Contacts of the helix formed by residues 60 - 72 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A PHE* 5.7 2.9 - - - -
56A LEU* 4.2 23.9 - - + +
57A HIS* 2.8 17.9 + - + +
59A LYS* 1.3 84.4 - - - +
61A VAL* 1.3 66.5 + - - +
62A THR* 3.1 8.6 + - - +
63A ILE* 3.0 22.5 + - + +
64A LEU* 3.7 6.7 + - - +
82A ALA* 5.1 0.4 - - - -
272A GLY* 3.1 29.5 - - - -
273A VAL* 3.3 16.3 + - - +
274A LYS 5.4 0.3 + - - -
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A HIS 3.8 0.8 + - - -
58A ASN* 3.0 19.6 + - - +
59A LYS 3.5 1.2 + - - -
60A ASP* 1.3 75.7 - - - +
62A THR* 1.3 64.4 + - + +
64A LEU* 2.9 18.2 + - + +
65A LYS* 3.1 11.9 + - + +
76A ILE* 4.2 24.9 - - + -
77A THR 5.5 0.2 - - - +
78A SER* 4.1 17.0 - - - +
82A ALA* 3.6 24.2 - - + -
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LYS 4.7 6.4 + - - +
60A ASP* 4.3 9.4 + - - -
61A VAL* 1.3 79.8 - - + +
63A ILE* 1.3 64.4 + - - +
65A LYS* 3.0 18.9 + - - +
66A SER* 3.0 13.0 + - - -
272A GLY* 5.7 2.3 - - - -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 5.7 0.5 - - - +
25A PHE* 5.2 4.3 - - + -
56A LEU* 4.1 16.4 - - + -
60A ASP* 3.0 20.7 + - + +
62A THR* 1.3 80.7 + - - +
64A LEU* 1.3 64.7 + - - +
66A SER* 3.0 19.3 + - - -
67A ILE* 3.1 18.0 + - + +
271A ILE* 4.7 21.5 - - + -
272A GLY* 5.7 2.9 - - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 3.8 12.3 - - + -
56A LEU* 3.5 25.1 - - + -
60A ASP 4.1 6.7 - - - +
61A VAL* 2.9 11.5 + - - +
63A ILE* 1.3 75.0 - - - +
65A LYS* 1.3 51.4 + - - +
67A ILE* 3.0 13.8 + - + +
68A ARG* 2.7 35.0 + - - +
76A ILE* 3.9 19.8 - - + +
82A ALA* 3.8 18.2 - - + +
83A ARG 3.5 41.5 - - - +
84A ILE* 3.7 24.3 - - + +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.1 11.6 + - + +
62A THR* 3.0 14.7 + - - +
64A LEU* 1.3 77.9 - - - +
66A SER* 1.3 51.5 + - - +
68A ARG* 3.0 5.9 + - - +
69A GLU* 2.6 38.2 + - - +
76A ILE* 3.9 14.5 - - + +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.2 27.8 - - - +
62A THR 3.0 10.4 + - - -
63A ILE* 3.0 13.0 + - - -
65A LYS* 1.3 74.1 - - - +
67A ILE* 1.3 52.8 + - - +
69A GLU* 3.0 8.1 + - - +
70A TYR* 2.7 35.2 + - - +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.9 7.6 - - + -
22A ILE* 4.3 35.4 - - + +
25A PHE* 4.9 14.6 - - + -
54A ILE* 4.1 26.0 - - + -
63A ILE* 3.1 13.3 + - + +
64A LEU* 3.0 21.2 + - + +
66A SER* 1.3 75.4 - - - +
68A ARG* 1.3 63.5 + - - +
70A TYR* 3.0 9.3 + - - +
71A LEU* 2.9 43.7 + - + +
84A ILE* 4.2 15.3 - - + -
86A PHE* 5.0 1.8 - - + -
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Residues in contact with ARG 68 (chain A).
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 2.7 16.3 + - - +
65A LYS* 3.3 12.1 - - - +
67A ILE* 1.3 71.2 - - - +
69A GLU* 1.3 58.8 + - - +
71A LEU 3.1 0.9 + - - -
72A GLY* 2.8 55.1 + - - -
73A ALA* 3.2 36.5 - - - +
74A GLY 2.6 36.1 + - - +
75A ILE* 5.6 0.8 - - - +
76A ILE* 4.2 15.3 - - + -
84A ILE* 4.3 5.4 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS 2.6 19.5 + - - +
66A SER* 3.4 9.2 - - - +
68A ARG* 1.3 75.3 - - - +
70A TYR* 1.3 64.2 + - - +
72A GLY* 4.1 4.6 + - - -
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASN* 6.1 2.0 - - + -
17A ILE* 3.7 28.3 - - + -
19A PRO* 3.2 35.6 - - + +
22A ILE* 3.6 20.9 - - + -
66A SER 2.7 12.8 + - - +
67A ILE 3.0 7.6 + - - +
69A GLU* 1.3 81.0 - - - +
71A LEU* 1.3 82.7 + - + +
72A GLY 3.7 0.2 + - - -
98A HIS* 4.1 15.5 - + - -
102A TYR* 4.2 9.9 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 5.2 5.4 - - + -
52A PHE* 6.3 0.9 - - + -
67A ILE* 2.9 39.0 + - + +
70A TYR* 1.3 98.8 - - + +
72A GLY* 1.3 63.1 + - - +
73A ALA* 3.4 13.6 + - + +
86A PHE* 3.9 22.4 - - + -
94A VAL* 4.2 30.5 - - + +
95A VAL* 5.4 5.4 - - + -
98A HIS* 4.2 24.9 - - + +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 2.8 35.5 + - - -
69A GLU* 4.1 3.7 + - - -
70A TYR 3.5 2.0 - - - -
71A LEU* 1.3 74.0 - - - +
73A ALA* 1.3 60.3 + - - +
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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