Contacts of the helix formed by residues 56 - 76 (chain J) in PDB entry 5A0Q
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 ALA 56 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ASN* 3.1 23.8 - - - +
27J PHE* 5.2 6.3 - - + -
38J PHE* 3.9 24.7 - - + -
40J LYS* 5.7 0.4 - - - +
54J GLY 3.6 0.6 + - - -
55J LEU* 1.3 71.2 - - - +
57J THR* 1.3 60.7 + - + +
59J VAL* 3.5 7.4 - - - +
60J GLN* 3.0 35.7 + - - +
123K ALA* 3.7 24.0 - - + -
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Residues in contact with THR 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J LEU* 3.7 13.1 - - + +
56J ALA* 1.3 78.9 - - - +
58J ASP* 1.3 73.3 + - - +
60J GLN* 3.8 2.7 - - - +
61J THR* 2.5 38.2 + - - -
89K ALA* 5.2 4.8 - - - +
92K LEU* 4.3 12.6 - - + +
121K LEU* 3.4 42.8 - - + +
122K ALA* 2.9 30.7 - - - +
123K ALA* 4.4 3.1 - - + +
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Residues in contact with ASP 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J LEU* 3.6 13.8 + - - +
56J ALA 3.4 0.2 - - - -
57J THR* 1.3 87.0 + - - +
59J VAL* 1.3 60.0 + - - +
61J THR* 4.0 6.4 + - - -
62J VAL* 2.9 33.1 + - - +
102J TYR* 2.9 34.6 - - + +
103J TYR* 3.1 47.8 + - - +
104J THR* 3.6 8.8 - - + +
92K LEU* 5.7 1.2 - - - +
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Residues in contact with VAL 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J PHE* 4.6 7.0 - - + -
39J GLN 4.5 8.5 - - - +
40J LYS* 4.7 7.4 - - + +
42J PHE* 3.7 28.5 - - + -
52J LEU* 3.8 27.7 - - + +
53J ALA* 4.0 9.4 - - - -
54J GLY 4.1 1.3 - - - +
55J LEU 2.7 30.0 + - - +
56J ALA* 3.3 9.6 + - - +
58J ASP* 1.3 74.2 - - - +
60J GLN* 1.3 62.6 + - + +
62J VAL 4.0 0.2 - - - -
63J ALA* 3.0 30.0 + - - +
104J THR* 3.5 17.9 - - - +
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Residues in contact with GLN 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J PHE* 3.8 20.3 - - + -
42J PHE* 5.3 6.3 - - + -
56J ALA 3.0 16.5 + - - +
57J THR* 4.1 2.9 - - - +
59J VAL* 1.3 78.8 - - + +
61J THR* 1.4 61.0 + - - +
63J ALA* 3.8 5.4 - - - +
64J GLN* 2.9 33.4 + - + +
85K ARG* 3.3 28.4 - - - +
122K ALA 3.8 3.9 - - - +
123K ALA* 3.5 9.0 - - - -
124K LEU* 3.1 50.3 + - - +
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Residues in contact with THR 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J THR* 2.5 29.3 + - - -
58J ASP* 3.9 11.3 + - - -
59J VAL 3.3 0.6 - - - -
60J GLN* 1.4 72.2 - - - +
62J VAL* 1.3 59.5 + - - +
64J GLN* 3.7 4.2 - - - +
65J ARG* 3.0 64.1 + - + +
102J TYR* 4.0 28.0 - - + -
85K ARG* 4.8 0.2 - - - +
86K ARG* 4.8 7.0 - - - +
89K ALA* 4.1 17.6 - - + +
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Residues in contact with VAL 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J LEU* 3.7 23.3 - - + -
58J ASP* 2.9 18.3 + - - +
61J THR* 1.3 77.0 - - + +
63J ALA* 1.3 59.0 + - - +
65J ARG* 4.5 4.7 - - + +
66J LEU* 2.9 29.9 + - + +
90J VAL* 4.3 15.0 - - + -
93J LEU* 4.2 13.5 - - + -
94J LEU* 3.6 34.1 - - + -
102J TYR* 4.7 11.7 - - + -
104J THR* 3.7 10.1 - - + -
106J PRO* 5.5 0.2 - - + -
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Residues in contact with ALA 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J PHE* 3.8 39.3 - - + -
50J ILE* 6.2 1.3 - - - -
52J LEU* 4.5 6.4 - - + +
59J VAL 3.0 20.9 + - - +
60J GLN* 3.8 5.6 - - - +
61J THR 3.3 0.2 - - - -
62J VAL* 1.3 76.6 - - - +
64J GLN* 1.3 59.1 + - + +
66J LEU* 4.2 3.8 - - - +
67J LYS* 3.1 29.8 + - - +
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Residues in contact with GLN 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 2.8 40.5 - - + +
102C GLN* 2.6 43.1 - - - +
60J GLN* 2.9 24.2 + - - +
61J THR 3.7 3.6 - - - +
63J ALA* 1.3 74.6 - - + +
65J ARG* 1.3 66.5 + - + +
67J LYS* 3.5 4.1 + - - +
68J PHE* 3.2 16.3 + - - +
82K ASN* 4.0 0.6 + - - -
85K ARG* 1.9 38.3 - - - +
86K ARG* 2.9 17.7 - - - +
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Residues in contact with ARG 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 4.2 22.2 - - - +
61J THR* 3.0 44.6 + - + +
62J VAL* 4.2 1.8 - - + +
64J GLN* 1.3 79.3 - - + +
66J LEU* 1.4 56.9 + - - +
68J PHE* 3.4 10.2 - - + +
69J ARG* 3.1 31.4 + - + +
93J LEU* 4.0 28.3 - - + -
97J LYS* 5.7 4.9 - - - +
102J TYR* 4.5 18.1 + - + -
86K ARG* 5.0 16.1 - - - +
89K ALA* 5.5 5.9 - - - +
90K ASP* 3.6 22.0 + - - -
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Residues in contact with LEU 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J ILE* 3.6 28.3 - - + -
62J VAL* 2.9 20.9 + - + +
63J ALA* 4.2 4.3 - - - +
65J ARG* 1.4 73.7 - - - +
67J LYS* 1.3 59.3 + - - +
68J PHE 3.2 0.2 - - - -
69J ARG* 3.3 2.4 + - + +
70J LEU* 2.9 36.1 + - + +
86J LEU* 3.8 27.8 - - + -
89J MET* 3.8 28.9 - - + -
90J VAL* 3.6 34.3 - - + +
93J LEU* 4.1 7.8 - - + +
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Residues in contact with LYS 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLN* 5.2 0.7 - - - +
98C LEU* 5.7 8.1 - - + -
43J PRO 4.0 22.1 + - - +
63J ALA 3.1 18.0 + - - +
64J GLN* 4.1 4.7 - - - +
65J ARG 3.5 0.2 - - - -
66J LEU* 1.3 77.7 - - - +
68J PHE* 1.3 56.1 + - - +
70J LEU* 4.3 14.6 - - + +
71J ASN* 2.8 63.0 + - - +
74J GLU* 4.2 12.3 + - - -
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Residues in contact with PHE 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 4.2 11.9 - - + -
95C GLN* 3.3 47.5 - - + +
96C ARG* 4.1 18.8 - - + -
99C LEU* 4.2 22.9 - - + -
64J GLN 3.2 14.1 + - - +
65J ARG* 3.4 15.9 - - + +
67J LYS* 1.3 76.0 - - - +
69J ARG* 1.4 77.4 + - + +
70J LEU 3.2 0.2 + - - -
71J ASN* 3.2 3.8 + - - +
72J LEU* 3.1 52.2 + - + +
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Residues in contact with ARG 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.9 8.6 - - - +
100B TYR* 5.4 3.3 + - - -
65J ARG* 3.1 16.2 + - + +
66J LEU* 3.9 4.5 - - - +
68J PHE* 1.4 90.9 - - + +
70J LEU* 1.3 59.9 + - - +
72J LEU* 3.7 12.6 + - + +
73J TYR* 3.6 17.7 + - - +
89J MET* 3.2 47.0 + - + +
92J ASN* 4.2 10.7 - - - +
93J LEU* 3.5 35.7 - - - +
96J GLU* 3.2 36.6 + - - -
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Residues in contact with LEU 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J LEU* 2.9 23.1 + - + +
67J LYS* 3.9 17.5 - - + +
69J ARG* 1.3 76.1 - - - +
71J ASN* 1.3 58.5 + - - +
73J TYR* 3.3 9.2 + - + +
74J GLU* 2.9 48.8 + - + +
81J ILE* 3.7 42.8 - - + -
86J LEU* 3.8 26.5 - - + -
89J MET* 4.0 13.7 - - + -
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Residues in contact with ASN 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLN* 3.2 38.0 + - - +
98C LEU* 4.8 6.9 - - - +
67J LYS* 2.8 50.6 + - - +
68J PHE 3.8 1.3 - - - +
70J LEU* 1.3 74.2 - - - +
72J LEU* 1.3 64.8 + - - +
74J GLU* 3.1 20.0 + - - +
75J LEU* 3.0 33.5 + - + +
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ASN* 5.9 1.1 - - - +
91C ARG* 3.9 32.2 - - + +
92C LEU* 3.7 34.5 - - + -
95C GLN* 4.0 13.7 - - + -
68J PHE* 3.1 34.5 + - + +
69J ARG* 3.9 12.6 - - + +
70J LEU 3.3 0.6 - - - -
71J ASN* 1.3 76.3 - - - +
73J TYR* 1.3 58.4 + - - +
75J LEU* 4.2 4.9 - - - +
76J LYS* 3.2 34.2 + - - +
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Residues in contact with TYR 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B TYR* 2.4 35.2 + + - -
100B TYR* 4.0 33.2 - + + +
102B GLU* 3.5 3.4 + - - -
105B PRO* 3.9 3.3 - - - +
108B GLN* 4.5 4.0 - - - -
112B ARG* 4.6 5.8 - - - -
69J ARG 3.6 9.2 + - - +
70J LEU* 3.3 12.3 + - + +
71J ASN 3.2 0.2 - - - -
72J LEU* 1.3 75.8 - - - +
74J GLU* 1.3 60.0 + - + +
75J LEU 3.1 2.5 - - - -
76J LYS* 3.1 4.4 + - + -
77J GLU* 2.5 69.3 + - - +
79J ARG* 3.4 37.9 + - - -
81J ILE* 4.7 23.1 - - + -
85J THR* 5.4 0.9 - - + -
89J MET* 5.2 2.5 - - + -
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Residues in contact with GLU 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 6.0 0.3 - - - +
67J LYS* 4.2 9.1 + - - -
70J LEU* 2.9 42.6 + - + +
71J ASN* 3.1 31.4 + - - +
73J TYR* 1.3 73.4 - - + +
75J LEU* 1.3 59.2 + - + +
77J GLU 2.9 23.5 - - - +
78J GLY* 3.9 8.2 - - - -
79J ARG 4.8 8.7 - - - +
80J GLN* 5.3 7.5 - - - +
81J ILE* 4.7 13.2 - - + +
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Residues in contact with LEU 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 3.5 33.5 - - + +
68C LEU 3.3 23.1 - - - +
69C ASN* 4.0 14.6 - - - +
70C GLU* 5.4 4.9 - - + +
91C ARG* 3.2 48.8 + - + +
95C GLN* 4.1 23.1 - - + +
71J ASN* 3.0 23.7 + - + +
72J LEU* 4.2 2.9 - - - +
74J GLU* 1.3 78.6 - - + +
76J LYS* 1.3 64.9 + - - +
77J GLU* 3.2 4.2 + - - -
78J GLY* 4.7 0.5 + - - -
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Residues in contact with LYS 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLN* 3.1 30.0 + - - +
111B GLN* 3.7 24.4 + - - +
112B ARG* 3.8 24.9 - - + +
88C ASN* 3.9 23.3 + - - +
91C ARG* 4.1 25.5 + - - +
72J LEU* 3.2 22.0 + - - +
73J TYR* 3.1 8.6 + - + +
75J LEU* 1.3 79.9 - - - +
77J GLU* 1.3 62.9 + - - +
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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