Contacts of the helix formed by residues 81 - 105 (chain A) in PDB entry 1AJ3
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 LYS 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 5.7 0.9 - - + -
70A GLY* 3.6 18.8 - - - +
73A LEU* 4.1 18.2 - - + -
74A SER* 2.9 43.0 + - - +
77A ASN* 3.2 14.6 + - - +
78A THR 3.1 3.8 + - - +
80A GLY* 1.3 73.3 - - - +
82A GLU* 1.3 75.1 + - - +
84A ILE* 2.7 44.8 + - + +
85A GLN* 2.8 50.6 + - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A THR* 3.0 49.0 + - - +
79A ILE* 4.6 2.1 - - - +
80A GLY 2.9 4.0 + - - +
81A LYS* 1.3 111.1 + - - +
83A GLU* 1.3 61.5 + - - +
85A GLN* 3.2 19.3 + - - +
86A GLN* 3.3 8.0 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.7 19.1 - - - -
80A GLY* 2.8 25.4 + - - +
82A GLU* 1.3 76.8 - - - +
84A ILE* 1.3 94.1 + - + +
86A GLN* 3.1 24.7 + - - +
87A ARG* 3.3 9.2 + - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A HIS 6.3 0.9 - - - +
12A PHE* 3.4 44.0 - - + -
13A PHE* 4.8 30.3 - - + +
16A MET* 5.0 8.3 - - + -
73A LEU* 4.3 7.4 - - + -
80A GLY 4.8 0.7 - - - +
81A LYS* 2.7 31.2 + - + +
83A GLU* 1.3 90.3 + - + +
85A GLN* 1.3 54.5 + - - +
87A ARG* 2.9 11.7 + - - +
88A LEU* 2.7 34.1 + - + +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 6.1 2.6 - - - +
81A LYS* 2.8 41.3 + - - +
82A GLU* 3.2 14.5 + - - +
84A ILE* 1.3 75.9 - - - +
86A GLN* 1.3 52.6 + - - +
88A LEU* 3.0 19.6 + - + +
89A ALA* 2.7 34.3 + - + +
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU 3.3 5.2 + - - +
83A GLU* 3.1 16.4 + - - +
85A GLN* 1.3 78.8 - - - +
87A ARG* 1.3 58.9 + - - +
89A ALA* 2.9 30.5 - - + +
90A GLN* 3.6 2.6 + - - +
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.0 22.4 - - + -
16A MET* 3.6 27.5 - - - -
17A ASP* 3.0 35.9 + - - +
20A GLU* 3.0 51.8 + - - +
83A GLU* 3.3 8.5 + - - +
84A ILE* 2.9 15.7 + - - +
86A GLN* 1.3 77.6 - - - +
88A LEU* 1.3 57.4 + - - +
90A GLN* 2.9 35.8 + - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.9 5.6 - - + -
16A MET* 3.8 22.0 - - + -
66A VAL* 3.2 35.9 - - + +
67A LEU* 4.0 31.2 - - + +
70A GLY* 5.9 1.6 - - - -
84A ILE* 2.7 16.3 + - + +
85A GLN* 3.3 22.7 - - + +
87A ARG* 1.3 73.4 - - - +
89A ALA* 1.3 60.8 + - - +
91A PHE* 2.8 32.9 + - + +
92A VAL* 3.2 22.3 + - + +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 2.7 13.1 + - + +
86A GLN* 2.9 20.8 + - + +
88A LEU* 1.3 79.1 - - - +
90A GLN* 1.3 59.7 + - - +
92A VAL* 3.5 10.7 + - - +
93A ASP* 3.1 22.3 + - - +
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 2.9 30.5 + - - +
24A LYS* 3.5 8.0 + - - -
86A GLN 3.6 2.5 + - - +
87A ARG* 2.9 20.3 + - + +
89A ALA* 1.3 76.5 - - - +
91A PHE* 1.3 53.7 + - - +
93A ASP* 3.1 11.8 + - - +
94A HIS* 2.7 77.0 + - + +
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 3.4 21.5 - - + -
19A GLU* 2.8 48.7 - - + -
20A GLU* 3.3 32.7 + - - +
22A TRP* 4.4 2.0 - + - -
23A ILE* 3.8 21.0 - - + +
63A ILE* 2.9 55.0 - - + -
66A VAL* 4.6 6.1 - - + -
87A ARG 3.7 0.4 + - - -
88A LEU* 2.8 16.8 + - + +
90A GLN* 1.3 78.7 - - - +
92A VAL* 1.3 62.8 + - + +
94A HIS* 3.2 4.9 + - - +
95A TRP* 3.0 22.1 + - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 5.4 4.9 - - + -
67A LEU* 4.4 17.7 - - + -
88A LEU* 3.2 32.3 + - + +
89A ALA* 3.7 8.5 - - - +
91A PHE* 1.3 77.1 - - + +
93A ASP* 1.3 53.8 + - - +
95A TRP* 3.1 11.1 + - + +
96A LYS* 2.7 37.6 + - + +
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 3.1 15.8 + - - +
90A GLN* 3.3 14.2 + - - +
92A VAL* 1.3 76.0 - - - +
94A HIS* 1.3 90.7 + - - +
96A LYS* 2.9 48.4 + - - +
97A GLU* 3.0 17.0 + - - +
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Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 3.2 13.5 - - - +
23A ILE* 3.7 19.3 - - + -
24A LYS* 3.0 26.7 + - + +
90A GLN* 2.7 42.6 + - + +
91A PHE 3.4 8.5 - - - +
93A ASP* 1.3 87.1 + - - +
95A TRP* 1.3 63.8 + - - +
97A GLU* 3.1 10.8 + - - +
98A LEU* 3.0 28.9 + - + +
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Residues in contact with TRP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.9 18.1 - - + +
26A LYS* 4.7 6.7 - - + -
52A LEU* 5.6 3.6 - - + -
56A LEU* 3.8 19.5 - - + -
59A HIS* 3.3 45.1 - + + -
60A GLU* 2.8 28.2 + - + +
63A ILE* 3.8 31.4 - - + +
64A GLN* 5.5 3.4 - - - -
91A PHE 3.0 12.7 + - - +
92A VAL* 3.5 12.8 - - + +
94A HIS* 1.3 75.1 - - - +
96A LYS* 1.3 65.1 + - - +
98A LEU* 3.0 30.6 + - + +
99A LYS* 2.7 48.6 + - - +
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL* 2.7 18.6 + - + +
93A ASP* 2.9 49.6 + - - +
95A TRP* 1.3 73.7 - - - +
97A GLU* 1.3 94.1 + - - +
99A LYS* 3.1 9.7 + - - +
100A GLN* 3.0 25.7 + - + +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ASP* 3.0 15.7 + - - +
94A HIS* 3.1 9.4 + - - +
96A LYS* 1.3 110.3 + - - +
98A LEU* 1.3 68.0 + - + +
100A GLN* 2.9 37.5 + - - +
101A LEU* 2.9 24.7 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.6 11.0 - - + -
26A LYS* 5.0 13.9 - - + -
27A LYS* 3.9 35.7 - - + -
30A VAL* 5.3 5.8 - - + -
52A LEU* 5.3 12.2 - - + +
94A HIS* 3.0 19.8 + - + +
95A TRP* 3.0 37.8 + - + +
97A GLU* 1.3 79.1 - - + +
99A LYS* 1.3 62.5 + - - +
101A LEU* 3.2 16.1 + - + +
102A ALA* 2.9 24.0 + - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.2 27.8 - - + +
60A GLU* 2.9 13.6 + - - -
95A TRP* 2.7 56.7 + - - +
96A LYS* 3.4 11.2 - - - +
98A LEU* 1.3 72.9 - - - +
100A GLN* 1.3 63.1 + - - +
102A ALA* 3.1 8.9 + - + +
103A ALA* 2.9 24.9 + - + +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LYS* 3.0 15.4 + - + +
97A GLU* 2.9 49.2 + - - +
99A LYS* 1.3 74.8 - - - +
101A LEU* 1.3 72.0 + - + +
103A ALA* 3.2 8.7 + - - +
104A ALA* 3.0 22.9 + - + +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 6.1 7.0 - - + -
52A LEU* 6.2 0.7 - - + -
97A GLU 2.9 9.0 + - - +
98A LEU* 3.5 21.5 - - + +
100A GLN* 1.3 84.8 - - + +
102A ALA* 1.3 63.2 + - - +
104A ALA* 3.1 10.2 + - + +
105A ARG* 2.9 28.5 + - + +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A HIS* 3.9 13.0 - - + +
52A LEU* 3.8 41.4 - - + +
53A GLU* 6.0 2.7 - - + +
56A LEU* 6.0 3.8 - - + -
98A LEU 2.9 13.1 + - - +
99A LYS* 3.4 11.9 - - + +
101A LEU* 1.3 75.0 - - - +
103A ALA* 1.3 63.7 + - - +
105A ARG* 3.2 6.8 + - - +
106A GLY 3.0 18.5 + - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A HIS* 5.8 0.7 - - - -
99A LYS* 2.9 14.8 + - + +
100A GLN* 3.4 11.7 - - - +
102A ALA* 1.3 76.9 - - - +
104A ALA* 1.3 63.2 + - - +
106A GLY* 3.1 3.4 + - - -
107A GLN* 2.7 36.5 + - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLN* 3.0 12.9 + - + +
101A LEU* 3.4 13.5 - - + +
103A ALA* 1.3 74.4 - - - +
105A ARG* 1.3 67.9 + - - +
107A GLN* 3.1 23.3 + - - +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.6 41.7 - - - +
46A ARG* 6.1 0.4 - - - +
48A LYS* 6.3 1.3 - - + -
49A HIS* 4.0 25.3 - - + +
52A LEU* 5.6 4.5 - - + -
101A LEU* 2.9 19.2 + - + +
102A ALA* 3.2 11.9 + - - +
104A ALA* 1.3 79.0 + - - +
106A GLY* 1.3 64.1 + - - +
107A GLN 3.3 5.5 + - - -
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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
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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