Contacts of the helix formed by residues 67 - 87 (chain A) in PDB entry 4GGF
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 ASN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.1 12.5 - - - -
27A HIS* 3.3 17.7 - - + +
61A ASN* 5.6 0.4 - - - +
63A ASP* 5.7 1.6 + - - -
65A ALA* 3.9 1.2 - - + -
66A VAL* 1.3 75.3 - - - +
68A PHE* 1.3 57.8 + - - +
69A GLN* 3.1 27.1 + - - +
70A GLU* 2.7 38.5 + - - +
71A PHE* 2.9 24.9 + - - +
68L THR* 5.7 8.9 - - + +
81L MET* 3.3 30.5 - - - +
85L ARG* 3.6 12.8 - - - +
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Residues in contact with PHE 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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12A ILE* 4.9 0.4 - - + -
13A ILE* 3.7 31.6 - - + -
16A TYR* 3.5 49.9 + + + -
17A HIS* 4.9 1.3 - + - -
27A HIS* 4.5 3.5 + - + +
67A ASN* 1.3 77.2 - - - +
69A GLN* 1.3 63.5 + - - +
71A PHE* 3.3 16.8 + + - +
72A LEU* 3.0 41.2 + - + +
87C THR* 3.7 19.7 - - + -
88C TRP* 3.7 15.9 - + + -
91C HIS* 3.6 35.0 - + + +
205C GOL 4.0 16.4 + - - +
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 3.1 25.4 + - - +
68A PHE* 1.3 80.9 - - - +
70A GLU* 1.3 62.1 + - + +
72A LEU* 3.3 19.6 + - + +
73A ILE* 3.6 8.8 + - - +
88C TRP* 3.1 47.9 - - + -
205C GOL 4.2 4.2 + - - -
81L MET* 4.3 10.7 - - + +
84L ALA* 6.1 0.5 - - - +
85L ARG* 2.9 37.4 + - + +
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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
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58A LEU* 3.1 30.9 - - - +
60A ILE* 2.9 28.4 + - + +
61A ASN* 3.0 9.0 + - - +
65A ALA 3.1 4.8 - - - +
66A VAL* 3.2 8.5 - - + -
67A ASN* 2.7 43.7 + - - +
69A GLN* 1.3 75.1 - - + +
71A PHE* 1.3 65.1 + - - +
73A ILE* 3.0 27.9 + - - +
101A CA 2.5 29.8 - - - -
81L MET* 3.7 12.9 - - + +
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Residues in contact with PHE 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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12A ILE* 3.7 20.6 - - + -
15A VAL* 4.6 4.5 - - + -
16A TYR* 3.6 44.9 - + + -
34A LEU* 5.8 1.3 - - + -
37A LEU* 3.8 28.9 - - + -
58A LEU* 5.3 0.7 - - - -
66A VAL* 3.5 11.1 - - + +
67A ASN 2.9 14.1 + - - +
68A PHE* 3.3 20.4 + + - +
70A GLU* 1.3 76.9 - - - +
72A LEU* 1.3 66.1 + - + +
74A LEU* 3.0 37.0 + - + +
75A VAL* 3.1 35.6 + - + +
8C LEU* 4.3 14.6 - - + -
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Residues in contact with LEU 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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12A ILE* 4.4 4.0 - - + -
68A PHE* 3.0 52.1 + - + +
69A GLN* 3.6 10.1 - - - +
70A GLU 3.2 0.8 - - - -
71A PHE* 1.3 78.0 - - + +
73A ILE* 1.3 57.2 + - - +
75A VAL* 3.6 21.8 - - + +
76A ILE* 2.9 37.4 + - + +
84C ALA* 3.7 36.6 - - + +
87C THR* 4.1 14.4 - - + -
88C TRP* 4.0 17.7 - - + +
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Residues in contact with ILE 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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58A LEU* 3.8 11.2 - - + +
60A ILE* 3.9 34.5 - - + -
69A GLN 3.6 6.8 + - - +
70A GLU* 3.0 21.7 + - + +
71A PHE 3.0 0.6 - - - -
72A LEU* 1.3 78.9 - - - +
74A LEU* 1.3 62.5 + - - +
76A ILE* 3.4 4.6 + - + +
77A LYS* 3.0 32.9 + - + +
60K ILE* 3.5 36.1 - - + -
73K ILE* 4.5 7.0 - - + -
103K GOL 3.6 22.2 - - - +
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Residues in contact with LEU 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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34A LEU* 4.6 4.3 - - + -
37A LEU* 3.9 27.4 - - + -
38A LEU* 4.1 15.9 - - + -
46A ILE* 4.3 0.4 - - + -
54A TRP* 3.7 43.3 - - + -
58A LEU* 3.8 27.1 - - + +
71A PHE* 3.0 24.8 + - + +
73A ILE* 1.3 77.8 - - - +
75A VAL* 1.3 58.5 + - - +
77A LYS* 3.3 0.7 + - - -
78A MET* 2.8 59.6 + - + +
8C LEU* 5.4 0.2 - - + -
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Residues in contact with VAL 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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12A ILE* 3.9 32.3 - - + -
71A PHE* 3.1 48.0 + - + +
72A LEU* 3.6 16.8 - - + +
73A ILE 3.2 0.2 - - - -
74A LEU* 1.3 77.2 - - + +
76A ILE* 1.3 59.8 + - + +
78A MET* 3.3 6.9 + - - +
79A GLY* 2.8 28.1 + - - -
8C LEU* 4.6 6.5 - - + -
12C ILE* 4.4 12.6 - - + +
15C ILE* 5.7 3.1 - - + -
80C ILE* 4.2 6.2 - - + +
84C ALA* 6.3 2.5 - - + -
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Residues in contact with ILE 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 LEU* 2.9 25.2 + - + +
73A ILE* 3.7 5.4 - - + +
75A VAL* 1.3 76.8 - - + +
77A LYS* 1.3 58.9 + - - +
79A GLY* 3.2 2.1 + - - -
80A VAL* 2.9 29.3 + - + +
80C ILE* 3.8 23.0 - - + +
81C MET* 3.6 28.0 - - + -
84C ALA* 3.7 26.5 - - + -
60K ILE* 4.1 15.7 - - + +
61K ASN* 3.7 36.3 - - + +
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Residues in contact with LYS 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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46A ILE* 4.8 2.6 - - + +
49A LYS* 4.6 4.7 - - - +
54A TRP* 4.0 31.0 - - + -
57A GLU* 4.1 13.3 + - - -
73A ILE* 3.0 25.1 + - + +
74A LEU 3.9 2.5 - - - +
76A ILE* 1.3 77.3 - - - +
78A MET* 1.3 62.1 + - - +
80A VAL* 4.0 5.1 - - - +
81A ALA* 3.0 26.3 + - - +
56K LYS 5.3 4.6 + - - -
57K GLU 5.1 2.0 + - - -
59K ASP 5.3 1.1 - - - -
60K ILE* 3.6 41.7 - - + +
62K THR* 6.1 1.8 - - - -
103K GOL 4.0 21.8 + - - -
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Residues in contact with MET 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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41A GLU 3.9 5.6 - - - +
42A SER* 3.9 28.3 - - - -
43A PRO* 3.9 14.8 - - + -
45A TYR* 4.6 1.6 + - - -
46A ILE* 3.9 25.7 - - + +
74A LEU* 2.8 45.5 + - + +
75A VAL* 3.6 4.3 - - - +
77A LYS* 1.3 71.2 - - - +
79A GLY* 1.3 58.4 + - - +
81A ALA* 3.4 1.6 + - - +
82A ALA* 2.9 31.7 + - - +
8C LEU* 3.8 32.5 - - + -
9C GLU* 4.6 5.2 - - + -
12C ILE* 3.7 18.8 - - + +
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Residues in contact with GLY 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 VAL 2.8 14.6 + - - -
78A MET* 1.3 70.6 - - - +
80A VAL* 1.3 65.8 + - - +
82A ALA* 3.3 1.9 + - - +
83A HIS* 3.0 19.2 + - - +
12C ILE* 3.8 19.2 - - - +
16C ILE* 4.1 0.7 - - - +
76C PHE* 3.4 15.7 - - - -
80C ILE* 3.5 20.2 - - - -
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Residues in contact with VAL 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 ILE 2.9 22.2 + - - +
77A LYS* 4.0 5.6 - - - +
79A GLY* 1.3 72.4 - - - +
81A ALA* 1.3 64.2 + - - +
83A HIS* 3.8 3.3 + - - +
84A LYS* 3.1 24.2 + - + +
76C PHE* 3.9 7.4 - - + -
77C GLU* 3.9 27.2 - - + +
80C ILE* 4.1 19.5 - - + -
60K ILE 5.8 0.4 - - - +
61K ASN* 4.0 22.4 - - - +
62K THR* 3.6 20.2 - - - +
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Residues in contact with ALA 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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45A TYR* 3.8 23.6 - - + -
46A ILE* 4.5 7.0 - - + -
77A LYS 3.0 19.0 + - - +
78A MET 3.8 2.9 - - - +
80A VAL* 1.3 79.1 - - - +
82A ALA* 1.3 58.4 + - - +
84A LYS* 3.2 12.7 + - - +
85A LYS* 2.9 35.4 + - + +
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Residues in contact with ALA 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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45A TYR* 3.5 15.9 + - - +
78A MET 2.9 17.9 + - - +
79A GLY 3.9 0.4 - - - +
81A ALA* 1.3 74.6 - - - +
83A HIS* 1.3 60.8 + - - +
85A LYS* 3.3 5.2 + - - +
86A SER* 3.0 27.4 + - - -
12C ILE* 4.0 10.1 - - + -
16C ILE* 3.6 20.6 - - + +
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Residues in contact with HIS 83 (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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79A GLY 3.0 17.6 + - - +
80A VAL 3.8 3.4 + - - +
82A ALA* 1.3 75.2 - - - +
84A LYS* 1.3 65.9 + - - +
86A SER* 2.7 24.1 + - - -
87A HIS* 3.6 11.7 - + - -
16C ILE* 3.5 12.5 - - + +
19C PHE* 4.3 0.8 - + - -
20C HIS* 3.5 15.0 - + - -
30C ASP* 2.8 18.7 + - - -
76C PHE* 3.5 50.3 - + + +
77C GLU* 4.9 12.4 + - - -
202C MN 2.1 36.3 + - - -
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Residues in contact with LYS 84 (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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80A VAL* 3.1 16.9 + - + +
81A ALA* 3.5 13.7 - - - +
83A HIS* 1.3 83.9 + - - +
85A LYS* 1.3 79.9 + - - +
87A HIS* 3.1 17.6 + - - +
88A GLU* 2.3 57.0 + - + +
77C GLU* 5.9 2.2 - - - +
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Residues in contact with LYS 85 (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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45A TYR* 3.9 54.6 - - + +
48A LYS* 5.9 1.8 - - - +
81A ALA* 2.9 23.8 + - - +
82A ALA* 3.7 7.0 - - - +
83A HIS 3.3 0.2 - - - -
84A LYS* 1.3 89.8 - - - +
86A SER* 1.3 62.4 + - - +
88A GLU* 3.1 43.1 + - - +
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Residues in contact with SER 86 (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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82A ALA 3.0 13.1 + - - -
83A HIS* 2.7 19.8 + - - -
84A LYS 3.1 0.2 - - - -
85A LYS* 1.3 75.5 - - - +
87A HIS* 1.3 72.6 + - - +
88A GLU 3.5 2.5 + - - +
16C ILE* 4.7 7.2 - - - -
20C HIS* 3.6 19.9 - - - -
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Residues in contact with HIS 87 (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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83A HIS* 3.6 16.2 - + - -
84A LYS* 3.1 9.8 + - - +
86A SER* 1.3 89.6 + - - +
88A GLU* 1.3 62.9 + - + +
89A GLU* 4.2 3.1 + - - -
20C HIS* 3.0 18.0 + + - -
30C ASP* 3.3 9.6 + - + -
202C MN 1.9 36.7 + - - -
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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