Contacts of the helix formed by residues 55 - 77 (chain C) in PDB entry 4GG6
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 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 1.3 85.8 - - - +
56C PRO* 1.3 73.6 - - - +
57C GLN* 2.9 32.7 + - - +
58C PHE* 3.2 39.9 + - + -
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Residues in contact with PRO 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 4.0 13.8 - - + +
39C LYS* 3.6 37.5 - - + +
40C GLU* 4.0 0.4 - - - -
41C THR* 3.3 26.2 - - - +
54C PHE* 3.4 10.5 - - + +
55C ASP* 1.3 91.0 - - - +
57C GLN* 1.3 62.4 + - + +
59C ALA* 3.0 15.8 + - - +
60C LEU* 3.1 16.6 + - + +
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LYS* 4.6 11.9 - - - +
55C ASP* 2.9 23.1 + - - +
56C PRO* 1.3 79.5 - - + +
58C PHE* 1.3 59.9 + - + +
60C LEU* 3.2 26.0 + - - +
61C THR* 2.9 35.8 + - - +
66F ARG* 3.8 23.8 + - - +
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Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TYR* 5.3 1.6 - - - +
54C PHE* 3.7 17.5 - + + -
55C ASP* 3.2 43.7 + - + +
57C GLN* 1.3 78.4 - - + +
59C ALA* 1.3 57.7 + - - +
61C THR* 3.8 5.2 - - + -
62C ASN* 3.0 37.7 + - - +
108E ASP* 4.2 10.3 - - + -
110E ARG* 3.4 72.9 - - + +
111E GLY 3.8 18.2 - - - -
112E GLY* 5.5 1.6 - - - -
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TYR* 3.6 42.6 - - + -
34C VAL* 3.8 21.5 - - + -
36C LEU* 4.5 3.8 - - + -
54C PHE* 4.1 3.3 - - + -
56C PRO 3.0 11.6 + - - +
58C PHE* 1.3 77.4 - - - +
60C LEU* 1.3 65.8 + - - +
62C ASN* 3.2 3.1 + - - +
63C ILE* 3.1 29.2 + - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 5.6 0.9 - - + -
36C LEU* 3.4 42.8 - - + +
39C LYS* 3.5 36.6 - - + -
56C PRO* 3.1 14.2 + - + +
57C GLN* 3.4 33.9 - - - +
59C ALA* 1.3 76.4 - - - +
61C THR* 1.3 61.2 - - - +
63C ILE* 3.6 6.1 + - - +
64C ALA* 3.3 21.1 + - - +
66F ARG* 3.6 22.3 + - - +
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Residues in contact with THR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLN* 2.9 19.7 + - - +
58C PHE* 3.8 7.6 - - - -
60C LEU* 1.3 74.2 - - - +
62C ASN* 1.3 71.9 + - - +
64C ALA* 3.1 15.3 + - - +
65C VAL* 3.2 12.2 + - + +
110E ARG 4.9 11.2 - - - +
66F ARG* 3.4 26.3 + - - +
110F VAL* 3.4 35.1 - - + +
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Residues in contact with ASN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 2.9 31.6 + - - +
22C TYR* 3.5 18.4 + - + -
58C PHE* 3.0 23.2 + - - +
59C ALA 3.2 6.0 + - - +
61C THR* 1.3 80.6 - - - +
63C ILE* 1.3 57.4 + - - +
65C VAL* 3.3 12.4 + - - +
66C LEU* 3.1 30.6 + - + +
11D PHE* 4.9 9.5 - - - -
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 4.7 6.7 - - + +
12C LEU 3.4 29.2 - - - +
13C TYR* 3.8 26.7 - - + -
20C GLY* 5.1 0.4 - - - -
21C GLN 3.8 17.5 - - - +
22C TYR* 4.8 4.0 - - + -
36C LEU* 4.1 26.7 - - + -
59C ALA 3.1 17.5 + - - +
60C LEU* 4.1 5.6 - - - +
62C ASN* 1.3 73.3 - - - +
64C ALA* 1.3 61.8 + - - +
65C VAL 3.1 0.7 - - - -
66C LEU* 3.2 11.6 + - + +
67C LYS* 2.9 28.1 + - + +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU 3.3 13.7 + - - +
61C THR* 3.1 12.7 + - - +
63C ILE* 1.3 77.6 - - - +
65C VAL* 1.3 58.6 + - - +
67C LYS* 3.7 7.4 + - - +
68C HIS* 3.4 16.5 + - - +
57F TYR* 3.6 34.8 - - + +
58F ASN* 4.9 2.9 + - - +
66F ARG* 4.3 15.3 - - - +
110F VAL* 5.2 0.4 - - + -
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C THR* 3.4 16.2 - - + +
62C ASN* 3.4 11.2 - - - +
63C ILE 3.1 0.4 - - - -
64C ALA* 1.3 75.2 - - - +
66C LEU* 1.3 57.5 - - + +
68C HIS* 3.3 2.9 + - + +
69C ASN* 2.8 59.4 + - - +
57F TYR* 4.2 13.5 - - - +
110F VAL* 3.8 27.1 - - + -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 3.5 41.1 - - + +
12C LEU* 3.5 16.8 - - - +
13C TYR* 3.9 12.8 - - + +
62C ASN 3.1 20.1 + - - +
63C ILE* 3.2 11.6 + - + +
65C VAL* 1.3 79.2 - - + +
67C LYS* 1.3 54.4 + - - +
69C ASN* 3.6 7.0 - - + +
70C LEU* 2.7 37.9 + - - +
9D TYR* 3.8 27.0 - - + -
11D PHE* 3.8 25.8 - - + +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 3.7 38.6 - - + +
63C ILE 2.9 16.7 + - - +
64C ALA* 3.8 7.9 - - - +
66C LEU* 1.3 77.0 - - - +
68C HIS* 1.3 60.5 + - - +
70C LEU* 3.6 2.6 + - - +
71C ASN* 3.5 25.1 + - - +
58F ASN* 5.5 3.1 - - - +
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Residues in contact with HIS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA 3.4 10.5 + - - +
65C VAL* 3.3 6.8 + - + +
66C LEU 3.3 0.2 - - - -
67C LYS* 1.3 77.5 - - - +
69C ASN* 1.3 81.7 + - - +
71C ASN* 3.0 24.6 + - + +
72C ILE* 3.3 33.9 + - + +
37F LEU* 3.5 33.0 - - + +
57F TYR* 4.0 14.4 - - - +
58F ASN* 4.0 20.2 + - - +
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Residues in contact with ASN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL* 2.8 40.9 + - - +
66C LEU* 3.6 4.9 - - - +
68C HIS* 1.3 86.1 - - - +
70C LEU* 1.3 63.0 + - - +
72C ILE* 3.2 7.9 + - - +
73C VAL* 3.2 26.2 + - + +
9D TYR* 3.0 37.5 + - + +
30D TYR* 4.4 14.1 - - - -
37D TYR* 4.5 2.3 + - - +
61D TRP* 4.6 11.4 - - - -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TYR* 3.5 42.8 - - + +
15C SER* 4.1 7.6 - - - +
66C LEU 2.7 20.0 + - - +
67C LYS 3.8 5.2 - - - +
68C HIS 3.2 0.2 - - - -
69C ASN* 1.3 73.4 - - - +
71C ASN* 1.3 59.2 + - - +
73C VAL* 4.8 0.2 - - - -
74C ILE* 3.0 50.5 + - + +
7D PHE 3.9 13.0 - - - +
8D VAL 3.9 12.3 - - - +
9D TYR* 3.6 25.3 - - + -
32D TYR* 3.8 24.9 - - + -
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Residues in contact with ASN 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LYS 3.5 13.1 + - - +
68C HIS* 3.0 15.8 + - - +
70C LEU* 1.3 79.8 - - - +
72C ILE* 1.3 61.5 + - + +
74C ILE* 3.7 11.7 + - - +
75C LYS* 3.5 42.1 + - - +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C HIS* 3.3 43.0 + - + +
69C ASN* 3.2 8.1 + - - +
71C ASN* 1.3 77.7 - - + +
73C VAL* 1.3 62.1 + - + +
74C ILE 3.2 0.2 - - - -
75C LYS* 3.4 15.1 + - + +
76C ARG* 2.9 53.0 + - + +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASN* 3.2 17.8 + - - +
70C LEU 4.2 1.1 - - - +
72C ILE* 1.3 76.5 - - + +
74C ILE* 1.3 60.2 + - - +
76C ARG* 4.3 13.0 - - - +
77C SER* 2.9 28.6 + - - -
9D TYR* 3.7 8.1 - - + -
32D TYR* 3.5 40.3 - - + -
37D TYR* 3.4 30.1 - - + +
53D LEU* 3.8 23.3 - - + -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C SER* 5.3 3.4 - - - -
70C LEU* 3.0 38.9 + - + +
71C ASN* 3.8 11.9 - - - +
72C ILE 3.2 0.2 - - - -
73C VAL* 1.3 76.9 - - - +
75C LYS* 1.3 61.5 - - + +
77C SER* 3.2 5.4 + - - -
79C SER* 2.7 53.2 + - - +
7D PHE* 3.7 34.1 - - + -
32D TYR* 3.3 26.5 - - + +
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ASN* 3.5 32.8 + - - +
72C ILE* 3.4 14.5 + - + +
73C VAL 3.4 0.2 - - - -
74C ILE* 1.3 81.6 - - + +
76C ARG* 1.3 57.8 + - - +
78C ASN* 2.9 20.7 + - - +
79C SER* 4.8 1.8 - - - +
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Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 2.9 43.2 + - + +
73C VAL* 4.0 10.3 - - - +
75C LYS* 1.3 76.4 - - - +
77C SER* 1.3 56.9 + - - +
78C ASN* 3.2 3.3 + - - +
37D TYR* 4.0 21.2 - - - -
53D LEU* 2.7 55.8 + - + +
54D GLY* 4.3 0.4 - - - -
56D PRO* 3.6 37.8 - - + +
57D ALA* 4.2 15.0 - - - +
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL 2.9 14.0 + - - -
74C ILE 3.2 7.8 + - - -
75C LYS 3.2 0.2 - - - -
76C ARG* 1.3 74.3 - - - +
78C ASN* 1.3 64.6 + - - +
80C THR* 2.7 47.3 + - - -
32D TYR* 3.1 28.1 + - - -
53D LEU* 4.0 12.8 - - - +
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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