Contacts of the helix formed by residues 62 - 87 (chain C) in PDB entry 4PHZ
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 TRP 62 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 3.9 10.8 - + - -
42C GLU* 3.4 31.9 - - + -
45C PHE* 2.5 43.2 + - + +
46C GLY* 3.8 4.9 - - - -
49C ALA 3.7 22.2 - - - -
50C GLY* 3.7 9.6 - - - -
58C PHE* 2.9 34.4 + + + +
61C TYR* 1.3 83.0 - - + +
63C MET* 1.3 59.7 + - - +
64C SER 3.1 4.8 + - - -
65C ILE* 3.4 33.8 + - + +
66C LEU 3.4 5.7 + - - -
144C PRO* 3.9 40.4 - - + -
147C ILE* 3.3 28.9 - - + +
148C ILE* 4.2 14.4 - - + -
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Residues in contact with MET 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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58C PHE* 3.0 33.1 + - + -
59C GLN* 3.7 32.3 - - + +
62C TRP* 1.3 72.8 - - - +
64C SER* 1.3 64.7 + - - +
66C LEU* 3.9 24.7 - - + +
67C TRP* 3.0 60.1 + - + +
142C PHE* 4.2 28.5 - - + -
147C ILE* 4.7 1.3 - - - -
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 5.1 0.7 + - - -
59C GLN 3.2 15.7 + - - -
60C THR* 3.6 17.7 + - - -
61C TYR 4.0 4.5 + - - -
63C MET* 1.3 77.2 - - - +
65C ILE* 1.3 75.8 + - - +
67C TRP* 3.3 5.7 + - - +
68C THR* 2.9 33.5 + - - -
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 3.8 25.8 - - + +
61C TYR 3.4 23.8 - - - +
62C TRP* 3.4 22.4 + - + +
64C SER* 1.3 86.9 + - - +
66C LEU* 1.3 56.8 + - - +
68C THR* 3.2 6.6 + - + -
69C GLU* 2.9 56.5 + - + +
147C ILE* 3.8 10.3 - - + -
148C ILE* 4.6 10.3 - - + -
152C MET* 5.2 2.7 - - - -
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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
----------------------------------------------------------
62C TRP 3.4 5.6 + - - +
63C MET* 3.9 33.9 - - + +
64C SER 3.4 0.4 - - - -
65C ILE* 1.3 79.2 - - - +
67C TRP* 1.3 68.0 + - + +
68C THR 3.4 0.2 + - - -
69C GLU* 3.5 6.9 + - - -
70C ILE* 3.6 37.7 + - + +
142C PHE* 4.0 26.7 - - + -
147C ILE* 3.9 21.5 - - + +
151C TYR* 3.6 40.8 - - + -
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Residues in contact with TRP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C MET* 3.0 53.8 + - + +
64C SER* 3.8 4.3 - - - +
66C LEU* 1.3 86.7 - - + +
68C THR* 1.3 58.1 + - - +
71C PRO* 3.1 25.1 - - - +
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Residues in contact with THR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 2.9 20.0 + - - -
65C ILE* 3.2 8.0 + - + +
67C TRP* 1.3 76.4 - - - +
69C GLU* 1.3 69.6 + - + +
71C PRO* 3.2 17.0 - - - +
72C LEU* 3.2 30.8 + - + +
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Residues in contact with GLU 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 ILE* 2.9 39.3 + - + +
66C LEU* 3.5 16.7 - - - +
67C TRP 3.7 0.2 - - - -
68C THR* 1.3 79.3 - - + +
70C ILE* 1.3 59.9 + - + +
72C LEU* 3.2 5.3 + - - -
73C GLU* 2.6 52.1 + - + +
147C ILE* 3.0 24.5 - - - +
151C TYR* 3.3 26.7 - - - +
152C MET* 3.2 23.8 - - + +
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Residues in contact with ILE 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 LEU* 3.6 30.4 + - + +
69C GLU* 1.3 85.1 - - + +
71C PRO* 1.4 74.8 - - + +
73C GLU* 3.7 13.4 - - - +
74C LEU* 3.0 26.0 + - + +
151C TYR* 3.6 36.8 - - + +
155C PRO* 5.9 1.3 - - + -
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Residues in contact with PRO 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 TRP* 3.1 29.2 - - - +
68C THR* 3.2 11.2 - - - +
70C ILE* 1.4 95.1 - - + +
72C LEU* 1.3 59.0 - - - +
74C LEU* 3.3 8.7 + - + +
75C VAL* 3.1 27.0 + - - +
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Residues in contact with LEU 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 THR* 3.2 33.6 + - + +
69C GLU* 3.5 5.8 - - - +
71C PRO* 1.3 79.1 - - - +
73C GLU* 1.3 60.3 + - + +
75C VAL* 3.6 7.4 + - + +
76C SER* 3.0 41.7 + - - +
302C PGT 6.4 2.0 - - + -
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Residues in contact with GLU 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 GLU* 2.6 35.8 + - + +
70C ILE* 3.7 9.1 - - - +
72C LEU* 1.3 75.0 - - + +
74C LEU* 1.3 61.7 + - - +
76C SER* 3.5 6.5 + - - -
77C GLY* 3.0 25.8 + - - -
151C TYR 2.9 28.6 - - - +
152C MET* 3.2 21.0 - - - +
155C PRO* 3.2 29.1 - - + +
156C ILE* 4.3 11.7 - - + +
159C VAL* 3.8 11.5 - - + +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.0 19.9 + - + +
71C PRO* 3.7 8.3 - - + +
73C GLU* 1.3 75.9 - - - +
75C VAL* 1.3 63.3 + - + +
77C GLY* 4.2 1.1 - - - +
78C LEU* 3.3 41.2 + - + +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO 3.1 17.3 + - - +
72C LEU* 4.1 6.5 - - + +
74C LEU* 1.3 78.5 - - + +
76C SER* 1.3 58.2 + - - +
78C LEU* 3.8 4.8 - - + +
79C GLY* 2.7 34.5 + - - -
302C PGT 4.6 6.5 - - + +
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Residues in contact with SER 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 LEU* 3.0 31.3 + - - +
73C GLU* 3.7 7.8 - - - -
75C VAL* 1.3 77.5 - - - +
77C GLY* 1.3 53.6 + - - +
80C LEU* 2.8 37.9 + - - +
159C VAL* 4.5 10.5 - - - -
302C PGT 3.7 30.9 - - - +
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Residues in contact with GLY 77 (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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73C GLU 3.0 15.9 + - - -
74C LEU* 4.2 2.0 - - - -
75C VAL 3.2 0.4 - - - -
76C SER* 1.3 76.1 - - - +
78C LEU* 1.3 58.4 + - - +
80C LEU* 3.9 2.3 - - - +
81C ALA* 3.1 26.9 + - - +
159C VAL* 3.9 22.6 - - - +
162C VAL* 4.5 8.6 - - - +
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Residues in contact with LEU 78 (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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74C LEU* 3.3 33.3 + - + +
75C VAL* 4.3 4.9 - - + +
77C GLY* 1.3 72.2 - - - +
79C GLY* 1.3 60.1 + - - +
81C ALA* 3.4 8.5 - - + +
82C GLY* 2.9 27.5 + - - -
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Residues in contact with GLY 79 (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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75C VAL* 2.7 23.5 + - - -
78C LEU* 1.3 74.7 - - - +
80C LEU* 1.3 63.0 + - - +
82C GLY* 3.9 0.3 - - - -
83C TYR* 3.0 26.0 + - - +
302C PGT 3.5 20.8 - - - +
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Residues in contact with LEU 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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76C SER 2.8 20.5 + - - +
77C GLY 3.9 3.4 - - - +
79C GLY* 1.3 70.5 - - - -
81C ALA* 1.3 63.6 + - - +
83C TYR* 4.1 0.2 - - - +
84C LEU* 3.3 28.1 + - + +
110C TRP* 3.7 29.2 - - + -
159C VAL* 3.9 25.4 - - + +
160C ILE* 5.0 2.7 - - + -
162C VAL* 5.4 1.8 - - + -
163C GLY* 3.9 19.7 - - - +
166C PHE* 5.5 0.2 - - - +
302C PGT 3.7 61.3 - - + +
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Residues in contact with ALA 81 (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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77C GLY 3.1 19.5 + - - +
78C LEU* 3.4 14.1 - - + +
79C GLY 3.1 0.2 + - - -
80C LEU* 1.3 73.3 - - - +
82C GLY* 1.3 68.1 + - - +
84C LEU* 3.0 14.4 + - - +
85C TRP* 3.1 13.2 + - - +
162C VAL* 4.7 13.0 - - + +
166C PHE* 4.6 25.2 - - + -
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Residues in contact with GLY 82 (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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78C LEU 2.9 17.9 + - - -
81C ALA* 1.3 72.4 - - - +
83C TYR* 1.3 62.1 + - - +
85C TRP* 3.2 7.9 + - - +
86C LYS* 2.8 30.9 + - - +
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Residues in contact with TYR 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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79C GLY 3.0 16.4 + - - +
80C LEU 4.1 1.3 - - - +
82C GLY* 1.3 74.6 - - - +
84C LEU* 1.3 75.2 + - + +
86C LYS* 3.3 4.9 + - + +
87C THR* 2.9 56.8 + - + +
171C ARG* 5.2 0.2 + - - -
302C PGT 3.4 74.2 + - + +
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 3.3 33.3 + - + +
81C ALA 3.0 4.4 + - - +
83C TYR* 1.3 95.8 - - + +
85C TRP* 1.3 62.7 + - - +
87C THR* 3.7 3.6 - - - +
88C ARG 3.2 4.5 + - - -
110C TRP* 4.1 18.2 - - + -
163C GLY 4.1 14.8 - - - +
166C PHE* 4.3 12.8 - - + -
167C TYR* 4.2 11.7 - - + +
170C THR* 3.3 10.7 + - - +
171C ARG* 3.0 54.6 + - - +
302C PGT 4.0 11.7 - - + -
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Residues in contact with TRP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA 3.1 11.8 + - - +
82C GLY* 3.6 11.0 - - - +
84C LEU* 1.3 75.4 - - - +
86C LYS* 1.3 61.9 + - + +
88C ARG* 2.8 85.8 + - - +
166C PHE* 4.5 20.7 - + + -
169C LYS* 4.6 19.1 - - + -
170C THR* 3.6 26.4 - - + +
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY* 2.8 20.6 + - - +
83C TYR* 3.6 6.3 - - + +
85C TRP* 1.3 81.8 - - + +
87C THR* 1.3 61.1 + - + +
88C ARG* 3.1 3.8 + - - +
90C ARG* 2.8 32.4 + - - +
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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
----------------------------------------------------------
83C TYR* 2.9 50.9 + - + +
84C LEU* 3.7 5.0 - - - +
86C LYS* 1.3 73.0 - - + +
88C ARG* 1.3 63.9 + - - +
171C ARG* 2.5 37.1 + - - -
302C PGT 3.2 29.6 + - - +
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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