Contacts of the helix formed by residues 50 - 72 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.4 13.3 - - - +
54A LEU* 6.1 0.2 - - - +
48B PRO* 3.2 20.0 + - + +
49B LEU* 1.3 80.0 - - - +
51B ARG* 1.3 65.9 + - - +
52B ALA* 3.5 7.3 + - - +
53B HIS* 2.8 26.9 + - - +
54B LEU 2.9 18.0 + - - -
32E G 3.7 21.3 - - - +
33E T 3.3 13.5 - - - +
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.5 36.5 - - - +
47A SER* 2.8 48.1 + - - +
49A LEU* 3.9 20.5 - - + +
50B THR* 1.3 75.8 - - - +
52B ALA* 1.4 55.0 + - - +
54B LEU* 3.4 17.9 + - - +
55B THR* 2.7 49.7 + - - +
58B GLU* 4.8 1.8 + - - -
33E T 2.9 21.0 + - - +
34E C 2.8 56.5 + - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.2 7.0 + - - +
51B ARG* 1.4 79.8 - - - +
53B HIS* 1.3 58.3 + - - +
55B THR* 3.3 6.3 + - - -
56B GLU* 2.9 33.7 + - - +
33E T 4.5 0.4 + - - -
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.8 14.4 - - + -
58A GLU* 3.4 18.9 + - - -
47B SER* 3.8 11.2 - - - -
48B PRO* 3.3 36.5 - - + +
50B THR* 2.8 21.2 + - - +
52B ALA* 1.3 80.3 - - - +
54B LEU* 1.3 62.9 + - - +
56B GLU* 3.1 34.0 + - + +
57B VAL* 3.2 30.7 + - + +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 3.5 2.7 - - - +
48A PRO 4.1 13.2 - - - +
49A LEU* 4.0 13.5 - - + -
53A HIS* 3.9 15.3 - - + +
54A LEU* 4.4 29.8 - - + +
57A VAL* 4.5 6.5 - - + -
48B PRO 5.2 0.2 + - - -
49B LEU* 5.9 0.2 - - + -
50B THR 2.9 17.6 + - - +
51B ARG* 3.5 29.8 - - - +
53B HIS* 1.3 77.1 - - - +
55B THR* 1.3 58.6 + - - +
57B VAL* 3.3 0.9 + - - +
58B GLU* 2.7 62.9 + - + +
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 5.7 0.7 + - - -
51B ARG* 2.7 32.1 + - - +
52B ALA* 3.6 7.0 - - - -
54B LEU* 1.3 74.1 - - - +
56B GLU* 1.3 66.8 + - - +
58B GLU* 3.9 12.5 + - - +
59B SER* 2.9 34.2 + - - -
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA* 2.9 21.9 + - - +
53B HIS* 3.1 34.9 + - + +
55B THR* 1.3 75.0 - - - +
57B VAL* 1.3 63.2 + - + +
59B SER* 3.4 4.4 + - - -
60B ARG* 3.1 23.5 + - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.7 3.4 - - + -
57A VAL* 3.0 30.5 - - + -
58A GLU* 4.3 21.5 - - + +
61A LEU* 4.3 23.9 - - + +
53B HIS* 3.2 36.2 + - + +
54B LEU* 3.7 7.9 - - - +
56B GLU* 1.3 79.7 - - + +
58B GLU* 1.3 64.9 + - - +
60B ARG* 4.2 0.8 - - - +
61B LEU* 3.1 21.0 + - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 2.6 31.2 + - - -
53A HIS* 3.3 10.2 + - - -
57A VAL* 4.2 16.4 - - + -
51B ARG* 4.8 1.0 + - - -
54B LEU* 2.7 53.1 + - + +
55B THR* 3.9 11.7 + - - +
57B VAL* 1.3 73.1 - - - +
59B SER* 1.3 60.2 + - - +
61B LEU* 3.8 5.4 - - + +
62B GLU* 2.9 26.3 + - - +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 2.9 26.5 + - - -
56B GLU* 3.4 5.0 + - - -
58B GLU* 1.3 81.6 - - - +
60B ARG* 1.3 58.5 + - - +
62B GLU* 3.3 8.7 + - - +
63B ARG* 3.1 26.9 + - - +
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Residues in contact with ARG 60 (chain B).
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* 3.9 19.7 - - + -
65A GLU* 2.7 44.0 + - - -
77A LEU* 4.0 9.9 - - - +
78A ASP* 3.4 26.0 + - - -
81A LEU* 3.3 35.8 - - + +
56B GLU 3.1 13.6 + - - +
57B VAL* 4.2 2.5 - - - +
59B SER* 1.3 77.6 + - - +
61B LEU* 1.3 71.7 + - - +
62B GLU 3.0 0.9 - - - -
63B ARG* 4.2 4.2 - - - +
64B LEU* 3.0 25.9 + - + +
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Residues in contact with LEU 61 (chain B).
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* 4.2 19.1 - - + +
60A ARG* 3.9 42.2 - - + -
61A LEU* 3.9 25.4 - - + +
64A LEU* 3.9 18.8 - - + -
57B VAL 3.1 17.6 + - - +
58B GLU* 3.8 4.5 - - - +
60B ARG* 1.3 79.8 - - - +
62B GLU* 1.3 64.2 + - - +
64B LEU* 3.1 1.8 + - - -
65B GLU* 2.9 43.4 + - - +
81B LEU* 4.2 1.1 - - + -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU 2.9 18.3 + - - +
59B SER* 3.6 8.9 - - - +
60B ARG 3.0 0.4 - - - -
61B LEU* 1.3 78.6 - - - +
63B ARG* 1.3 58.0 + - - +
65B GLU* 3.2 17.9 + - + +
66B GLN* 2.9 44.7 + - + +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE 5.0 0.8 + - - -
81A LEU* 3.0 43.9 + - + +
82A LYS 4.3 4.4 + - - -
83A MET 2.8 29.0 + - - -
84A ASP* 4.4 9.7 + - - +
89A ILE* 5.4 5.1 - - - +
59B SER 3.1 14.4 + - - +
60B ARG* 3.2 5.1 + - - +
62B GLU* 1.3 80.3 - - - +
64B LEU* 1.3 58.5 + - - +
66B GLN* 2.8 43.2 + - - +
67B LEU* 3.0 30.7 + - - +
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Residues in contact with LEU 64 (chain B).
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* 3.6 32.1 - - + -
64A LEU* 3.5 24.9 - - + -
65A GLU* 4.0 11.4 - - - +
68A PHE* 3.9 21.3 - - + -
77A LEU* 4.4 10.3 - - + -
81A LEU* 3.2 39.5 - - + -
60B ARG* 3.0 30.5 + - - +
63B ARG* 1.3 72.9 - - - +
65B GLU* 1.3 67.4 + - - +
66B GLN 3.1 0.2 + - - -
67B LEU* 3.2 5.3 + - + +
68B PHE* 2.9 24.1 + - - +
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Residues in contact with GLU 65 (chain B).
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* 4.8 2.1 + - - -
64A LEU* 3.7 16.4 - - + -
61B LEU* 2.9 29.8 + - + +
62B GLU* 3.5 22.0 - - + +
64B LEU* 1.3 77.9 - - - +
66B GLN* 1.3 62.8 + - + +
68B PHE* 3.2 13.8 + - - +
69B LEU* 3.3 18.4 + - + +
77B LEU* 4.2 22.3 - - + +
81B LEU* 3.6 27.5 - - - +
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 2.9 30.5 + - + +
63B ARG* 2.8 52.7 + - - +
65B GLU* 1.3 78.5 - - + +
67B LEU* 1.3 66.5 + - - +
69B LEU* 3.3 19.2 + - - +
70B LEU* 3.6 11.6 + - - +
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Residues in contact with LEU 67 (chain B).
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* 3.6 23.1 - - + -
72A PHE* 3.9 11.9 - - + -
77A LEU* 4.1 7.4 - - + -
80A ILE* 4.2 15.7 - - + +
81A LEU* 3.9 23.6 - - + -
89A ILE* 4.2 15.3 - - + -
93A LEU* 3.8 33.2 - - + -
63B ARG* 3.0 18.5 + - - +
64B LEU* 3.8 3.8 - - + +
66B GLN* 1.3 75.3 - - - +
68B PHE* 1.3 66.2 + - - +
70B LEU* 2.9 22.3 + - + +
71B ILE* 3.5 13.3 + - + +
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Residues in contact with PHE 68 (chain B).
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* 4.1 15.3 - - + -
67A LEU* 4.1 17.7 - - + -
68A PHE* 3.7 15.9 - + + -
64B LEU 2.9 18.0 + - - +
65B GLU* 3.2 9.4 + - - +
67B LEU* 1.3 78.4 - - - +
69B LEU* 1.3 61.6 + - + +
71B ILE* 3.0 7.9 + - - +
72B PHE* 2.8 55.7 + + + -
73B PRO 3.6 12.8 - - - -
76B ASP* 3.8 15.0 - - + -
77B LEU* 3.3 50.0 - - + -
80B ILE* 4.4 13.0 - - + -
92B LEU* 5.2 2.2 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 3.3 11.6 + - + +
66B GLN* 3.5 13.9 - - - +
67B LEU 3.2 0.2 - - - -
68B PHE* 1.3 85.6 - - + +
70B LEU* 1.3 62.9 + - + +
71B ILE 3.1 1.8 - - - -
72B PHE 3.6 20.5 - - - +
74B ARG* 3.7 41.3 - - + +
77B LEU* 4.2 11.0 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 4.5 26.2 - - + +
89A ILE* 3.7 36.6 - - + -
90A LYS* 3.9 41.1 - - + +
93A LEU* 4.4 14.4 - - + +
66B GLN 3.6 14.6 + - - +
67B LEU* 2.9 16.0 + - - +
69B LEU* 1.3 78.1 - - - +
71B ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 71 (chain B).
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* 4.4 17.3 - - + -
71A ILE* 4.6 10.1 - - + -
72A PHE* 4.4 12.8 - - + -
93A LEU* 4.3 16.6 - - + -
96A LEU* 5.5 13.9 - - + -
67B LEU* 4.0 27.4 - - + +
68B PHE* 3.0 7.4 + - - +
70B LEU* 1.3 86.9 - - - +
72B PHE* 1.3 100.2 + - + +
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Residues in contact with PHE 72 (chain B).
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* 4.6 7.9 - - + -
68A PHE* 6.3 0.7 - + - -
71A ILE* 4.8 8.5 - - + -
68B PHE* 2.8 54.3 + + + +
69B LEU* 3.6 16.4 - - - +
70B LEU 3.7 0.2 - - - -
71B ILE* 1.3 109.7 - - + +
73B PRO* 1.3 80.6 - - + +
74B ARG 3.7 0.2 + - - -
76B ASP* 4.3 3.8 - - + +
92B LEU* 5.6 7.2 - - + -
93B LEU* 3.8 28.3 - - + -
96B LEU* 3.9 29.6 - - - -
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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
------------------------------------------------------------
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