Contacts of the helix formed by residues 57 - 73 (chain C) in PDB entry 3PHW
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 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ALA* 4.1 0.9 - - - -
50C MET* 3.6 30.2 - - - +
52C ASN 4.5 0.5 + - - -
53C LYS* 3.4 18.0 - - - -
54C THR* 2.6 41.8 + - - +
56C HIS* 1.3 75.8 - - - +
58C TYR* 1.3 66.9 + - - +
59C HIS 2.9 1.7 + - - -
60C TYR* 2.9 21.8 + - - +
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Residues in contact with TYR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP* 5.4 0.4 - - - -
39C ASN* 3.3 41.2 + - + -
42C TYR* 3.8 12.8 - - + +
43C HIS* 3.3 52.9 + + - +
46C ALA* 4.2 5.0 - - - +
54C THR 4.5 1.4 + - - -
55C ASP 3.3 18.4 - - - -
56C HIS* 3.1 3.9 - + - -
57C SER* 1.3 79.1 - - - +
59C HIS* 1.3 102.6 + + - +
61C ILE* 2.9 16.5 + - - +
62C LYS* 3.1 32.1 + - + +
96C ASP* 4.3 8.7 + - - -
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Residues in contact with HIS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C HIS* 3.3 33.4 + + + +
57C SER 2.9 0.8 + - - -
58C TYR* 1.3 118.1 + + - +
60C TYR* 1.3 56.7 + - - +
62C LYS* 3.3 9.6 + - - +
63C ARG* 3.0 26.3 + - - +
96C ASP* 6.0 0.2 - - - -
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET* 3.6 33.2 - - + -
57C SER 2.9 12.4 + - - +
59C HIS* 1.3 75.8 - - - +
61C ILE* 1.3 62.0 + - + +
63C ARG* 3.2 25.8 + - - +
64C LEU* 2.9 65.8 + - + +
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Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 3.8 18.8 - - + +
45C ILE* 3.8 25.4 - - + -
46C ALA* 3.8 26.7 - - + +
49C THR* 3.8 18.8 - - - +
50C MET* 3.6 21.5 - - + -
58C TYR* 2.9 10.0 + - - +
60C TYR* 1.3 77.6 - - + +
62C LYS* 1.3 56.9 + - - +
64C LEU* 3.3 21.0 + - + +
65C THR* 2.7 30.4 + - - -
108C LEU* 3.8 21.5 - - + -
112C MET* 4.7 2.0 - - + -
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Residues in contact with LYS 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 4.3 11.1 - - - +
42C TYR* 3.6 31.6 - - + -
58C TYR* 3.1 32.0 + - + +
59C HIS* 3.6 12.3 - - - +
60C TYR 3.2 0.2 - - - -
61C ILE* 1.3 75.0 - - - +
63C ARG* 1.3 58.5 + - - +
65C THR* 3.2 9.1 + - - -
66C GLU* 3.0 26.5 + - - +
93C MET* 3.0 39.3 + - - +
94C LEU* 3.9 21.9 + - + +
95C SER 3.1 20.2 + - - -
96C ASP* 5.0 0.8 - - - +
97C ASN 5.0 0.2 - - - +
98C GLU 4.6 6.3 + - - -
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Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C HIS 3.0 14.9 + - - +
60C TYR* 3.4 29.5 - - + +
62C LYS* 1.3 76.2 - - - +
64C LEU* 1.3 62.9 + - + +
66C GLU* 3.2 22.1 + - - +
67C SER* 3.1 26.8 + - - +
94C LEU* 5.1 2.4 - - - +
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Residues in contact with LEU 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 TYR* 2.9 57.3 + - + +
61C ILE* 3.5 14.4 - - + +
62C LYS 3.3 0.2 - - - -
63C ARG* 1.3 77.2 - - + +
65C THR* 1.3 51.7 + - - +
67C SER* 3.4 6.4 + - - +
68C ALA* 2.8 35.3 + - - +
108C LEU* 3.8 11.0 - - + -
111C GLU* 3.6 20.6 - - + +
112C MET* 3.9 32.8 - - + -
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Residues in contact with THR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 3.6 7.9 - - - +
61C ILE 2.7 19.0 + - - -
62C LYS* 3.4 11.2 - - - -
63C ARG 3.2 0.4 - - - -
64C LEU* 1.3 74.7 - - - +
66C GLU* 1.3 58.9 + - - +
68C ALA* 3.6 4.6 - - + +
69C ALA* 2.9 28.2 + - - +
89C TYR* 4.1 5.2 - - - +
93C MET* 3.6 19.7 - - + -
104C GLU* 3.7 32.1 - - + -
107C MET* 4.4 7.6 - - + +
108C LEU* 3.3 25.0 - - + +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LYS 3.0 13.1 + - - +
63C ARG* 3.5 24.3 + - - +
65C THR* 1.3 74.1 - - - +
67C SER* 1.3 67.0 + - - +
69C ALA* 3.3 2.8 + - - +
70C ARG* 2.6 63.9 + - - +
90C LEU* 3.9 15.9 - - + +
93C MET* 3.6 12.9 - - + +
94C LEU* 3.9 24.0 - - + +
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Residues in contact with SER 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 3.1 16.8 + - - +
64C LEU* 3.7 11.5 - - - +
66C GLU* 1.3 77.5 + - - +
68C ALA* 1.3 68.9 + - - +
70C ARG* 3.3 20.0 + - - +
71C LYS* 3.5 16.5 + - - +
111C GLU* 4.0 16.8 - - - -
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU 2.8 21.7 + - - +
65C THR* 3.6 9.0 - - - +
67C SER* 1.3 73.0 - - - +
69C ALA* 1.3 56.7 + - - +
71C LYS* 2.9 6.2 + - - -
72C TYR* 2.9 33.5 + - - -
107C MET* 3.5 37.2 - - + +
108C LEU* 4.5 0.7 - - - +
111C GLU* 3.6 21.1 + - + -
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Residues in contact with ALA 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 THR 2.9 19.1 + - - +
66C GLU 3.7 3.8 - - - +
67C SER 3.2 0.6 - - - -
68C ALA* 1.3 72.9 - - - +
70C ARG* 1.3 66.8 + - - +
73C TYR* 3.0 31.3 + - + +
74C GLN* 4.7 1.2 + - - +
86C LEU* 3.9 6.4 - - + +
89C TYR* 3.9 26.7 - - + -
90C LEU* 3.9 10.3 - - + -
107C MET* 3.7 18.6 - - + -
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLU* 2.6 51.5 + - - +
67C SER* 3.3 10.5 + - - +
69C ALA* 1.3 77.0 - - - +
71C LYS* 1.3 63.4 + - + +
74C GLN* 5.2 5.7 - - - +
86C LEU* 4.0 23.2 - - + +
87C GLU* 5.9 4.2 - - - +
90C LEU* 3.5 24.3 - - + +
94C LEU* 5.7 0.2 - - - +
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Residues in contact with LYS 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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135A ASP 4.8 5.9 + - - +
136A GLY* 5.2 9.1 - - - -
137A ASP* 5.8 5.4 - - + +
67C SER* 3.8 11.2 - - - +
68C ALA 2.9 5.6 + - - +
69C ALA 3.8 0.4 - - - -
70C ARG* 1.3 84.3 - - + +
72C TYR* 1.3 89.3 + - + +
74C GLN* 5.2 5.9 + - - +
75C GLU* 5.0 6.8 - - - +
111C GLU* 2.8 37.6 + - - +
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Residues in contact with TYR 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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17A TYR* 4.7 5.2 - + - -
135A ASP* 2.7 54.4 + - + +
68C ALA* 2.9 26.6 + - + +
71C LYS* 1.3 98.8 + - + +
73C TYR* 1.3 68.0 + - - +
74C GLN 3.2 2.7 - - - -
75C GLU* 2.9 20.3 + - - +
76C GLU* 3.2 28.1 + - - +
107C MET* 3.9 20.2 - - + -
110C LYS* 3.6 37.2 + - + +
111C GLU* 3.9 21.3 - - - -
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Residues in contact with TYR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA* 3.0 25.4 + - + +
72C TYR* 1.3 76.1 - - - +
74C GLN* 1.3 71.7 - - + +
75C GLU 3.0 1.2 + - - -
76C GLU* 3.2 10.6 + - - -
79C ALA* 3.3 37.4 + - + +
82C VAL* 3.6 16.6 - - + +
84C LEU 2.8 32.0 + - - -
86C LEU* 3.7 35.7 - - + -
89C TYR* 3.5 45.1 - + + +
103C LEU* 4.0 12.6 - - + -
107C MET* 3.8 12.9 - - - -
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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