Contacts of the helix formed by residues 60 - 74 (chain n) in PDB entry 4B2Q
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 60 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56n ALA 3.5 9.1 + - - +
57n LEU* 3.5 16.2 - - - +
59n GLU* 1.3 76.5 - - - +
61n THR* 1.3 61.6 + - + +
63n LEU* 2.9 26.7 + - - +
64n PHE* 3.0 40.6 + - + -
59o GLU* 5.1 10.3 - - - +
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Residues in contact with THR 61 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18n GLY 3.8 7.9 - - - +
19n LEU* 3.6 2.4 - - - +
21n GLY* 4.8 1.3 - - - -
22n ALA* 3.7 10.2 + - - -
57n LEU 5.4 1.3 - - - +
58n SER 3.1 16.8 + - - +
60n ALA* 1.3 76.8 - - + +
62n GLY* 1.3 58.2 + - - +
63n LEU 3.3 0.8 + - - -
64n PHE* 4.4 7.6 - - + -
65n CYS* 3.4 30.7 + - - +
19o LEU* 3.2 33.0 - - + +
22o ALA* 3.5 16.8 - - + +
23o GLY* 3.3 26.7 - - - +
26o ILE* 6.0 0.2 - - + -
62o GLY* 5.6 1.1 - - - -
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Residues in contact with GLY 62 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61m THR* 5.7 0.7 - - - -
64m PHE* 4.8 5.4 - - - -
19n LEU* 3.6 17.7 - - - +
22n ALA* 3.8 19.0 - - - +
59n GLU* 3.0 17.2 + - - +
60n ALA 3.0 1.4 - - - -
61n THR* 1.3 79.7 + - - +
63n LEU* 1.3 62.5 + - - +
66n LEU* 3.2 23.6 - - - +
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Residues in contact with LEU 63 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64m PHE* 6.0 1.6 - - + -
56n ALA 5.9 0.9 - - - +
59n GLU* 3.1 42.0 - - + +
60n ALA* 2.9 9.7 + - - +
62n GLY* 1.3 83.3 - - - +
64n PHE* 1.3 63.7 + - + +
65n CYS 3.4 0.4 - - - -
66n LEU* 3.1 15.3 + - + +
67n MET* 2.9 45.4 + - + +
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Residues in contact with PHE 64 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60n ALA* 3.0 44.0 + - + +
61n THR* 4.3 4.3 - - + +
63n LEU* 1.3 77.7 - - + +
65n CYS* 1.3 62.6 + - - +
67n MET* 3.1 35.2 + - + +
68n VAL* 3.1 19.2 + - - +
19o LEU* 4.3 11.0 - - + -
59o GLU* 4.9 7.6 - - - -
62o GLY 4.9 7.4 - - - -
63o LEU* 6.0 1.6 - - + -
66o LEU* 3.5 49.3 - - + +
70o PHE* 5.7 3.6 - + - -
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Residues in contact with CYS 65 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15n SER* 3.4 25.7 + - - +
16n THR* 5.2 0.2 - - - -
18n GLY 3.5 17.7 - - - -
19n LEU* 3.5 21.4 - - + +
61n THR 3.4 13.5 + - - +
63n LEU 3.4 0.2 - - - -
64n PHE* 1.3 79.0 - - - +
66n LEU* 1.3 60.8 + - - +
68n VAL* 3.7 16.8 + - - +
69n SER* 3.8 9.5 + - - -
16o THR* 3.5 18.4 - - - -
19o LEU* 3.3 31.0 - - - -
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Residues in contact with LEU 66 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64m PHE* 3.5 62.1 - - + -
68m VAL* 5.9 2.9 - - + -
19n LEU* 3.7 10.5 - - + +
62n GLY 3.2 23.8 - - - +
63n LEU* 3.3 16.3 - - + +
64n PHE 3.0 0.4 - - - -
65n CYS* 1.3 79.0 - - - +
67n MET* 1.3 61.3 + - + +
69n SER* 2.7 28.2 + - - +
70n PHE* 3.1 34.0 - - + -
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Residues in contact with MET 67 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63n LEU* 2.9 31.6 + - + +
64n PHE* 3.1 37.9 + - + +
66n LEU* 1.3 76.7 - - + +
68n VAL* 1.3 65.0 + - + +
70n PHE* 3.2 13.3 + - + +
71n LEU* 3.1 35.8 + - + +
70o PHE* 6.3 2.2 - - + -
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Residues in contact with VAL 68 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15n SER* 3.7 17.3 - - - -
64n PHE* 3.1 18.6 + - + +
65n CYS 3.8 7.9 - - - +
66n LEU 3.3 0.4 - - - -
67n MET* 1.3 77.7 - - + +
69n SER* 1.3 59.4 + - - +
71n LEU* 3.4 15.0 + - + +
72n LEU* 3.2 28.6 - - + +
12o ALA 4.1 10.8 - - - +
16o THR* 3.7 26.0 - - + -
66o LEU* 5.8 3.4 - - + -
69o SER* 4.5 14.4 - - - +
70o PHE* 6.5 0.9 - - + -
73o LEU* 4.6 14.8 - - + -
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Residues in contact with SER 69 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68m VAL* 4.6 18.5 - - - +
12n ALA* 4.1 15.9 - - - -
15n SER* 3.6 17.8 + - - -
16n THR* 4.9 3.1 - - - -
65n CYS 3.8 5.0 + - - -
66n LEU* 2.7 27.9 + - - +
68n VAL* 1.3 80.3 - - - +
70n PHE* 1.3 69.5 + - - +
72n LEU* 3.3 2.8 + - - +
73n LEU* 3.2 32.1 + - - +
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Residues in contact with PHE 70 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64m PHE* 5.7 3.8 - + - -
67m MET* 6.3 2.2 - - + -
71m LEU* 5.1 8.5 - - + -
66n LEU* 3.1 51.4 - - + -
67n MET* 3.2 13.0 + - + +
69n SER* 1.3 77.8 + - - +
71n LEU* 1.3 55.1 + - + +
72n LEU 3.0 5.2 - - - -
73n LEU* 4.8 2.0 - - + -
74n PHE* 2.9 43.1 + + + +
75n GLY* 2.7 32.1 + - - -
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Residues in contact with LEU 71 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67n MET* 3.1 25.3 + - + +
68n VAL* 3.8 9.6 - - + +
69n SER 3.3 0.8 - - - -
70n PHE* 1.3 77.7 - - + +
72n LEU* 1.3 69.1 + - - +
75n GLY* 4.0 7.4 - - - -
76n VAL* 3.0 28.4 + - - +
70o PHE* 5.1 9.2 - - + -
73o LEU* 4.3 21.0 - - + +
74o PHE* 3.7 38.6 - - + -
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Residues in contact with LEU 72 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8n LYS* 3.3 38.3 - - - +
9n TYR* 5.2 1.0 - - - -
11n GLY* 3.4 38.4 - - - +
12n ALA* 3.6 5.2 - - + +
68n VAL* 3.2 27.6 - - + +
69n SER 3.3 6.9 + - - +
70n PHE 3.0 0.4 - - - -
71n LEU* 1.3 86.3 - - - +
73n LEU* 1.3 63.6 + - - +
76n VAL* 3.7 12.4 - - + +
9o TYR* 3.5 43.7 - - + +
12o ALA* 5.4 0.7 - - + -
13o GLY* 4.9 1.1 - - - +
73o LEU* 3.8 14.1 - - + -
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Residues in contact with LEU 73 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68m VAL* 4.6 13.7 - - + -
71m LEU* 4.1 34.3 - - + +
72m LEU* 3.8 8.3 - - + -
76m VAL* 5.4 3.1 - - - +
8n LYS 4.2 0.4 - - - +
9n TYR* 3.6 34.9 - - + -
12n ALA* 3.8 22.4 - - + -
69n SER* 3.2 21.7 + - - +
70n PHE* 5.8 1.6 - - + -
72n LEU* 1.3 86.7 - - - +
74n PHE* 1.3 82.2 + - + +
75n GLY 3.5 1.1 - - - -
76n VAL* 5.2 2.4 - - - +
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Residues in contact with PHE 74 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71m LEU* 3.7 42.4 - - + -
76m VAL* 5.5 9.0 - - - -
70n PHE* 2.9 36.5 + + + +
73n LEU* 1.3 87.7 - - + +
75n GLY* 1.3 57.9 + - - +
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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
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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