Contacts of the helix formed by residues 47 - 71 (chain C) in PDB entry 1SIW
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 GLY 47 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ARG 3.2 1.8 + - - -
46C LYS* 1.3 75.5 - - - +
48C MET* 1.3 58.0 + - - +
49C ASN* 3.4 3.3 + - - -
50C LEU* 3.6 8.7 + - - +
51C ALA* 3.0 32.8 + - - +
107C LEU* 5.7 0.2 - - - +
111C ARG* 5.6 1.8 - - - -
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Residues in contact with MET 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE 5.2 0.9 - - - +
90B ALA* 3.8 2.1 - - + +
40C SER* 4.5 0.2 - - - +
41C GLN* 4.2 20.4 - - + +
44C ASP 3.6 7.4 - - - +
45C ARG 3.1 12.1 + - - +
46C LYS 3.1 3.0 + - - -
47C GLY* 1.3 74.8 - - - +
49C ASN* 1.3 65.5 + - - +
51C ALA* 4.5 0.4 - - - -
52C SER* 2.9 38.4 + - - -
108C LEU* 3.7 27.4 - - + -
111C ARG* 3.3 51.1 - - - +
806C HEM 3.2 44.9 - - + +
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Residues in contact with ASN 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 3.7 21.4 + - + +
92B PRO* 4.0 26.9 - - - +
41C GLN* 5.6 1.9 - - - +
45C ARG 4.4 1.8 + - - -
47C GLY 3.4 1.0 - - - +
48C MET* 1.3 80.4 - - - +
50C LEU* 1.3 66.7 + - - +
53C ASN* 2.8 39.8 + - - +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 3.6 9.5 + - - +
49C ASN* 1.3 84.5 + - - +
51C ALA* 1.3 66.1 + - - +
53C ASN* 3.9 2.0 - - - +
54C LEU* 3.0 62.5 + - + +
107C LEU* 3.7 18.8 - - + -
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Residues in contact with ALA 51 (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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47C GLY 3.0 21.6 + - - +
48C MET* 4.3 1.6 - - - +
50C LEU* 1.3 83.4 - - - +
52C SER* 1.3 62.2 + - - +
55C PHE* 3.1 21.0 + - - +
104C GLY* 3.4 15.8 - - - +
107C LEU* 3.8 28.0 - - + -
108C LEU* 3.8 19.5 - - + +
111C ARG* 6.1 1.6 - - - -
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 2.6 29.5 + - - -
90B ALA* 4.3 1.1 - - - -
48C MET* 2.9 35.5 + - - -
51C ALA* 1.3 71.4 - - - +
53C ASN* 1.3 60.4 + - - +
55C PHE* 3.9 0.2 - - - -
56C HIS* 2.9 51.1 + - - +
108C LEU* 4.1 11.5 - - - +
806C HEM 4.5 4.2 - - - +
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Residues in contact with ASN 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY 4.8 6.6 - - - +
87B LYS 6.0 0.5 - - - -
89B PHE* 3.5 28.4 + - - +
90B ALA* 4.2 9.6 + - - +
49C ASN* 2.8 45.7 + - - +
50C LEU* 4.0 2.5 - - + +
52C SER* 1.3 76.4 - - - +
54C LEU* 1.3 67.4 + - + +
57C ILE* 2.9 46.5 + - + +
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Residues in contact with LEU 54 (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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50C LEU* 3.0 55.7 + - + +
51C ALA 3.8 3.4 - - - +
53C ASN* 1.3 77.0 - - + +
55C PHE* 1.3 58.7 - - - +
57C ILE* 4.4 1.5 - - - +
58C GLY* 3.0 23.0 + - - -
100C LEU* 3.4 44.6 - - + +
103C ILE* 3.9 26.7 - - + -
104C GLY* 3.9 4.7 - - - +
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Residues in contact with PHE 55 (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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51C ALA 3.1 15.4 + - - +
52C SER 4.0 1.3 - - - +
54C LEU* 1.3 80.7 - - - +
56C HIS* 1.3 66.8 + + - +
58C GLY* 3.9 0.2 - - - -
59C ILE* 2.7 47.6 + - + +
101C CYS* 3.7 26.4 - - - +
104C GLY* 3.9 0.6 - - - -
105C GLY* 3.5 32.1 - - - +
108C LEU* 3.7 16.8 - - + -
130C LEU* 4.4 10.5 - - + -
133C LEU* 4.0 20.6 - - + -
134C VAL* 5.7 0.9 - - + -
806C HEM 3.5 56.8 - + + -
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Residues in contact with HIS 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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89B PHE* 3.3 30.5 - + + -
52C SER* 2.9 38.4 + - - +
55C PHE* 1.3 82.6 - + - +
57C ILE* 1.3 61.5 + - - +
59C ILE* 3.1 4.2 - - + +
60C LEU* 2.9 37.3 + - + +
108C LEU* 5.7 0.9 - - + -
806C HEM 2.0 101.7 + + + -
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Residues in contact with ILE 57 (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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89B PHE* 4.3 17.5 - - + -
53C ASN* 2.9 40.2 + - + +
54C LEU* 4.4 2.0 - - - +
56C HIS* 1.3 76.7 - - - +
58C GLY* 1.3 62.4 + - - +
60C LEU* 3.9 6.6 - - - +
61C GLY* 3.1 18.7 + - - -
97C SER* 4.8 0.9 + - - -
100C LEU* 4.9 13.2 - - + -
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Residues in contact with GLY 58 (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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54C LEU 3.0 18.7 + - - -
55C PHE 3.9 0.2 - - - -
57C ILE* 1.3 75.7 - - - +
59C ILE* 1.3 64.3 + - - +
61C GLY* 3.0 12.5 + - - -
62C ILE* 3.0 15.8 + - - +
97C SER* 3.4 28.5 - - - -
100C LEU* 4.3 6.9 - - - +
101C CYS* 3.8 4.7 - - - -
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PHE* 2.7 34.2 + - + +
56C HIS* 3.1 22.2 - - + +
58C GLY* 1.3 71.5 - - - +
60C LEU* 1.3 64.8 + - + +
62C ILE* 3.5 5.8 + - + +
63C PHE* 3.0 26.0 + - + +
101C CYS* 3.7 17.7 - - - +
133C LEU* 4.7 4.5 - - + -
806C HEM 3.7 47.7 - - + +
807C HEM 3.5 37.5 - - + -
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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
----------------------------------------------------------
89B PHE* 3.7 29.6 - - + -
56C HIS* 2.9 25.3 + - - +
57C ILE* 3.9 6.3 - - - +
59C ILE* 1.3 78.2 - - + +
61C GLY* 1.3 66.3 + - - +
63C PHE* 3.3 13.0 + - + +
64C VAL* 3.0 32.9 + - + +
806C HEM 3.9 46.9 - - + -
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Residues in contact with GLY 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 ILE 3.1 9.9 + - - -
58C GLY 3.0 7.4 + - - -
60C LEU* 1.3 79.2 - - - +
62C ILE* 1.3 62.7 + - - +
64C VAL* 3.2 6.0 + - - +
65C GLY* 3.0 19.8 + - - -
94C GLY* 5.8 2.0 - - - -
97C SER* 3.5 18.6 - - - -
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Residues in contact with ILE 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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58C GLY 3.0 19.2 + - - +
59C ILE* 3.6 11.4 - - + +
60C LEU 3.2 0.2 - - - -
61C GLY* 1.3 75.2 - - - +
63C PHE* 1.3 59.6 + - - +
65C GLY* 3.1 3.6 + - - -
66C HIS* 2.8 57.7 + - + +
94C GLY* 3.2 28.9 - - - +
97C SER* 3.6 3.6 - - - -
98C GLY* 3.5 17.0 - - - +
101C CYS* 5.0 2.0 - - + -
807C HEM 3.5 53.4 - - + +
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Residues in contact with PHE 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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59C ILE* 3.0 17.2 + - + +
60C LEU* 3.3 17.0 + - + +
62C ILE* 1.3 77.6 - - - +
64C VAL* 1.3 73.6 + - + +
66C HIS* 3.9 5.1 - - + +
67C PHE* 2.9 51.2 + + + +
195C PHE* 6.6 0.2 - + - -
206C ILE* 6.3 2.7 - - + -
806C HEM 5.5 10.3 - - + -
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Residues in contact with VAL 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* 3.0 21.7 + - + +
61C GLY* 3.2 6.5 + - - +
63C PHE* 1.3 86.9 - - + +
65C GLY* 1.3 64.5 + - - +
67C PHE* 4.5 1.3 - - - -
68C PHE* 3.1 56.8 + - + +
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Residues in contact with GLY 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 GLY 3.0 13.6 + - - -
62C ILE* 3.5 3.1 - - - -
64C VAL* 1.3 77.7 - - - +
66C HIS* 1.3 58.3 + - - +
68C PHE* 4.5 1.3 - - - +
69C GLY* 2.8 31.2 + - - -
90C ALA* 6.6 0.7 - - - -
94C GLY* 6.4 2.2 - - - -
807C HEM 6.1 0.7 - - - -
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Residues in contact with HIS 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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62C ILE* 2.8 42.9 + - + +
63C PHE* 3.9 6.3 - - + +
65C GLY* 1.3 72.8 - - - +
67C PHE* 1.3 64.2 + - - +
69C GLY* 5.1 0.2 - - - -
70C MET* 3.1 45.3 + - + +
71C LEU* 5.0 1.0 - - - +
807C HEM 2.0 105.3 + + + -
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Residues in contact with PHE 67 (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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63C PHE* 2.9 45.5 + + + +
64C VAL* 3.7 3.6 - - - +
66C HIS* 1.3 76.1 - - - +
68C PHE* 1.3 93.9 + + - +
71C LEU* 3.2 64.7 + - + +
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Residues in contact with PHE 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 VAL* 3.1 46.5 + - + +
65C GLY* 4.5 1.3 - - - +
67C PHE* 1.3 105.3 - + + +
69C GLY* 1.3 59.8 + - - +
72C THR* 2.7 37.9 + - - +
86C LYS* 5.4 4.0 + - - +
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Residues in contact with GLY 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 GLY 2.8 18.4 + - - -
66C HIS* 4.1 0.4 - - - -
68C PHE* 1.3 80.1 - - - +
70C MET* 1.3 63.1 + - - +
72C THR 4.7 4.0 + - - +
86C LYS* 5.0 17.7 + - - +
156C MET* 5.3 13.7 - - - +
160C VAL* 3.7 17.5 - - - +
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Residues in contact with MET 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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66C HIS* 3.1 60.6 + - + +
69C GLY* 1.3 78.5 - - - +
71C LEU* 1.3 69.5 + - + +
72C THR 3.6 0.9 - - - -
156C MET* 6.1 2.5 - - + -
159C LEU 5.3 1.8 - - - +
160C VAL* 3.9 20.3 - - + +
162C TRP* 6.0 0.2 - - - -
163C ALA* 4.0 22.8 - - + +
164C GLN* 3.2 28.3 + - - +
188C LEU* 5.8 0.4 - - - -
807C HEM 3.9 48.7 - - + -
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Residues in contact with LEU 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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66C HIS 5.0 0.2 - - - +
67C PHE* 3.2 54.1 + - + +
70C MET* 1.3 90.9 - - + +
72C THR* 1.3 65.2 + - - +
163C ALA* 4.9 7.2 - - + +
164C GLN* 3.7 7.7 + - + +
167C VAL* 4.3 33.4 - - + -
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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
------------------------------------------------------------
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