Contacts of the helix formed by residues 60 - 72 (chain H) in PDB entry 6BCH
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 ASP 60 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25H PHE* 5.8 2.1 - - - -
56H LEU* 4.1 25.9 - - + +
57H HIS* 2.9 18.8 + - - +
58H ASN 2.9 0.2 + - - -
59H LYS* 1.3 86.0 - - - +
61H VAL* 1.3 63.5 + - - +
62H THR* 3.1 7.9 + - - +
63H ILE* 3.0 21.0 + - + +
64H LEU* 3.7 3.0 + - - +
82H ALA* 5.1 0.9 - - - -
272H GLY* 3.0 29.9 - - - -
273H VAL* 3.1 18.4 + - - +
274H LYS 5.3 0.3 + - - -
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Residues in contact with VAL 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H HIS 4.1 0.4 + - - -
58H ASN* 3.0 24.2 + - + +
59H LYS 3.5 1.4 - - - -
60H ASP* 1.3 75.7 - - - +
62H THR* 1.3 65.0 + - + +
64H LEU* 2.9 18.2 + - - +
65H LYS* 3.1 11.1 + - + +
76H ILE* 4.2 24.2 - - + -
78H SER* 4.0 19.5 - - - +
82H ALA* 3.6 24.0 - - + -
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Residues in contact with THR 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H LYS 4.7 6.2 + - - +
60H ASP* 4.3 9.4 + - - -
61H VAL* 1.3 78.7 - - + +
63H ILE* 1.3 64.7 + - - +
65H LYS* 3.0 19.2 + - - +
66H SER* 3.0 13.2 + - - -
272H GLY* 5.8 2.4 - - - -
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ILE* 5.7 0.9 - - - +
25H PHE* 5.3 4.9 - - + -
56H LEU* 4.2 15.7 - - + -
60H ASP* 3.0 19.6 + - + +
62H THR* 1.3 80.1 + - - +
64H LEU* 1.3 65.3 + - - +
66H SER* 3.0 18.9 + - - -
67H ILE* 3.1 18.1 + - + +
271H ILE* 4.8 21.1 - - + -
272H GLY* 5.6 4.5 - - - -
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Residues in contact with LEU 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ILE* 4.0 13.7 - - + +
56H LEU* 3.7 23.8 - - + -
60H ASP 4.1 6.1 - - - +
61H VAL* 2.9 11.5 + - - +
63H ILE* 1.3 75.8 - - + +
65H LYS* 1.3 51.3 + - - +
67H ILE* 3.0 14.7 + - + +
68H ARG* 2.7 34.1 + - - +
76H ILE* 3.9 19.6 - - + +
82H ALA* 3.8 18.2 - - + +
83H ARG* 3.5 41.5 - - - +
84H ILE* 3.8 24.3 - - + +
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Residues in contact with LYS 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H VAL* 3.1 12.0 + - + +
62H THR* 3.0 14.2 + - - +
64H LEU* 1.3 77.1 - - - +
66H SER* 1.3 52.0 + - - +
68H ARG* 3.0 5.1 + - + +
69H GLU* 2.6 37.8 + - - +
76H ILE* 3.8 14.5 - - + +
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Residues in contact with SER 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASN* 5.7 0.2 - - - -
17H ILE* 3.3 37.5 + - - +
62H THR 3.0 9.5 + - - -
63H ILE* 3.0 12.4 + - - -
65H LYS* 1.3 75.5 - - - +
67H ILE* 1.3 53.0 + - - +
69H GLU* 3.0 8.7 + - - +
70H TYR* 2.7 34.5 + - - +
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Residues in contact with ILE 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ILE* 4.9 7.0 - - + -
22H ILE* 4.2 35.2 - - + +
25H PHE* 4.9 14.8 - - + -
54H ILE* 4.1 25.1 - - + -
63H ILE* 3.1 14.3 + - + +
64H LEU* 3.0 19.8 + - + +
66H SER* 1.3 75.9 - - - +
68H ARG* 1.3 62.1 + - - +
70H TYR* 3.0 8.7 + - - +
71H LEU* 2.9 43.4 + - + +
84H ILE* 4.1 15.7 - - + -
86H PHE* 5.0 1.8 - - + -
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Residues in contact with ARG 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H LEU 2.7 16.5 + - - +
65H LYS* 3.3 13.0 - - - +
67H ILE* 1.3 71.8 - - - +
69H GLU* 1.3 58.1 + - - +
71H LEU 3.1 0.9 + - - -
72H GLY* 2.8 54.9 + - - -
73H ALA* 3.3 38.2 - - - +
74H GLY 2.6 36.3 + - - +
75H ILE* 5.6 0.6 - - - +
76H ILE* 4.2 13.9 - - + -
84H ILE* 4.3 5.4 - - + +
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Residues in contact with GLU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H LYS 2.6 20.1 + - - +
66H SER* 3.4 9.4 - - - +
68H ARG* 1.3 75.2 - - - +
70H TYR* 1.3 64.9 + - - +
72H GLY* 4.1 3.7 + - - -
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Residues in contact with TYR 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASN* 6.1 2.2 - - + -
17H ILE* 3.7 28.7 - - + -
19H PRO* 3.2 35.0 - - + +
22H ILE* 3.6 21.1 - - + -
66H SER 2.7 13.5 + - - +
67H ILE 3.3 7.4 - - - +
69H GLU* 1.3 80.9 - - - +
71H LEU* 1.3 84.6 + - + +
98H HIS* 4.2 13.9 - + - -
102H TYR* 4.2 10.6 + + - -
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Residues in contact with LEU 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ILE* 5.2 6.5 - - + -
52H PHE* 6.4 0.7 - - + -
67H ILE* 2.9 39.0 + - + +
68H ARG 4.3 0.2 - - - +
70H TYR* 1.3 98.4 - - + +
72H GLY* 1.3 61.9 + - - +
73H ALA* 3.5 14.5 + - + +
86H PHE* 3.9 22.4 - - + -
94H VAL* 4.1 30.5 - - + +
95H VAL* 5.4 5.2 - - + -
98H HIS* 4.3 25.1 - - + +
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Residues in contact with GLY 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H ARG* 2.8 36.2 + - - -
69H GLU 4.1 3.3 + - - -
70H TYR 3.5 2.4 + - - -
71H LEU* 1.3 74.0 - - - +
73H ALA* 1.3 60.6 + - - +
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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
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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