Contacts of the helix formed by residues 60 - 81 (chain A) in PDB entry 6BQG
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 ILE 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO 5.3 2.7 - - - +
57A ALA* 3.0 18.9 + - + +
58A LEU 2.9 1.8 + - - -
59A SER* 1.3 83.9 + - - +
61A VAL* 1.3 66.2 + - - +
62A ILE* 3.0 3.1 + - - -
63A ILE* 3.2 43.9 + - + +
64A ILE* 4.4 0.8 - - + +
111A LEU* 3.7 16.8 - - + -
114A ILE* 5.6 4.0 - - + -
355A TRP* 4.7 15.7 - - + -
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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
----------------------------------------------------------
58A LEU* 2.9 28.0 + - + +
59A SER* 2.9 8.1 + - - +
60A ILE* 1.3 78.1 - - - +
62A ILE* 1.3 66.1 + - + +
64A ILE* 2.7 44.2 + - + +
65A ILE* 3.1 28.7 + - + +
111A LEU* 4.5 11.4 - - + +
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Residues in contact with ILE 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 SER* 3.2 17.5 - - - +
60A ILE* 3.0 1.5 - - - +
61A VAL* 1.3 85.5 - - + +
63A ILE* 1.3 67.9 + - + +
65A ILE* 3.3 17.3 + - + +
66A MET* 3.3 31.5 + - + +
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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
----------------------------------------------------------
60A ILE* 3.2 32.3 + - + +
62A ILE* 1.3 79.8 - - + +
64A ILE* 1.3 74.3 + - + +
66A MET* 3.2 15.8 + - - +
67A THR* 3.2 26.0 + - - +
107A MET* 5.4 2.2 - - - -
355A TRP* 3.9 28.0 - - + -
359A VAL* 4.3 22.9 - - + -
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Residues in contact with ILE 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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60A ILE 4.4 2.5 - - - +
61A VAL* 2.7 30.7 + - + +
63A ILE* 1.3 72.7 - - - +
65A ILE* 1.3 65.7 + - + +
67A THR* 3.1 11.6 + - - -
68A ILE* 3.3 24.1 + - + +
103A GLY 3.7 21.8 - - - +
107A MET* 4.0 39.0 - - + +
108A PRO* 4.5 7.9 - - + -
111A LEU* 4.0 27.1 - - + -
355A TRP* 4.1 17.9 - - + -
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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
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61A VAL* 3.1 30.2 + - + +
62A ILE* 3.7 9.9 - - + +
64A ILE* 1.3 80.2 - - + +
66A MET* 1.3 62.6 + - + +
68A ILE* 4.5 8.9 - - + +
69A GLY* 3.5 18.0 + - - -
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Residues in contact with MET 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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62A ILE* 3.3 26.0 + - + +
63A ILE* 3.2 17.0 + - - +
64A ILE 3.2 0.8 - - - -
65A ILE* 1.3 79.6 - - + +
67A THR* 1.3 55.3 + - - +
70A GLY* 2.8 28.8 + - - -
362A GLY* 5.6 1.4 - - - +
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Residues in contact with THR 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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63A ILE* 3.2 11.8 + - - +
64A ILE 3.1 8.7 + - - -
66A MET* 1.3 75.1 - - - +
68A ILE* 1.3 68.1 + - - +
70A GLY* 3.2 7.6 + - - -
71A ASN* 3.0 27.4 + - - +
99A ASP 3.8 22.4 - - - +
103A GLY* 3.9 7.2 - - - -
107A MET* 3.7 30.6 - - + +
358A TYR 5.1 0.2 + - - -
359A VAL* 5.6 1.9 - - - -
361A SER* 3.8 7.2 - - - +
362A GLY* 3.7 22.2 - - - -
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Residues in contact with ILE 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 ILE* 3.3 23.6 + - + +
65A ILE* 4.5 10.1 - - + +
67A THR* 1.3 77.5 - - - +
69A GLY* 1.3 62.8 + - - +
71A ASN 3.5 0.3 + - - -
72A ILE* 3.1 39.7 + - + +
100A MET* 3.6 18.7 - - + +
103A GLY 3.5 34.5 - - - +
104A LEU* 4.0 29.6 - - + +
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Residues in contact with GLY 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 ILE 3.5 11.9 + - - -
68A ILE* 1.3 76.9 - - - +
70A GLY* 1.3 66.3 + - - +
72A ILE* 3.0 14.4 + - - +
73A LEU* 3.0 31.0 + - - +
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Residues in contact with GLY 70 (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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66A MET 2.8 21.9 + - - -
67A THR* 3.2 2.4 + - - -
69A GLY* 1.3 76.6 - - - +
71A ASN* 1.3 59.0 + - - +
73A LEU* 3.7 12.0 + - - +
74A VAL* 3.5 12.5 + - - +
362A GLY* 5.8 1.6 - - - -
365A PRO* 3.4 24.8 - - - +
379A PHE* 4.1 4.5 - - - -
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Residues in contact with ASN 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 THR* 3.0 26.0 + - - +
68A ILE 4.2 0.2 - - - +
69A GLY 3.2 0.4 - - - -
70A GLY* 1.3 73.3 - - - +
72A ILE* 1.3 66.9 + - - +
73A LEU 3.2 0.2 - - - -
74A VAL* 3.0 8.4 + - - +
75A ILE* 2.9 26.6 + - - +
96A ALA* 3.3 35.2 - - + +
99A ASP* 3.2 30.7 - - - +
100A MET* 3.7 16.2 - - + +
361A SER 3.8 5.3 + - - -
362A GLY* 4.9 0.2 - - - -
365A PRO* 3.1 26.4 - - - +
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Residues in contact with ILE 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 ILE* 3.1 35.7 + - + +
69A GLY* 3.0 12.9 + - - +
71A ASN* 1.3 76.5 - - - +
73A LEU* 1.3 59.7 + - + +
75A ILE* 3.0 11.6 + - + +
76A MET* 2.7 53.7 + - + +
100A MET* 3.7 18.8 - - - -
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Residues in contact with LEU 73 (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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69A GLY 3.0 19.0 + - - +
70A GLY* 3.8 8.3 - - - +
71A ASN 3.2 0.2 - - - -
72A ILE* 1.3 78.6 - - + +
74A VAL* 1.3 56.1 + - - +
76A MET* 3.2 15.5 + - + +
77A ALA* 2.8 28.6 + - - +
379A PHE* 3.4 43.0 - - + +
382A TYR* 3.7 31.7 - - + +
383A LEU* 3.9 31.9 - - + -
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Residues in contact with VAL 74 (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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70A GLY 3.5 16.6 - - - +
71A ASN* 3.0 8.6 + - - +
73A LEU* 1.3 77.0 - - - +
75A ILE* 1.3 61.5 + - - +
77A ALA* 3.1 3.3 + - - +
78A VAL* 3.0 36.7 + - + +
92A LEU* 4.5 13.0 - - + +
93A MET* 4.9 0.4 - - - -
96A ALA* 4.0 18.4 - - + -
365A PRO* 3.7 22.7 - - + +
368A TYR* 6.2 4.0 - - + -
375A TYR* 4.1 19.7 - - + +
379A PHE* 3.5 19.3 - - + -
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Residues in contact with ILE 75 (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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71A ASN 2.9 18.6 + - - +
72A ILE* 3.5 9.0 - - + +
74A VAL* 1.3 74.4 - - - +
76A MET* 1.3 59.2 + - + +
78A VAL* 3.7 1.4 + - - +
79A SER* 2.7 38.6 + - - +
93A MET* 4.2 24.6 - - + +
96A ALA* 3.9 13.9 - - + -
97A ILE* 3.9 28.7 - - + +
100A MET* 4.3 24.2 - - + -
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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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72A ILE* 2.7 37.1 + - + +
73A LEU* 3.4 23.6 - - + +
75A ILE* 1.3 71.7 - - + +
77A ALA* 1.3 59.4 + - - +
79A SER* 2.9 4.6 + - - -
80A MET* 2.7 43.4 + - + +
382A TYR* 3.5 35.7 - - + +
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Residues in contact with ALA 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 LEU 2.8 19.0 + - - +
74A VAL 3.1 5.1 + - - +
76A MET* 1.3 72.1 - - - +
78A VAL* 1.3 62.7 + - - +
81A GLU* 3.1 30.4 + - - +
84A LEU* 3.6 21.2 - - + +
375A TYR* 3.6 18.8 - - + -
378A ALA* 4.1 8.3 - - + -
379A PHE* 4.3 1.3 - - + -
382A TYR* 3.4 19.0 - - + -
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Residues in contact with VAL 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 VAL* 3.0 21.1 + - + +
75A ILE 4.3 2.9 - - - +
77A ALA* 1.3 77.0 - - - +
79A SER* 1.3 59.7 + - - +
81A GLU 4.6 0.2 - - - -
84A LEU* 3.4 25.5 - - + +
85A HIS* 3.7 19.2 + - - -
89A ASN* 3.8 20.9 - - + +
90A TYR* 3.8 26.3 - - + -
93A MET* 4.2 22.0 - - + -
375A TYR* 3.6 24.5 - - + +
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Residues in contact with SER 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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75A ILE* 2.7 29.0 + - - +
76A MET* 2.9 5.5 + - - -
78A VAL* 1.3 78.0 - - - +
80A MET* 1.3 70.1 + - - +
85A HIS* 3.2 21.0 + - - -
93A MET* 4.9 6.6 - - - -
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Residues in contact with MET 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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76A MET* 2.7 28.3 + - + +
79A SER* 1.3 76.6 - - - +
81A GLU* 1.3 66.0 + - + +
82A LYS* 3.4 2.9 + - - +
85A HIS* 4.6 1.4 - - - -
382A TYR* 3.3 28.5 - - + +
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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
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77A ALA 3.1 20.5 + - - +
78A VAL 4.1 0.9 - - - +
80A MET* 1.3 76.7 - - - +
82A LYS* 1.3 57.1 + - - +
83A LYS* 3.6 4.1 + - - +
84A LEU* 3.6 28.8 + - + +
85A HIS* 2.7 29.0 + - - -
374A ILE* 4.7 12.2 - - + +
378A ALA* 3.9 21.7 - - + +
381A ASN* 5.7 3.1 + - - +
382A TYR* 3.5 20.4 + - - +
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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
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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