Contacts of the helix formed by residues 63 - 82 (chain A) in PDB entry 7BQQ
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 GLU 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 3.4 28.0 - - + +
60A SER* 3.0 19.4 + - - +
62A SER* 1.3 79.8 + - - +
64A VAL* 1.3 63.7 + - - +
65A ILE 3.1 3.1 + - - -
66A LYS* 2.8 53.5 + - - +
67A ASP* 4.4 4.5 + - - +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.8 24.5 - - + +
53A LEU* 4.0 11.9 - - + -
54A ALA* 3.7 30.1 - - + +
57A LYS* 3.8 24.7 - - + -
59A THR* 3.8 9.6 - - + -
60A SER 3.5 0.4 + - - -
61A PRO 3.3 21.5 - - - +
63A GLU* 1.3 75.6 - - - +
65A ILE* 1.3 67.1 + - + +
66A LYS 3.3 0.2 - - - -
67A ASP* 3.1 14.3 + - + +
68A LEU* 3.0 29.5 + - + +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.1 44.9 - - + +
36A LEU* 3.8 18.2 - - + -
37A GLN* 4.1 17.0 - - + +
50A LEU* 3.6 34.5 - - + -
61A PRO 3.4 18.4 - - - +
62A SER* 3.3 22.2 - - - +
63A GLU 3.1 0.4 - - - -
64A VAL* 1.3 77.3 - - + +
66A LYS* 1.3 56.2 + - - +
68A LEU* 3.7 4.7 - - + +
69A ALA* 2.9 30.5 + - - +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 5.9 1.2 - - - +
33A ARG* 3.8 42.0 - - - +
62A SER 3.9 13.0 - - - +
63A GLU* 2.8 44.3 + - - +
64A VAL 3.3 0.2 - - - -
65A ILE* 1.3 74.6 - - - +
67A ASP* 1.3 63.4 + - - +
69A ALA* 3.8 3.5 + - - +
70A GLU* 3.6 23.6 + - - +
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 5.8 13.0 + - - +
63A GLU 4.5 7.8 - - - +
64A VAL* 3.1 13.1 + - + +
66A LYS* 1.3 78.6 - - - +
68A LEU* 1.3 67.8 + - + +
69A ALA 3.5 0.2 + - - -
70A GLU* 3.5 14.7 + - - +
71A GLN* 3.1 20.1 - - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.7 18.6 - - + -
50A LEU* 5.4 0.7 - - + -
53A LEU* 3.9 22.0 - - + -
57A LYS* 6.2 2.7 - - - -
64A VAL* 3.0 22.7 + - + +
65A ILE* 3.3 9.4 + - + +
67A ASP* 1.3 78.9 - - + +
69A ALA* 1.3 60.7 + - - +
71A GLN* 3.3 29.5 + - - +
72A VAL* 3.6 2.6 + - - +
94A PHE* 3.6 35.4 - - + -
97A ASP* 3.8 18.4 - - + +
98A LEU* 3.5 33.0 - - + -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 3.5 29.3 - - + +
32A VAL* 3.5 17.1 - - + +
33A ARG* 3.6 18.8 - - + +
36A LEU* 3.4 4.0 - - + +
65A ILE 2.9 18.0 + - - +
66A LYS* 4.0 5.2 - - - +
68A LEU* 1.3 75.5 - - - +
70A GLU* 1.3 64.2 + - - +
72A VAL 3.5 1.0 + - - -
73A TRP* 3.1 23.4 + - - +
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 2.8 41.3 + - + +
66A LYS 3.6 13.0 + - - +
67A ASP* 3.5 12.5 + - - +
68A LEU 3.4 0.2 - - - -
69A ALA* 1.3 77.9 - - - +
71A GLN* 1.3 57.3 + - + +
73A TRP* 3.2 4.2 + - - +
74A ARG* 2.8 74.5 + - + +
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Residues in contact with GLN 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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67A ASP* 3.1 20.2 - - - +
68A LEU* 3.5 19.7 - - - +
69A ALA 3.2 0.6 - - - -
70A GLU* 1.3 75.2 - - + +
72A VAL* 1.3 62.1 + - - +
74A ARG* 3.7 4.6 + - - +
75A ALA* 3.2 21.0 + - - +
90A LEU* 4.0 23.7 - - + +
93A LYS* 3.5 27.2 + - + +
94A PHE* 3.7 28.7 - - + +
97A ASP* 2.8 24.6 + - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 3.8 11.4 - - + -
32A VAL* 3.7 27.1 - - + -
68A LEU 3.6 1.7 + - - +
69A ALA 3.5 0.6 + - - +
70A GLU 3.3 0.2 - - - -
71A GLN* 1.3 74.7 - - - +
73A TRP* 1.3 65.8 + - - +
75A ALA* 3.0 9.2 + - - +
76A MET* 3.0 41.3 + - - +
91A ILE* 5.9 1.8 - - + -
94A PHE* 3.4 53.6 - - + -
108A PHE* 3.7 16.2 - - + -
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Residues in contact with TRP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 5.1 0.2 - - + -
20A MET* 4.5 3.4 - - - -
25A PRO* 3.3 38.8 + - + +
28A VAL* 3.3 38.6 - - + -
29A LYS* 3.6 28.2 - - + +
32A VAL* 4.8 2.2 - - + -
69A ALA 3.1 17.8 + - - +
70A GLU 3.8 2.2 - - - +
72A VAL* 1.3 74.2 - - - +
74A ARG* 1.3 91.0 + - - +
76A MET* 3.0 19.7 + - + -
77A GLU* 3.0 61.0 + - + +
80A ARG* 3.9 30.3 - - - -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 5.6 3.0 - - - +
26A GLU* 4.4 5.3 + - - -
29A LYS* 4.1 12.5 - - - +
70A GLU* 2.8 53.9 + - + +
71A GLN* 4.0 3.6 - - - +
73A TRP* 1.3 92.1 - - - +
75A ALA* 1.3 59.2 + - - +
77A GLU* 2.8 37.6 + - - +
78A ARG* 3.2 30.6 + - + +
90A LEU* 3.6 22.4 - - + -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 4.1 8.5 - - + -
71A GLN 3.2 13.5 + - - +
72A VAL* 3.0 11.7 + - - +
74A ARG* 1.3 75.0 - - - +
76A MET* 1.3 56.9 + - - +
79A ALA* 3.0 30.1 + - - +
87A ALA* 3.3 30.0 - - - +
90A LEU* 3.8 11.6 - - + +
91A ILE* 3.8 18.8 - - + -
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Residues in contact with MET 76 (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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13A MET* 3.5 34.1 - - + +
16A MET* 4.4 2.0 - - + -
17A ALA* 3.2 24.2 - - + +
20A MET* 3.6 23.8 - - - -
28A VAL* 3.7 19.7 - - + -
32A VAL* 3.8 9.2 - - + -
72A VAL* 3.0 35.7 + - + +
73A TRP* 3.0 17.3 + - + +
75A ALA* 1.3 72.7 - - - +
77A GLU* 1.3 60.5 + - - +
79A ALA* 3.2 2.6 + - - +
80A ARG 2.9 23.7 + - - -
112A MET* 3.6 26.9 - - + -
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Residues in contact with GLU 77 (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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73A TRP* 3.0 50.6 + - + +
74A ARG* 2.8 46.7 + - - +
76A MET* 1.3 75.0 - - - +
78A ARG* 1.3 75.7 + - - +
80A ARG* 3.2 12.7 + - - +
81A GLU* 3.0 35.6 + - + +
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Residues in contact with ARG 78 (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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74A ARG* 3.2 21.8 + - + +
75A ALA 3.9 2.9 - - - +
77A GLU* 1.3 85.1 + - - +
79A ALA* 1.3 59.9 + - - +
81A GLU* 3.2 11.1 + - - +
82A GLY 3.2 5.4 + - - -
83A ASP* 2.8 73.4 + - - +
86A THR* 3.6 18.0 + - + +
87A ALA 4.3 7.2 - - - +
90A LEU* 4.1 13.0 - - + -
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Residues in contact with ALA 79 (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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10A THR 4.8 0.2 - - - +
13A MET* 3.7 4.9 - - + -
14A ARG* 3.6 51.4 + - + +
75A ALA 3.0 19.9 + - - +
76A MET 3.2 5.4 + - - +
78A ARG* 1.3 75.0 - - - +
80A ARG* 1.3 60.0 + - - +
82A GLY* 3.4 11.8 + - - -
83A ASP 4.3 6.1 - - - +
84A LYS* 4.9 1.3 - - - +
87A ALA* 4.0 14.3 - - + +
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Residues in contact with ARG 80 (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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14A ARG 5.5 1.6 - - - +
17A ALA* 2.9 42.3 + - + +
18A GLU* 4.5 7.6 - - + +
20A MET* 3.8 13.5 + - - +
21A ASP* 3.6 41.0 + - - +
22A GLY 4.9 0.6 - - - +
23A GLN* 6.0 0.2 - - - +
28A VAL* 5.6 0.8 - - - +
73A TRP* 3.9 26.8 - - - -
76A MET 2.9 12.6 + - - +
77A GLU* 3.2 13.8 + - - +
79A ALA* 1.3 71.8 - - - +
81A GLU* 1.3 66.2 + - + +
82A GLY* 3.2 5.8 + - - -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 3.0 20.5 + - + +
78A ARG* 3.2 15.2 + - - +
80A ARG* 1.3 78.2 - - + +
82A GLY* 1.3 58.1 + - - +
83A ASP* 3.5 5.2 - - + +
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Residues in contact with GLY 82 (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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14A ARG* 5.9 7.1 + - - -
78A ARG 3.2 1.6 + - - -
79A ALA 3.4 9.3 + - - -
80A ARG 3.2 5.3 - - - -
81A GLU* 1.3 78.8 - - - +
83A ASP* 1.3 58.5 + - - +
84A LYS* 3.4 9.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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