Contacts of the helix formed by residues 50 - 72 (chain A) in PDB entry 3COQ
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 THR 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.1 20.8 + - + +
49A LEU* 1.3 77.9 - - - +
51A ARG* 1.3 66.5 + - - +
52A ALA* 3.0 7.3 + - - +
53A HIS* 3.2 22.5 + - - +
54A LEU 3.0 17.3 + - - -
49B LEU* 3.4 11.6 - - - +
12D G 3.3 26.5 - - - +
13D T 3.3 10.5 - - - +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 1.3 72.4 - - - +
52A ALA* 1.3 54.5 + - - +
54A LEU* 3.5 11.8 - - - +
55A THR* 2.6 48.9 + - - +
58A GLU* 5.1 1.2 + - - -
46B ARG* 4.2 28.5 - - - +
47B SER* 2.9 48.7 + - - +
48B PRO* 4.9 0.2 - - - +
49B LEU* 3.7 28.0 - - - +
13D T 2.7 19.3 + - - +
14D C 2.5 49.2 + - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 3.1 7.0 - - - +
51A ARG* 1.3 78.5 - - - +
53A HIS* 1.3 62.5 + - - +
55A THR* 3.5 7.0 + - - -
56A GLU* 2.9 25.8 + - - +
13D T 4.4 0.8 + - - +
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.8 12.2 - - - -
48A PRO* 3.4 35.8 - - + +
50A THR* 3.2 17.9 + - - +
51A ARG 3.2 0.2 - - - -
52A ALA* 1.3 79.2 - - - +
54A LEU* 1.4 67.7 + - - +
55A THR 3.1 0.9 - - - -
56A GLU* 3.2 9.7 + - + +
57A VAL* 3.0 37.0 + - + +
54B LEU* 3.9 12.8 - - + -
58B GLU* 3.3 20.5 + - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR 3.0 12.5 + - - +
51A ARG* 3.5 23.8 - - - +
53A HIS* 1.4 77.3 - - - +
55A THR* 1.3 57.4 + - - +
57A VAL* 3.3 1.6 + - - +
58A GLU* 2.8 57.1 + - + +
47B SER* 3.3 23.1 - - - +
48B PRO 3.8 17.0 - - - +
49B LEU* 3.9 15.9 - - + +
50B THR 6.1 0.2 - - - +
53B HIS* 3.8 14.6 - - + +
54B LEU* 4.4 30.2 - - + +
57B VAL* 4.6 4.9 - - + -
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Residues in contact with THR 55 (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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51A ARG* 2.6 36.8 + - - +
52A ALA* 3.6 7.0 - - - -
53A HIS 3.1 0.2 - - - -
54A LEU* 1.3 75.3 - - - +
56A GLU* 1.3 67.9 + - - +
58A GLU* 3.7 13.0 + - - +
59A SER* 2.9 33.1 + - - +
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Residues in contact with GLU 56 (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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52A ALA 2.9 17.8 + - - +
53A HIS* 3.2 13.7 + - + +
55A THR* 1.3 74.7 - - - +
57A VAL* 1.3 65.6 + - + +
59A SER* 2.9 16.7 + - - -
60A ARG* 3.0 44.0 + - - +
63A ARG* 4.4 13.9 + - - -
81B LEU 5.5 0.2 - - - +
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Residues in contact with VAL 57 (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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53A HIS* 3.0 44.0 + - + +
54A LEU 3.7 2.9 - - - +
56A GLU* 1.3 76.4 - - + +
58A GLU* 1.3 64.2 + - - +
60A ARG* 2.8 21.4 + - - +
61A LEU* 3.0 10.9 + - - +
54B LEU* 4.5 2.7 - - + -
57B VAL* 3.0 37.9 - - + +
58B GLU* 4.2 17.5 - - + +
61B LEU* 4.2 14.1 - - + -
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Residues in contact with GLU 58 (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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51A ARG* 5.1 0.9 + - - -
54A LEU* 2.8 51.0 + - + +
55A THR* 3.9 13.0 + - - +
57A VAL* 1.3 73.0 - - - +
59A SER* 1.3 62.7 + - - +
61A LEU* 3.8 7.6 - - + +
62A GLU* 3.0 27.0 + - + +
47B SER* 2.6 36.1 + - - -
53B HIS* 3.4 5.2 + - - -
57B VAL* 4.3 13.2 - - + -
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Residues in contact with SER 59 (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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55A THR* 2.9 25.2 + - - +
56A GLU* 2.9 12.5 + - - -
58A GLU* 1.3 74.3 - - - +
60A ARG* 1.3 63.6 + - - +
62A GLU* 3.6 5.0 + - - +
63A ARG* 3.1 50.5 + - - +
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Residues in contact with ARG 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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56A GLU* 3.0 39.8 + - - +
57A VAL* 2.8 13.1 + - - +
59A SER* 1.3 73.9 - - - +
61A LEU* 1.3 68.6 + - - +
63A ARG* 2.8 29.7 + - - +
64A LEU* 3.0 13.0 + - - +
61B LEU* 3.9 23.1 - - + +
65B GLU* 4.8 2.2 + - - -
81B LEU* 3.3 57.5 + - + +
82B LYS* 6.3 0.8 - - - +
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Residues in contact with LEU 61 (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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57A VAL 3.0 14.3 + - - +
58A GLU* 3.8 7.9 - - + +
60A ARG* 1.3 77.4 - - - +
62A GLU* 1.4 52.3 + - - +
64A LEU* 3.2 1.7 + - - +
65A GLU* 2.7 44.6 + - + +
57B VAL* 4.3 32.3 - - + +
60B ARG* 3.9 22.7 - - + -
61B LEU* 3.9 23.7 - - + +
64B LEU* 3.6 28.7 - - + -
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Residues in contact with GLU 62 (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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58A GLU* 3.0 20.4 + - + +
59A SER* 3.8 6.3 - - - +
60A ARG 3.1 0.2 - - - -
61A LEU* 1.4 73.9 - - - +
63A ARG* 1.3 69.4 + - + +
65A GLU* 3.6 10.1 - - - +
66A GLN* 3.0 53.6 + - - +
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Residues in contact with ARG 63 (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 GLU* 4.4 8.9 + - - -
59A SER* 3.1 45.5 + - - +
60A ARG* 2.8 14.4 + - - +
62A GLU* 1.3 79.1 - - + +
64A LEU* 1.3 66.4 + - - +
66A GLN* 3.0 6.3 + - - +
67A LEU* 2.9 22.6 + - - +
80B ILE* 3.3 18.4 - - + +
81B LEU* 2.7 31.0 + - - +
82B LYS* 4.2 7.8 + - - +
83B MET 2.8 31.1 + - - +
84B ASP* 4.7 11.7 + - - +
89B ILE* 4.3 16.4 - - + +
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Residues in contact with LEU 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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60A ARG 3.0 10.7 + - - +
61A LEU* 3.8 5.6 - - - +
63A ARG* 1.3 78.1 - - - +
65A GLU* 1.3 64.7 + - - +
67A LEU* 3.2 8.5 + - + -
68A PHE* 2.9 45.8 + - + -
61B LEU* 3.9 12.3 - - + -
64B LEU* 3.5 34.1 - - + -
65B GLU* 3.6 30.3 - - + +
68B PHE* 4.1 18.2 - - + -
77B LEU* 4.4 9.2 - - + -
80B ILE* 4.9 8.5 - - + -
81B LEU* 4.6 9.0 - - + -
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Residues in contact with GLU 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 LEU* 2.7 34.7 + - + +
62A GLU* 3.6 16.4 - - - +
63A ARG 3.1 0.2 - - - -
64A LEU* 1.3 74.2 - - - +
66A GLN* 1.3 58.2 - - + +
68A PHE* 3.4 4.4 + - - +
69A LEU* 3.0 24.1 + - - +
77A LEU* 4.1 11.6 - - - +
60B ARG* 2.7 46.4 + - - -
64B LEU* 4.3 5.6 - - - +
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Residues in contact with GLN 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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62A GLU* 3.0 37.7 + - - +
63A ARG* 3.3 8.5 - - - +
65A GLU* 1.3 76.3 - - - +
67A LEU* 1.3 64.7 + - - +
69A LEU* 2.9 31.8 + - - +
70A LEU* 3.4 10.7 + - - +
86B LEU* 2.8 38.0 - - + +
89B ILE* 4.2 16.8 - - + -
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Residues in contact with LEU 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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63A ARG 2.9 12.0 + - - +
64A LEU* 3.6 12.6 - - + +
66A GLN* 1.3 73.3 - - - +
68A PHE* 1.3 69.0 + - + +
70A LEU* 3.2 8.9 + - + +
71A ILE* 3.2 34.4 + - + +
68B PHE* 4.1 26.7 - - + -
72B PHE* 4.6 5.6 - - + -
80B ILE* 4.1 24.7 - - + -
89B ILE* 3.3 39.6 - - + +
92B LEU* 4.6 4.7 - - + -
93B LEU* 4.1 17.3 - - + -
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Residues in contact with PHE 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 LEU* 2.9 46.8 + - + +
65A GLU* 3.6 5.4 - - - +
67A LEU* 1.3 80.4 - - + +
69A LEU* 1.4 63.0 + - - +
70A LEU 3.1 0.2 - - - -
71A ILE* 3.6 8.5 - - + +
72A PHE* 2.9 52.2 + + - +
77A LEU* 4.0 22.2 - - + +
64B LEU* 3.9 21.5 - - + -
67B LEU* 3.6 23.8 - - + -
68B PHE* 3.7 36.6 - + + -
71B ILE* 4.4 11.7 - - + -
72B PHE* 6.3 0.4 - + - -
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Residues in contact with LEU 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 GLU 3.0 11.8 + - - +
66A GLN* 2.9 25.6 + - - +
68A PHE* 1.4 76.3 - - - +
70A LEU* 1.3 72.1 + - + +
72A PHE 4.3 3.8 - - - +
73A PRO* 3.4 32.2 - - + +
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Residues in contact with LEU 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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66A GLN 3.7 14.1 - - - +
67A LEU* 3.2 6.5 + - - +
68A PHE 3.1 0.2 - - - -
69A LEU* 1.3 89.3 - - + +
71A ILE* 1.3 67.5 + - - +
73A PRO* 3.5 12.7 - - - +
89B ILE* 4.4 11.4 - - + +
90B LYS* 3.6 49.6 - - + +
93B LEU* 3.8 21.9 - - + +
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Residues in contact with ILE 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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67A LEU* 3.2 27.1 + - + +
68A PHE* 3.3 12.5 + - + +
70A LEU* 1.3 76.2 - - - +
72A PHE* 1.3 98.8 + - + +
73A PRO* 3.0 10.6 - - - +
96A LEU* 4.4 18.9 - - + +
71B ILE* 4.6 9.4 - - + -
72B PHE* 4.8 9.6 - - + -
93B LEU* 3.3 44.0 - - + -
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Residues in contact with PHE 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 PHE* 2.9 49.4 + + - +
69A LEU* 3.5 10.2 - - - +
71A ILE* 1.3 96.7 - - + +
73A PRO* 1.3 66.9 - - - +
74A ARG 3.1 17.8 + - - +
75A GLU 4.3 3.1 + - - +
77A LEU* 4.1 24.5 - - + +
80A ILE* 4.0 20.0 - - + -
92A LEU* 5.9 0.4 - - + -
93A LEU* 3.5 33.4 - - + -
96A LEU* 4.9 7.2 - - + -
67B LEU* 3.9 11.0 - - + -
71B ILE* 4.4 5.2 - - + -
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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