLU 3.1 13.6 + - - -
94Q ASN* 3.0 7.2 + - - -
96Q VAL* 1.3 76.5 - - - +
98Q ASN* 1.3 65.6 + - - +
100Q ASP* 3.3 8.3 + - - +
101Q HIS* 3.1 23.7 + - - +
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Residues in contact with ASN 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4920 C 4.5 2.6 + - - -
4930 U 5.2 3.0 + - - -
5000 G 3.1 29.5 - - - +
5010 G 2.9 38.4 + - - +
14Q ALA* 5.1 2.2 - - + -
15Q LYS 3.1 20.1 - - - +
94Q ASN* 2.8 31.8 + - - +
95Q ALA 3.4 6.1 - - - +
97Q GLY* 1.3 76.9 - - - +
99Q ALA* 1.3 63.5 + - - +
101Q HIS* 3.2 16.6 + - - +
102Q GLN* 3.3 23.8 + - - +
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Residues in contact with ALA 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q ALA* 3.9 16.3 - - + +
95Q ALA 2.8 12.9 + - - +
96Q VAL* 3.4 11.4 - - - +
98Q ASN* 1.3 76.4 - - - +
100Q ASP* 1.3 62.4 + - - +
102Q GLN* 3.1 10.2 + - - -
104Q PHE* 3.1 27.6 + - - -
106Q GLY* 3.8 3.8 - - - -
109Q MET* 3.0 34.8 - - + -
147Q LEU* 4.4 1.1 - - + -
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Residues in contact with ASP 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Q VAL* 3.0 32.3 + - - +
97Q GLY* 3.7 8.1 - - - +
98Q ASN 3.2 0.4 - - - -
99Q ALA* 1.3 72.1 - - - +
101Q HIS* 1.3 56.9 + - - +
102Q GLN 2.9 10.0 + - - -
103Q GLY* 3.0 13.9 + - - -
104Q PHE 3.2 10.3 - - - +
105Q ASP* 4.1 1.6 - - - +
106Q GLY 3.1 23.1 + - - -
107Q GLU* 5.9 0.3 - - - +
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Residues in contact with HIS 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4910 C 4.4 9.0 + - - -
4920 C 3.2 56.7 + - - +
5010 G 4.3 13.4 + - - -
5020 A 6.0 2.7 - - - -
97Q GLY 3.1 16.8 + - - +
98Q ASN* 3.2 9.4 + - - +
100Q ASP* 1.3 73.8 - - - +
102Q GLN* 1.3 61.9 + - + +
103Q GLY 3.5 0.2 - - - -
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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