Contacts of the helix formed by residues 60 - 74 (chain r) 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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56r ALA 3.5 9.8 + - - +
57r LEU* 3.5 16.6 - - - +
58r SER 3.1 0.2 - - - -
59r GLU* 1.3 77.7 - - - +
61r THR* 1.3 58.9 + - + +
63r LEU* 2.9 25.9 + - - +
64r PHE* 3.0 42.1 + - + -
59s GLU* 5.3 8.7 - - - +
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Residues in contact with THR 61 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18r GLY 3.8 9.6 - - - +
19r LEU* 3.6 2.4 - - - +
21r GLY* 4.8 0.9 - - - -
22r ALA* 3.7 10.8 + - - -
57r LEU 5.4 1.6 - - - +
58r SER 3.1 16.6 + - - +
60r ALA* 1.3 78.4 - - + +
62r GLY* 1.3 58.3 + - - +
63r LEU 3.3 1.2 + - - -
64r PHE* 4.4 7.2 - - + -
65r CYS* 3.4 30.1 + - - +
19s LEU* 3.1 33.9 - - + +
22s ALA* 3.7 14.1 - - + -
23s GLY* 3.3 28.1 - - - +
62s GLY* 5.8 0.7 - - - -
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Residues in contact with GLY 62 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61q THR* 5.7 0.7 - - - -
64q PHE* 5.0 4.9 - - - -
19r LEU* 3.6 17.6 - - - +
22r ALA* 3.8 18.5 - - - +
59r GLU* 3.0 18.9 + - - +
61r THR* 1.3 79.8 + - - +
63r LEU* 1.3 62.6 + - - +
66r LEU* 3.2 23.6 - - - +
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Residues in contact with LEU 63 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64q PHE* 6.1 1.6 - - + -
56r ALA 5.9 0.9 - - - +
59r GLU* 3.1 42.0 - - + +
60r ALA* 2.9 9.9 + - - +
62r GLY* 1.3 82.4 - - - +
64r PHE* 1.3 63.7 + - + +
65r CYS 3.4 0.4 - - - -
66r LEU* 3.1 15.0 + - + +
67r MET* 2.9 44.9 + - + +
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Residues in contact with PHE 64 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60r ALA* 3.0 44.4 + - + +
61r THR* 4.3 4.9 - - + +
63r LEU* 1.3 76.6 - - + +
65r CYS* 1.3 61.5 + - - +
67r MET* 3.1 34.6 + - + +
68r VAL* 3.1 18.8 + - + +
19s LEU* 4.2 13.0 - - + -
59s GLU* 5.2 6.7 - - - -
62s GLY 5.1 5.2 - - - -
63s LEU* 6.3 0.9 - - + -
66s LEU* 3.7 48.7 - - + -
70s PHE* 5.7 3.4 - + - -
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Residues in contact with CYS 65 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15r SER* 3.4 25.8 + - - +
16r THR* 5.9 0.2 - - - +
18r GLY 3.5 13.5 - - - -
19r LEU* 3.5 21.0 - - + +
61r THR 3.4 14.2 + - - +
63r LEU 3.4 0.2 - - - -
64r PHE* 1.3 78.3 - - - +
66r LEU* 1.3 61.3 + - - +
68r VAL* 3.7 16.6 + - - +
69r SER* 3.8 9.4 + - - -
16s THR* 3.4 31.9 - - - -
19s LEU* 3.5 21.1 - - - -
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Residues in contact with LEU 66 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64q PHE* 3.6 61.2 - - + -
19r LEU* 3.7 12.0 - - + +
62r GLY 3.2 24.5 - - - +
63r LEU* 3.1 16.5 + - + +
64r PHE 3.0 0.4 - - - -
65r CYS* 1.3 78.5 - - - +
67r MET* 1.3 60.7 + - + +
69r SER* 2.7 27.3 + - - +
70r PHE* 3.1 34.2 - - + -
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Residues in contact with MET 67 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63r LEU* 2.9 32.5 + - + +
64r PHE* 3.1 37.7 + - + +
66r LEU* 1.3 76.7 - - + +
68r VAL* 1.3 66.0 + - + +
70r PHE* 3.2 13.6 + - + +
71r LEU* 3.1 34.8 + - + +
70s PHE* 6.6 0.4 - - + -
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Residues in contact with VAL 68 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15r SER* 3.7 17.7 - - - -
64r PHE* 3.1 19.2 + - + +
65r CYS 3.8 7.6 - - - +
66r LEU 3.3 0.4 - - - -
67r MET* 1.3 78.3 - - + +
69r SER* 1.3 59.9 + - - +
71r LEU* 3.4 15.9 + - + +
72r LEU* 3.2 29.7 - - + +
12s ALA 4.1 11.2 - - - +
13s GLY* 4.5 0.4 - - - -
16s THR* 3.6 26.2 - - + -
19s LEU* 6.3 0.4 - - + -
66s LEU* 6.1 2.0 - - + -
69s SER* 4.8 12.3 - - - +
73s LEU* 4.8 12.8 - - + -
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Residues in contact with SER 69 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68q VAL* 4.6 17.9 - - - +
12r ALA* 4.1 15.5 - - - -
15r SER* 3.6 18.9 + - - -
16r THR* 4.9 3.6 - - - -
65r CYS 3.8 4.6 + - - -
66r LEU* 2.7 28.6 + - - +
68r VAL* 1.3 79.4 - - - +
70r PHE* 1.3 69.5 + - - +
72r LEU* 3.3 3.3 + - - +
73r LEU* 3.2 32.8 + - - +
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Residues in contact with PHE 70 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64q PHE* 5.6 4.0 - + - -
67q MET* 6.3 1.8 - - + -
68q VAL* 6.5 1.6 - - + -
71q LEU* 5.1 8.1 - - + -
66r LEU* 3.1 50.9 - - + -
67r MET* 3.2 12.4 + - + +
69r SER* 1.3 78.7 + - - +
71r LEU* 1.3 54.1 + - + +
72r LEU 3.0 5.2 - - - -
73r LEU* 4.8 2.2 - - + -
74r PHE* 2.9 42.9 + + + +
75r GLY* 2.7 32.1 + - - -
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Residues in contact with LEU 71 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67r MET* 3.1 29.5 + - + +
68r VAL* 3.8 9.2 - - + +
69r SER 3.3 0.8 - - - -
70r PHE* 1.3 79.3 - - + +
72r LEU* 1.3 66.9 + - - +
75r GLY* 4.0 8.1 - - - -
76r VAL* 3.0 28.5 + - - +
9s TYR* 5.2 0.3 - - - -
70s PHE* 5.5 6.5 - - + -
73s LEU* 4.3 21.3 - - + +
74s PHE* 4.0 35.0 - - + -
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Residues in contact with LEU 72 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8r LYS* 3.3 38.3 - - - +
9r TYR* 5.2 0.7 - - - -
11r GLY* 3.4 38.8 - - - +
12r ALA* 3.6 5.2 - - + +
68r VAL* 3.2 27.6 - - + +
69r SER 3.3 6.5 + - - +
70r PHE 3.0 0.8 - - - -
71r LEU* 1.3 87.1 - - - +
73r LEU* 1.3 64.9 + - - +
76r VAL* 3.7 13.2 - - + +
9s TYR* 3.6 43.1 - - + +
12s ALA* 5.7 0.7 - - + -
13s GLY* 4.9 1.1 - - - +
73s LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 73 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68q VAL* 4.5 15.3 - - + -
71q LEU* 4.4 31.2 - - + +
72q LEU* 3.8 10.1 - - + -
76q VAL* 5.5 2.6 - - - +
8r LYS 4.2 0.4 - - - +
9r TYR* 3.6 34.0 - - + -
12r ALA* 3.8 22.4 - - + -
69r SER* 3.2 21.4 + - - +
70r PHE* 5.5 1.6 - - + -
72r LEU* 1.3 86.9 - - - +
74r PHE* 1.3 82.2 + - + +
75r GLY 3.5 0.7 - - - -
76r VAL* 5.2 2.4 - - - +
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Residues in contact with PHE 74 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71q LEU* 3.6 45.1 - - + -
76q VAL* 5.4 10.8 - - - -
70r PHE* 2.9 38.3 + + + +
73r LEU* 1.3 89.9 - - + +
75r GLY* 1.3 58.3 + - - +
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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