Contacts of the helix formed by residues 75 - 95 (chain C) 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 SER 75 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.7 2.5 - - - -
30C ASP 4.5 1.3 - - - -
31C THR* 4.2 16.4 - - - +
69C ASN* 5.8 2.2 + - - -
73C GLN 3.8 1.4 + - - -
74C LEU* 1.3 76.3 - - - +
76C PHE* 1.3 58.5 + - - +
77C GLU* 3.6 17.2 + - - +
78C GLU* 3.0 36.7 + - - +
79C PHE* 2.9 27.2 + - - +
63K ASP* 5.3 0.7 - - - +
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Residues in contact with PHE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 3.4 27.6 - - - -
80A VAL* 3.9 7.4 - - - -
83A HIS* 3.5 47.0 - + + +
12C ILE* 5.8 0.7 - - + -
15C ILE* 3.9 22.0 - - + -
16C ILE* 3.8 31.0 - - + -
19C PHE* 3.4 36.1 - + + -
30C ASP* 4.5 2.0 + - - -
75C SER* 1.3 74.4 - - - +
77C GLU* 1.3 60.9 + - - +
79C PHE* 3.1 5.9 + + - +
80C ILE* 2.8 52.8 + - + +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.9 27.0 - - + +
83A HIS* 4.9 9.9 + - - -
84A LYS* 5.9 2.8 - - - +
75C SER* 3.7 19.6 - - - +
76C PHE* 1.3 81.3 + - - +
78C GLU* 1.3 58.4 + - - +
80C ILE* 3.2 18.8 - - - +
61K ASN* 2.8 49.2 + - - +
62K THR* 3.8 11.2 + - - +
63K ASP* 4.1 11.0 - - + -
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Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.2 32.9 - - - +
67C ASP* 3.7 1.0 - - - +
68C THR* 3.2 18.9 + - - +
69C ASN* 3.0 29.8 + - - +
73C GLN 3.0 9.9 - - - +
74C LEU* 3.2 7.3 - - + +
75C SER* 3.0 25.7 + - - +
77C GLU* 1.3 74.6 - - - +
79C PHE* 1.3 66.0 + - - +
81C MET* 3.3 20.3 + - - +
203C CA 2.3 31.4 - - - -
61K ASN* 4.1 4.9 - - - +
63K ASP* 4.2 7.4 - - + +
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 5.0 2.7 - - + -
15C ILE* 4.0 12.8 - - + -
18C THR* 5.9 0.4 - - + -
19C PHE* 3.7 31.6 - + + -
32C LEU* 3.9 14.1 - - + -
37C PHE* 4.4 14.1 - + - -
40C LEU* 3.8 37.0 - - + -
66C LEU* 5.2 0.9 - - - -
74C LEU* 4.6 11.2 - - + +
75C SER 2.9 16.4 + - - +
76C PHE* 3.6 10.8 - + - +
78C GLU* 1.3 78.7 - - - +
80C ILE* 1.3 64.2 + - - +
82C LEU* 2.9 31.5 + - + +
83C MET* 3.5 47.2 + - + -
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Residues in contact with ILE 80 (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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75A VAL* 4.2 6.1 - - + +
76A ILE* 3.8 39.0 - - + +
79A GLY* 3.5 32.1 - - - -
80A VAL* 4.1 10.1 - - + -
12C ILE* 5.9 1.3 - - + -
15C ILE* 5.2 9.4 - - + -
76C PHE* 2.8 36.8 + - + +
77C GLU 3.2 19.5 - - - +
79C PHE* 1.3 75.7 - - - +
81C MET* 1.3 59.1 + - - +
83C MET* 3.1 17.1 + - + -
84C ALA* 2.9 26.3 + - - +
61K ASN* 4.3 2.0 - - + -
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Residues in contact with MET 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.6 28.7 - - + -
66C LEU* 4.1 9.4 - - + -
77C GLU 3.9 0.2 - - - +
78C GLU* 3.5 11.7 - - - +
79C PHE 3.1 0.4 - - - -
80C ILE* 1.3 73.8 - - - +
82C LEU* 1.3 54.3 + - - +
84C ALA* 3.1 4.9 + - - +
85C ARG* 2.7 53.3 + - - +
60K ILE* 5.0 2.0 - - + -
61K ASN* 3.1 49.8 - - + +
63K ASP* 5.1 0.4 - - - +
67K ASN* 3.5 25.4 - - - +
69K GLN* 4.0 11.0 - - + +
70K GLU* 3.9 16.4 - - + +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.9 33.0 - - + -
45C LEU* 4.2 14.1 - - + -
49C LEU* 4.7 9.0 - - + -
62C ILE* 4.2 19.3 - - + -
66C LEU* 3.8 19.9 - - + +
79C PHE* 2.9 15.3 + - + +
81C MET* 1.3 76.9 - - - +
83C MET* 1.3 71.4 + - + +
85C ARG* 3.2 12.5 + - + +
86C LEU* 2.9 52.2 + - + +
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Residues in contact with MET 83 (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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5A LEU* 4.0 27.4 - - + -
9A LEU* 4.1 21.0 - - + +
15C ILE* 3.8 21.1 - - + -
45C LEU* 4.0 25.8 - - + -
79C PHE* 3.5 52.7 + - + +
80C ILE* 3.1 12.9 + - + +
82C LEU* 1.3 83.8 - - + +
84C ALA* 1.3 63.1 + - - +
86C LEU* 3.9 5.2 - - + +
87C THR* 2.8 30.6 + - - -
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Residues in contact with ALA 84 (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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72A LEU* 3.7 20.2 - - + +
75A VAL* 6.3 2.5 - - + -
76A ILE* 3.7 33.9 - - + -
80C ILE* 2.9 10.8 + - + +
81C MET* 3.5 8.5 - - - +
83C MET* 1.3 75.5 - - - +
85C ARG* 1.3 65.4 + - + +
87C THR* 3.3 6.0 + - - -
88C TRP* 3.0 24.1 + - - +
69K GLN* 6.1 1.6 - - - +
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Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 6.0 1.4 - - - +
65C ASP* 2.8 33.9 + - - -
66C LEU* 3.8 25.4 - - - +
81C MET* 2.7 26.6 + - - +
82C LEU* 3.6 16.8 - - + +
84C ALA* 1.3 74.2 - - + +
86C LEU* 1.3 57.3 + - + +
88C TRP* 3.4 10.4 - - - +
89C ALA* 2.8 28.5 + - - +
27K HIS* 6.3 0.8 - - - +
67K ASN* 3.6 13.7 - - - +
69K GLN* 3.1 40.2 + - - +
88L TRP* 4.6 19.2 - - + -
92L GLU* 6.1 0.2 - - - -
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Residues in contact with LEU 86 (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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9A LEU* 3.9 13.9 - - + -
45C LEU* 3.8 39.7 - - + -
48C PHE* 4.2 10.6 - - + +
49C LEU* 4.0 29.2 - - + -
82C LEU* 2.9 37.0 + - + +
83C MET* 4.2 4.9 - - + -
85C ARG* 1.3 74.4 - - + +
87C THR* 1.3 67.5 + - - +
89C ALA* 3.7 6.4 - - + +
90C SER* 2.9 24.8 + - - -
109C LEU* 3.9 20.2 - - + +
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Residues in contact with THR 87 (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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9A LEU* 3.6 45.3 - - - +
12A ILE* 4.2 11.3 - - + +
13A ILE* 3.5 20.0 - - + +
68A PHE* 3.7 15.7 - - + -
72A LEU* 4.1 13.0 - - + +
83C MET 2.8 22.4 + - - -
84C ALA* 3.7 4.7 - - - -
86C LEU* 1.3 77.8 - - - +
88C TRP* 1.3 61.1 + - - +
90C SER* 3.4 3.1 + - - -
91C HIS* 3.1 19.2 + - - +
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Residues in contact with TRP 88 (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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68A PHE* 3.7 24.9 - + - -
69A GLN* 3.1 60.8 - - + -
72A LEU* 4.0 8.8 - - + +
84C ALA 3.0 13.5 + - - +
85C ARG* 3.4 12.8 - - - +
87C THR* 1.3 77.6 - - - +
89C ALA* 1.3 61.3 + - + +
91C HIS* 3.1 4.4 + - - +
92C GLU* 2.9 68.8 + - + +
205C GOL 3.8 20.6 - - - -
85L ARG* 4.6 13.0 - - + -
88L TRP* 4.4 27.3 - + - +
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Residues in contact with ALA 89 (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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85C ARG 2.8 20.8 + - - +
86C LEU* 3.3 10.1 + - + +
88C TRP* 1.3 76.7 - - + +
90C SER* 1.3 57.0 + - - +
92C GLU* 3.4 9.3 + - - +
93C LYS* 2.9 28.2 + - - +
109C LEU* 3.9 20.8 - - + +
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Residues in contact with SER 90 (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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10A ASN* 2.8 29.3 + - - -
13A ILE* 3.9 3.1 - - - -
48C PHE* 3.8 7.3 - - - -
86C LEU 2.9 17.2 + - - -
87C THR* 3.7 5.4 - - - -
89C ALA* 1.3 75.5 - - - +
91C HIS* 1.3 57.6 + - - +
93C LYS* 3.1 5.0 + - - +
94C MET* 2.9 32.8 + - - +
108C GLY* 3.6 4.9 - - - -
109C LEU* 3.0 35.4 + - - +
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Residues in contact with HIS 91 (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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13A ILE* 3.7 17.7 - - + +
17A HIS* 3.1 14.4 - + - -
27A HIS* 3.4 13.9 - + - -
68A PHE* 3.6 26.2 - + + -
87C THR 3.1 12.6 + - - +
88C TRP* 3.1 8.8 + - - +
90C SER* 1.3 75.6 - - - +
92C GLU* 1.3 64.5 + - - +
94C MET* 3.1 16.0 + - - +
95C HIS* 3.2 14.0 + + - -
105C HIS* 3.4 12.6 - + - -
201C MN 2.3 35.0 + - - -
205C GOL 3.2 39.7 + - - -
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Residues in contact with GLU 92 (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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88C TRP* 2.9 54.7 + - + +
89C ALA* 3.5 10.3 - - - +
91C HIS* 1.3 76.7 + - - +
93C LYS* 1.3 61.1 + - - +
95C HIS* 3.0 13.7 + - - +
96C GLU* 3.1 13.4 + - - +
205C GOL 3.1 43.9 + - - -
85L ARG* 6.2 0.2 - - - -
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Residues in contact with LYS 93 (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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89C ALA 2.9 14.2 + - - +
90C SER 3.1 9.6 + - - +
92C GLU* 1.3 76.3 - - - +
94C MET* 1.3 61.7 + - - +
95C HIS 3.1 0.9 + - - -
96C GLU* 3.1 36.2 + - - +
106C LYS* 4.4 5.5 - - - +
107C PRO* 3.5 20.7 + - - +
108C GLY 2.9 33.7 + - - -
109C LEU* 3.9 16.6 - - + +
110C GLY 5.0 2.5 - - - +
111C GLU 4.0 16.9 - - - -
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Residues in contact with MET 94 (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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10A ASN* 3.6 33.0 - - + +
13A ILE* 3.7 24.5 - - + -
14A ASP* 5.9 2.0 - - - +
90C SER* 2.9 20.4 + - - +
91C HIS* 3.1 11.8 + - - +
93C LYS* 1.3 76.4 - - - +
95C HIS* 1.3 58.2 + - - +
96C GLU 3.5 0.2 - - - -
98C ASP* 5.8 0.2 - - - -
104C HIS 3.9 3.3 - - - +
105C HIS* 3.6 45.3 - - + -
106C LYS* 2.9 51.4 + - - +
107C PRO 3.8 1.1 - - - -
108C GLY* 3.7 13.7 - - - +
111C GLU* 5.6 0.2 - - - +
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Residues in contact with HIS 95 (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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27A HIS* 3.1 9.2 + + - -
91C HIS* 3.2 32.1 + + - -
92C GLU 3.0 8.8 + - - +
94C MET* 1.3 77.3 - - - +
96C GLU* 1.3 64.5 + - - +
97C GLY 3.2 0.9 + - - -
98C ASP* 2.7 44.8 + - + +
103C HIS* 3.4 14.8 - + - -
104C HIS 3.4 20.4 + - - -
105C HIS* 3.3 4.8 - + - -
106C LYS* 4.8 0.4 - - - -
201C MN 2.3 35.6 + - - -
205C GOL 3.6 21.3 - - - +
61L HIS* 4.2 10.4 + + - +
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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