Contacts of the helix formed by residues 60 - 74 (chain m) 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 m).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56m ALA 3.5 8.7 + - - +
57m LEU* 3.5 16.8 - - - +
58m SER 3.1 0.2 - - - -
59m GLU* 1.3 77.9 - - - +
61m THR* 1.3 60.3 + - + +
63m LEU* 2.9 26.1 + - - +
64m PHE* 3.0 41.1 + - + -
59n GLU* 5.1 9.9 - - - +
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Residues in contact with THR 61 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18m GLY 3.8 9.5 - - - +
19m LEU* 3.6 2.3 - - - +
21m GLY* 4.8 1.1 - - - -
22m ALA* 3.7 11.1 + - - -
57m LEU 5.4 0.9 - - - +
58m SER 3.1 16.6 + - - +
60m ALA* 1.3 77.7 - - + +
62m GLY* 1.3 57.4 + - - +
63m LEU 3.3 0.8 + - - -
64m PHE* 4.4 7.0 - - + -
65m CYS* 3.4 30.3 + - - +
19n LEU* 3.1 34.1 - - + +
22n ALA* 3.5 15.9 - - + +
23n GLY* 3.3 27.5 - - - +
62n GLY* 5.7 1.1 - - - -
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Residues in contact with GLY 62 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61l THR* 5.7 0.7 - - - -
64l PHE* 4.9 5.0 - - - -
19m LEU* 3.6 16.9 - - - +
22m ALA* 3.8 18.6 - - - +
59m GLU* 3.0 18.6 + - - +
61m THR* 1.3 81.0 + - - +
63m LEU* 1.3 61.7 + - - +
66m LEU* 3.2 24.3 - - - +
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Residues in contact with LEU 63 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64l PHE* 5.9 2.0 - - + -
56m ALA 5.9 0.7 - - - +
59m GLU* 3.1 42.2 - - + +
60m ALA* 2.9 10.2 + - - +
62m GLY* 1.3 82.4 - - - +
64m PHE* 1.3 62.4 + - + +
65m CYS 3.4 0.2 - - - -
66m LEU* 3.1 15.3 + - + +
67m MET* 2.9 45.4 + - + +
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Residues in contact with PHE 64 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60m ALA* 3.0 47.2 + - + +
61m THR* 4.3 4.3 - - + +
63m LEU* 1.3 77.0 - - + +
65m CYS* 1.3 62.8 + - - +
67m MET* 3.1 36.1 + - + +
68m VAL* 3.1 18.7 + - - +
19n LEU* 4.1 12.3 - - + -
59n GLU* 4.9 7.2 - - - -
62n GLY 4.8 7.9 - - - -
63n LEU* 6.0 1.1 - - + -
66n LEU* 3.5 50.6 - - + +
70n PHE* 5.7 3.1 - + - -
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Residues in contact with CYS 65 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15m SER* 3.4 25.7 + - - +
18m GLY 3.5 13.5 - - - -
19m LEU* 3.5 22.0 - - + +
61m THR 3.4 13.9 + - - +
63m LEU 3.4 0.2 - - - -
64m PHE* 1.3 78.0 - - - +
66m LEU* 1.3 59.5 + - - +
68m VAL* 3.7 16.6 + - - +
69m SER* 3.8 9.5 + - - -
16n THR* 3.3 31.0 - - - -
19n LEU* 3.3 22.2 - - - -
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Residues in contact with LEU 66 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64l PHE* 3.6 59.9 - - + +
68l VAL* 5.7 3.1 - - + -
19m LEU* 3.7 11.9 - - + +
62m GLY 3.2 23.8 - - - +
63m LEU* 3.3 16.7 - - + +
64m PHE 3.0 0.6 - - - -
65m CYS* 1.3 79.1 - - - +
67m MET* 1.3 61.9 + - + +
69m SER* 2.7 28.1 + - - +
70m PHE* 3.1 34.9 - - + -
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Residues in contact with MET 67 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63m LEU* 2.9 31.6 + - + +
64m PHE* 3.1 37.2 + - + +
66m LEU* 1.3 76.5 - - + +
68m VAL* 1.3 65.8 + - + +
70m PHE* 3.2 12.8 + - + +
71m LEU* 3.1 35.8 + - + +
70n PHE* 6.3 2.5 - - + -
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Residues in contact with VAL 68 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15m SER* 3.7 17.5 - - - -
64m PHE* 3.1 18.6 + - + +
65m CYS 3.8 7.9 - - - +
66m LEU 3.3 0.4 - - - -
67m MET* 1.3 78.1 - - + +
69m SER* 1.3 60.4 + - - +
71m LEU* 3.4 15.5 + - + +
72m LEU* 3.2 28.9 - - + +
12n ALA 3.9 12.6 - - - +
16n THR* 3.5 27.4 - - + -
19n LEU* 6.1 0.4 - - + -
66n LEU* 5.9 2.2 - - + -
69n SER* 4.6 14.6 - - - +
73n LEU* 4.6 11.9 - - + -
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Residues in contact with SER 69 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68l VAL* 4.5 18.4 - - - +
12m ALA* 4.1 15.9 - - - -
15m SER* 3.6 19.1 + - - -
16m THR* 4.9 3.4 - - - -
65m CYS 3.8 5.0 + - - -
66m LEU* 2.7 27.9 + - - +
68m VAL* 1.3 79.1 - - - +
70m PHE* 1.3 68.7 + - - +
72m LEU* 3.3 3.1 + - - +
73m LEU* 3.2 32.6 + - - +
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Residues in contact with PHE 70 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64l PHE* 5.8 2.5 - + - -
67l MET* 6.4 1.8 - - + -
68l VAL* 6.5 1.6 - - + -
71l LEU* 4.9 10.1 - - + -
66m LEU* 3.1 51.8 - - + -
67m MET* 3.2 13.1 + - + +
69m SER* 1.3 77.8 + - - +
71m LEU* 1.3 54.9 + - + +
72m LEU 3.0 5.4 - - - -
73m LEU* 4.8 1.8 - - + -
74m PHE* 2.9 42.3 + + + +
75m GLY* 2.7 31.5 + - - -
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Residues in contact with LEU 71 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67m MET* 3.1 29.3 + - + +
68m VAL* 3.8 9.6 - - + +
69m SER 3.3 0.8 - - - -
70m PHE* 1.3 78.2 - - + +
72m LEU* 1.3 68.2 + - - +
75m GLY* 4.0 8.3 - - - -
76m VAL* 3.0 27.7 + - - +
70n PHE* 5.1 9.6 - - + -
73n LEU* 4.1 22.1 - - + +
74n PHE* 3.7 38.4 - - + -
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Residues in contact with LEU 72 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8m LYS* 3.3 38.2 - - - +
9m TYR* 5.2 1.2 - - - -
11m GLY* 3.4 38.1 - - - +
12m ALA* 3.6 5.2 - - + +
68m VAL* 3.2 28.7 - - + +
69m SER 3.3 7.1 + - - +
70m PHE 3.0 0.4 - - - -
71m LEU* 1.3 87.2 - - - +
73m LEU* 1.3 62.7 + - - +
76m VAL* 3.7 13.2 - - - +
9n TYR* 3.4 44.4 - - + +
12n ALA* 5.4 0.2 - - + -
13n GLY* 4.8 0.9 - - - +
73n LEU* 3.8 13.7 - - + -
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Residues in contact with LEU 73 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68l VAL* 4.6 12.6 - - + -
71l LEU* 4.4 31.6 - - + +
72l LEU* 3.7 14.6 - - + -
76l VAL* 5.4 3.9 - - - +
8m LYS 4.2 0.4 - - - +
9m TYR* 3.6 34.7 - - + -
12m ALA* 3.8 20.0 - - + -
69m SER* 3.2 20.7 + - - +
70m PHE* 5.8 1.6 - - + -
72m LEU* 1.3 87.0 - - - +
74m PHE* 1.3 80.5 + - + +
75m GLY 3.5 0.7 - - - -
76m VAL* 5.1 2.2 - - - +
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Residues in contact with PHE 74 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71l LEU* 3.6 43.5 - - + -
76l VAL* 5.1 14.4 - - - -
70m PHE* 2.9 37.4 + + + +
73m LEU* 1.3 89.9 - - + +
75m GLY* 1.3 58.9 + - - +
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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