Contacts of the helix formed by residues 52 - 68 (chain Q) in PDB entry 2J28
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 ARG 52 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B G 2.7 31.3 + - - +
536B G 2.8 29.9 + - - -
995B C 3.4 18.7 - - - -
48Q ASP 3.4 4.7 + - - +
49Q ARG* 2.6 73.8 + - - +
51Q GLN* 1.3 76.4 - - - +
53Q LYS* 1.3 90.3 + - - +
54Q ARG* 2.7 6.6 + - - -
55Q GLN* 2.8 31.2 + - + +
56Q PHE* 3.0 26.5 + - + +
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Residues in contact with LYS 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B C 5.3 1.0 - - + +
995B C 2.9 34.3 + - - -
996B A 5.3 5.5 + - - +
1156B A 5.7 7.9 - - - +
50Q ARG* 3.0 53.3 - - - +
51Q GLN 3.4 1.5 - - - +
52Q ARG* 1.3 97.7 - - - +
54Q ARG* 1.3 59.8 + - - +
56Q PHE* 3.1 7.1 + - - +
57Q ARG* 2.8 34.9 + - + +
60Q TRP* 5.8 0.3 - - - -
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Residues in contact with ARG 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B G 6.2 0.4 - - - +
976B G 4.4 3.6 + - - -
977B G 3.2 30.3 + - - -
1154B G 5.8 2.0 - - - -
1155B A 3.1 38.0 + - - +
1156B A 2.7 32.9 + - - -
51Q GLN* 2.8 37.0 + - - +
52Q ARG 2.7 4.9 + - - +
53Q LYS* 1.3 75.8 - - - +
55Q GLN* 1.3 69.8 + - + +
57Q ARG* 4.7 3.4 - - - -
58Q GLN* 2.7 42.0 + - + +
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Residues in contact with GLN 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B G 2.9 67.5 + - - +
536B G 4.7 5.4 + - - +
559B G 3.6 30.1 + - - +
52Q ARG* 2.8 27.6 + - + +
54Q ARG* 1.3 82.5 - - + +
56Q PHE* 1.3 63.9 + - + +
58Q GLN* 3.1 28.9 - - - +
59Q LEU* 3.5 8.8 + - - +
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Residues in contact with PHE 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B G 3.8 29.4 - - - -
995B C 3.3 65.7 - + - +
4J PHE 4.9 4.7 - - - -
5J THR* 5.0 6.3 - - + -
7J LYS* 5.6 0.4 - - - -
52Q ARG* 3.0 34.9 + - - -
53Q LYS* 3.1 7.4 + - - +
55Q GLN* 1.3 83.8 - - + +
57Q ARG* 1.3 56.0 + - - +
58Q GLN 3.2 0.9 - - - -
59Q LEU* 2.8 18.8 + - + +
60Q TRP* 2.7 65.1 + + + -
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Residues in contact with ARG 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B G 3.8 23.9 + - - +
998B C 2.6 48.7 + - - +
999B U 5.7 2.4 + - - -
1153B C 4.5 3.6 + - - -
1154B G 2.7 41.6 + - - +
1155B A 5.0 5.4 + - - -
53Q LYS* 2.8 23.2 + - + +
54Q ARG* 4.1 2.5 - - - +
56Q PHE* 1.3 73.9 - - - +
58Q GLN* 1.3 57.6 + - - +
60Q TRP* 3.9 24.8 - - + -
61Q ILE* 2.8 46.1 + - + +
92Q LYS* 2.8 24.9 - - + +
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Residues in contact with GLN 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008B A 5.4 5.9 - - - -
1009B A 3.6 48.9 + - - +
1154B G 4.9 1.9 + - - +
46J PRO* 5.1 12.8 - - - +
54Q ARG* 2.7 30.9 + - + +
55Q GLN* 3.1 23.9 - - - +
57Q ARG* 1.3 73.9 - - - +
59Q LEU* 1.3 65.7 + - - +
61Q ILE* 4.4 3.8 - - - +
62Q ALA* 3.2 26.8 + - - +
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Residues in contact with LEU 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J THR* 3.4 44.2 - - + +
7J LYS* 4.0 5.6 - - - +
41J LYS* 4.4 4.0 - - - +
45J THR* 3.7 27.1 - - + +
46J PRO* 3.8 18.4 - - + -
55Q GLN 3.5 12.1 - - - +
56Q PHE* 2.8 22.0 + - + +
58Q GLN* 1.3 86.2 - - - +
60Q TRP* 1.3 54.7 + - + +
62Q ALA* 2.9 7.1 + - + +
63Q ARG* 2.8 35.8 + - + +
96Q ASP* 3.4 9.4 - - - +
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Residues in contact with TRP 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B C 3.4 57.9 + - - -
996B A 4.2 4.7 - - - -
997B G 4.2 11.7 - - - -
4J PHE 4.2 3.8 + - - -
53Q LYS 5.8 0.4 - - - -
56Q PHE* 2.7 33.1 + - + +
57Q ARG* 3.9 25.6 - - + +
59Q LEU* 1.3 72.6 - - + +
61Q ILE* 1.3 66.2 + - + +
63Q ARG* 2.9 4.7 + - - -
64Q ILE* 2.8 25.5 + - + +
92Q LYS* 5.1 3.1 - - + -
93Q ILE* 3.4 59.5 + - + +
95Q ALA* 3.2 22.5 - - + +
96Q ASP* 3.2 24.5 + - - +
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Residues in contact with ILE 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009B A 3.1 32.3 - - - +
1010B A 3.6 16.2 - - - -
1153B C 3.1 33.7 - - - +
1154B G 3.3 14.4 - - - +
57Q ARG* 2.8 42.0 + - + +
58Q GLN 4.0 2.5 - - - +
60Q TRP* 1.3 73.3 - - + +
62Q ALA* 1.3 62.5 + - - +
64Q ILE* 3.3 10.3 + - - +
65Q ASN* 3.0 22.9 + - - +
75Q TYR* 4.2 20.9 - - + +
92Q LYS* 4.9 6.1 - - + -
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Residues in contact with ALA 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009B A 5.0 5.4 - - - +
1010B A 3.7 15.3 - - - +
41J LYS* 4.9 13.2 - - - -
46J PRO* 5.3 7.6 - - + -
58Q GLN* 3.2 14.8 + - - +
59Q LEU* 2.9 20.0 + - + +
61Q ILE* 1.3 76.3 - - - +
63Q ARG* 1.3 64.6 + - - +
64Q ILE 3.0 0.5 + - - -
65Q ASN* 3.1 3.6 + - - +
66Q ALA* 2.8 25.3 + - - +
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Residues in contact with ARG 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J THR* 4.7 0.7 - - - -
40J HIS 4.4 0.6 + - - -
41J LYS* 2.5 58.6 + - - +
43J GLU* 2.9 18.4 + - - +
44J TYR 2.6 30.3 + - - -
45J THR* 4.7 0.2 - - - -
59Q LEU* 2.8 21.5 + - + +
60Q TRP* 3.3 7.4 - - - +
62Q ALA* 1.3 70.3 - - - +
64Q ILE* 1.3 57.4 + - - +
66Q ALA* 3.0 6.7 - - - +
67Q ALA* 2.8 34.2 + - - +
95Q ALA* 3.6 17.0 - - + +
96Q ASP* 2.9 37.0 + - - +
99Q VAL* 3.3 31.5 - - + +
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Residues in contact with ILE 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q TRP* 2.8 24.8 + - + +
61Q ILE* 3.4 8.1 - - - +
62Q ALA 3.0 0.4 + - - -
63Q ARG* 1.3 66.8 - - - +
65Q ASN* 1.3 64.1 + - - +
66Q ALA 2.8 5.4 + - - -
67Q ALA* 3.1 3.8 + - - -
68Q ALA* 2.9 28.2 + - + +
75Q TYR* 3.4 34.5 - - + +
78Q PHE* 4.7 22.4 - - + -
79Q ILE* 5.1 6.3 - - + -
91Q ARG 4.2 19.1 - - - +
92Q LYS* 4.9 11.7 - - + -
94Q LEU* 5.0 3.4 - - + -
95Q ALA* 3.3 22.9 - - + +
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Residues in contact with ASN 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B A 4.0 20.2 + - - +
1011B G 3.2 17.3 + - - -
34J ARG* 6.1 1.4 - - - +
39J LYS* 5.9 2.5 - - - +
61Q ILE 3.0 15.0 + - - +
62Q ALA 3.9 2.5 - - - +
64Q ILE* 1.3 76.5 - - - +
66Q ALA* 1.3 61.1 + - - +
68Q ALA* 4.5 3.5 - - - +
69Q ARG* 3.5 21.8 + - - +
73Q ILE* 4.8 1.9 - - - +
74Q SER* 4.5 2.4 - - - -
75Q TYR* 3.0 45.5 + - + +
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Residues in contact with ALA 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J LYS* 2.8 28.7 - - - +
40J HIS* 2.9 15.8 - - - +
41J LYS* 3.8 12.1 - - + +
62Q ALA 2.8 12.9 + - - +
63Q ARG* 3.0 13.2 - - - +
64Q ILE 2.8 0.8 + - - -
65Q ASN* 1.3 75.7 - - - +
67Q ALA* 1.3 66.5 + - - +
69Q ARG* 2.8 29.6 + - - +
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Residues in contact with ALA 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J HIS* 3.5 15.2 + - - +
41J LYS 5.6 2.7 - - - +
63Q ARG* 2.8 20.4 + - - +
64Q ILE* 4.0 3.1 - - - +
66Q ALA* 1.3 70.2 - - - +
68Q ALA* 1.3 52.0 + - - +
69Q ARG 2.6 17.1 + - - -
70Q GLN* 2.6 25.6 + - - +
98Q ALA* 5.8 8.7 - - + -
99Q VAL* 6.1 4.0 - - + -
102Q LYS* 3.9 28.9 + - + +
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Residues in contact with ALA 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Q ILE* 2.9 22.0 + - + +
65Q ASN* 4.7 2.7 - - - -
67Q ALA* 1.3 72.7 - - - +
69Q ARG* 1.3 57.1 + - - +
70Q GLN* 2.8 19.4 + - - +
71Q ASN* 3.5 7.6 + - - +
73Q ILE* 3.0 32.5 - - + +
75Q TYR* 5.7 0.4 - - - -
78Q PHE* 3.4 39.0 - - + -
109Q VAL* 5.0 4.4 - - + +
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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