Contacts of the helix formed by residues 59 - 81 (chain A) in PDB entry 6U81
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 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.6 1.1 - - + -
53A ALA* 4.6 0.4 - - + -
58A ILE* 1.3 93.9 - - + +
60A GLU* 1.3 66.6 + - - +
61A PRO* 3.3 14.8 - - + -
62A ARG* 3.0 30.9 + - + +
63A VAL* 3.3 7.4 + - - +
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Residues in contact with GLU 60 (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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46A ILE* 3.7 7.1 - - - +
49A ARG* 2.6 50.8 + - + -
50A GLU* 3.9 21.8 - - + +
53A ALA* 3.6 19.1 - - + +
58A ILE 3.5 1.4 + - - -
59A PRO* 1.3 71.8 - - - +
61A PRO* 1.3 80.5 - - + +
63A VAL* 2.8 5.1 + - - +
64A GLN* 2.8 24.8 + - - +
96A ARG* 2.9 39.3 + - - -
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Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 3.4 13.0 - - + -
60A GLU* 1.3 104.3 - - + +
62A ARG* 1.3 77.7 + - - +
64A GLN* 3.3 8.7 + - + +
65A ILE* 3.0 28.8 + - - +
96A ARG* 5.6 0.7 - - - +
135A GLU* 5.7 0.7 - - - +
136A SER* 3.7 35.2 - - - +
137A ARG* 6.1 0.4 - - - +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.6 40.7 - - - +
24A LEU* 4.5 13.0 - - + -
26A TRP* 4.2 11.0 - - + -
58A ILE* 3.5 15.3 - - + -
59A PRO* 3.0 32.9 + - + +
61A PRO* 1.3 89.9 - - - +
63A VAL* 1.3 66.1 + - - +
65A ILE* 3.3 26.5 + - - +
66A TRP* 2.9 22.9 + - - +
135A GLU* 5.0 0.8 + - - -
136A SER* 5.6 1.8 - - - +
139A GLN* 4.7 9.7 + - - -
6B A 2.8 52.1 + - - +
7B T 4.7 1.8 + - - -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.6 4.7 - - + -
49A ARG* 4.2 20.6 - - + +
52A LEU* 4.0 11.2 - - + -
53A ALA* 3.9 23.8 - - + +
56A ILE* 4.5 8.7 - - + -
58A ILE* 3.3 24.7 - - + -
59A PRO 3.3 5.4 + - - +
60A GLU* 2.8 9.3 + - - +
62A ARG* 1.3 76.2 - - - +
64A GLN* 1.3 64.1 + - - +
66A TRP* 3.1 7.2 + - - +
67A PHE* 3.0 47.4 + - + -
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Residues in contact with GLN 64 (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 ARG* 3.7 26.6 - - - +
60A GLU* 2.8 22.4 + - - +
61A PRO* 3.6 11.5 - - - +
63A VAL* 1.3 75.0 - - - +
65A ILE* 1.3 65.9 + - + +
67A PHE* 3.2 4.1 + - - +
68A GLN* 3.0 51.4 + - + +
96A ARG* 2.8 25.3 + - - -
137A ARG* 3.8 10.9 + - - +
7C T 3.0 34.6 + - - +
8C T 5.0 2.1 + - - +
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Residues in contact with ILE 65 (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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61A PRO* 3.0 16.3 + - + +
62A ARG* 3.6 28.3 - - - +
64A GLN* 1.3 75.0 - - + +
66A TRP* 1.3 65.8 + - - +
68A GLN* 3.0 19.8 + - + +
69A ASN* 2.8 40.3 + - - +
139A GLN* 5.9 3.1 - - - +
5B A 4.7 2.7 - - + -
6B A 4.3 18.8 - - + +
7B T 3.8 27.8 - - + -
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Residues in contact with TRP 66 (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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26A TRP* 3.6 37.7 - + + +
31A SER* 5.2 0.4 - - - -
34A LEU* 3.4 58.2 - - + +
35A ARG* 3.8 12.3 - - + -
38A PHE* 3.8 23.8 - + + -
62A ARG 2.9 14.4 + - - +
63A VAL* 3.1 9.2 + - - +
65A ILE* 1.3 77.6 - - - +
67A PHE* 1.3 82.0 + + - +
69A ASN* 3.2 5.7 + - - +
70A GLU* 2.6 65.4 + - + +
73A ARG* 3.3 15.0 - - - +
5B A 3.7 17.6 + - - -
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Residues in contact with PHE 67 (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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34A LEU 4.5 0.2 - - - -
37A CYS* 3.9 22.7 - - + -
38A PHE* 3.6 35.0 - + - -
41A ASN 3.7 9.9 - - - -
42A PRO 3.8 5.4 - - - -
44A PRO* 3.5 41.7 - - + -
49A ARG* 5.1 2.7 - - + -
52A LEU* 4.0 11.0 - - + -
63A VAL* 3.0 41.8 + - + -
64A GLN* 3.6 8.5 - - - +
66A TRP* 1.3 96.6 - + - +
68A GLN* 1.3 58.1 + - - +
70A GLU* 4.3 1.8 - - - -
71A ARG* 2.9 46.2 + - - +
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Residues in contact with GLN 68 (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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64A GLN* 3.0 49.4 + - + +
65A ILE* 3.5 22.2 - - + +
67A PHE* 1.3 77.2 - - + +
69A ASN* 1.3 60.4 + - - +
71A ARG* 3.7 24.5 + - - +
72A SER* 3.0 27.5 + - - -
7B T 5.4 3.3 - - + +
8B C 5.5 4.3 + - - -
7C T 4.6 1.0 - - - +
8C T 3.5 39.2 + - + +
9C A 5.5 3.4 + - - +
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Residues in contact with ASN 69 (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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65A ILE* 2.8 31.8 + - - +
66A TRP 3.7 3.1 - - - +
68A GLN* 1.3 72.6 - - - +
70A GLU* 1.3 60.1 + - - +
72A SER* 3.2 8.4 + - - -
73A ARG* 2.7 50.6 + - + +
5B A 3.6 19.1 + - - +
6B A 2.9 48.4 + - - -
7B T 3.6 9.7 + - - +
10C G 5.6 0.3 - - - +
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Residues in contact with GLU 70 (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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35A ARG* 6.0 2.5 - - - +
38A PHE* 3.5 27.3 - - + -
66A TRP* 2.6 49.8 + - + +
67A PHE 3.9 1.1 - - - +
69A ASN* 1.3 73.6 - - - +
71A ARG* 1.3 51.1 + - - +
73A ARG* 2.6 46.3 + - - +
74A GLN* 2.7 65.4 + - - +
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Residues in contact with ARG 71 (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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38A PHE* 3.7 23.3 - - + -
42A PRO* 2.9 26.3 + - + +
43A TYR* 3.6 34.9 - - - +
44A PRO* 4.4 2.6 - - - +
67A PHE* 2.9 34.2 + - - +
68A GLN* 3.8 23.7 - - - +
70A GLU* 1.3 76.1 - - - +
72A SER* 1.3 53.4 + - - +
74A GLN* 3.0 3.8 + - - +
75A LEU* 2.6 44.0 + - + +
85A TRP* 4.7 4.9 - - + -
7C T 5.3 0.6 - - - +
8C T 2.9 45.9 + - - +
9C A 3.0 24.6 + - - +
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Residues in contact with SER 72 (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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68A GLN 3.0 14.1 + - - -
69A ASN* 3.5 14.0 + - - -
71A ARG* 1.3 77.3 - - - +
73A ARG* 1.3 61.8 + - - +
75A LEU* 3.9 11.0 - - - +
76A ARG* 3.0 35.1 + - - +
9C A 4.7 7.6 + - - -
10C G 3.2 34.0 + - - -
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Residues in contact with ARG 73 (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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66A TRP* 3.3 25.7 + - - +
69A ASN* 2.7 34.6 + - + +
70A GLU* 2.6 51.5 + - - +
72A SER* 1.3 74.8 - - - +
74A GLN* 1.3 60.7 + - - +
76A ARG* 3.4 25.9 + - - +
77A GLN* 3.1 22.2 + - - +
4B T 3.8 29.4 - - - +
5B A 2.8 25.0 + - - -
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Residues in contact with GLN 74 (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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38A PHE* 3.8 26.0 - - + -
70A GLU* 2.7 45.9 + - - +
71A ARG 3.5 4.0 - - - +
73A ARG* 1.3 70.5 - - + +
75A LEU* 1.3 63.0 + - - +
77A GLN* 3.1 6.9 + - - +
78A HIS* 2.9 58.4 + - - -
85A TRP* 3.6 20.4 - - + -
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Residues in contact with LEU 75 (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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71A ARG* 2.6 27.4 + - + +
72A SER* 3.9 8.5 - - - +
74A GLN* 1.3 72.8 - - - +
76A ARG* 1.3 62.0 + - - +
78A HIS* 3.7 3.7 + - - +
79A ARG* 3.2 42.0 + - - +
85A TRP* 3.3 50.9 - - + +
9C A 3.7 43.1 - - + +
10C G 3.8 16.2 - - - +
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Residues in contact with ARG 76 (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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72A SER* 3.0 26.4 + - - +
73A ARG* 3.7 29.4 + - - +
74A GLN 3.3 0.2 - - - -
75A LEU* 1.3 77.0 - - - +
77A GLN* 1.3 60.5 + - - +
79A ARG* 3.6 20.2 + - - +
80A ARG* 3.2 46.3 + - - +
4B T 5.6 7.9 - - - +
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Residues in contact with GLN 77 (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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73A ARG 3.1 15.7 + - - +
74A GLN* 3.1 11.7 + - - +
76A ARG* 1.3 73.9 - - - +
78A HIS* 1.3 72.4 + - + +
79A ARG 3.0 1.1 - - - -
80A ARG* 2.8 50.5 + - - +
81A GLU* 2.8 48.7 + - - +
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Residues in contact with HIS 78 (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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74A GLN* 2.9 53.2 + - - +
75A LEU 4.3 2.5 - - - +
77A GLN* 1.3 74.1 - - + +
79A ARG* 1.3 57.4 + - - +
81A GLU* 3.3 7.5 + - - +
82A SER* 2.9 7.3 + - - -
83A ARG* 2.9 69.7 + - + +
84A PRO 3.7 20.9 - - - -
85A TRP* 3.7 37.2 - + + -
86A PRO* 4.2 7.4 - - + +
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Residues in contact with ARG 79 (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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75A LEU* 3.2 30.8 + - - +
76A ARG* 3.6 20.9 + - - +
77A GLN 3.0 0.6 - - - -
78A HIS* 1.3 78.4 - - - +
80A ARG* 1.3 62.2 + - - +
82A SER* 3.4 13.4 + - - +
83A ARG 5.0 0.4 - - - -
10C G 3.1 33.3 + - - +
11C C 3.3 61.0 + - - +
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Residues in contact with ARG 80 (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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76A ARG* 3.2 41.0 + - - +
77A GLN* 2.8 38.7 + - - +
79A ARG* 1.3 77.9 - - - +
81A GLU* 1.3 58.9 + - + +
82A SER* 3.1 6.2 + - - -
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Residues in contact with GLU 81 (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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77A GLN* 2.8 55.0 + - - +
78A HIS* 3.9 7.4 + - - +
80A ARG* 1.3 70.0 - - + +
82A SER* 1.3 70.3 + - - +
83A ARG* 2.8 53.2 + - + +
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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
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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