Contacts of the helix formed by residues 57 - 73 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ALA* 4.0 2.0 - - - -
50E MET* 3.5 32.4 - - - +
52E ASN 4.5 1.2 + - - -
53E LYS* 3.4 16.2 - - - -
54E THR* 2.7 39.7 + - - -
56E HIS* 1.3 75.7 - - - +
58E TYR* 1.3 65.4 + - - +
60E TYR* 2.9 24.5 + - - +
61E ILE 3.8 0.3 + - - -
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Residues in contact with TYR 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP* 5.6 0.7 - - - -
39E ASN* 3.6 32.8 + - + -
42E TYR* 3.8 22.9 - - + -
43E HIS* 3.2 42.8 + + - +
46E ALA* 4.2 3.7 - - - +
54E THR 4.7 0.8 + - - -
55E ASP 3.5 17.0 - - - -
56E HIS* 3.2 4.8 - + - -
57E SER* 1.3 78.7 - - - +
59E HIS* 1.3 104.9 + + - +
61E ILE* 3.1 6.1 + - - +
62E LYS* 2.9 46.3 + - + +
96E ASP* 3.8 10.8 + - - +
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Residues in contact with HIS 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E HIS* 3.2 36.5 - + + +
57E SER 3.0 0.6 + - - -
58E TYR* 1.3 119.6 + + - +
60E TYR* 1.3 63.0 + - - +
62E LYS* 3.1 7.9 + - - +
63E ARG* 2.9 24.1 + - - +
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Residues in contact with TYR 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E MET* 3.7 35.4 - - + -
57E SER 2.9 13.5 + - - +
59E HIS* 1.3 78.5 - - - +
61E ILE* 1.3 70.0 + - + +
63E ARG* 3.2 13.2 + - + +
64E LEU* 2.9 64.5 + - + +
112E MET* 5.6 2.2 - - + -
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Residues in contact with ILE 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 3.8 37.0 - - + +
45E ILE* 3.8 33.2 - - + -
46E ALA* 4.0 12.6 - - + +
49E THR* 3.8 13.9 - - - +
50E MET* 4.0 6.1 - - + -
58E TYR 3.1 9.1 + - - +
60E TYR* 1.3 93.6 - - + +
62E LYS* 1.3 56.1 + - - +
64E LEU* 2.9 7.6 + - + +
65E THR* 2.8 29.6 + - - -
108E LEU* 3.9 16.4 - - + -
112E MET* 4.5 13.5 - - + -
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Residues in contact with LYS 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ASN* 4.1 12.3 - - - +
42E TYR* 3.4 38.6 - - + -
58E TYR* 2.9 36.9 + - + +
59E HIS* 3.1 10.1 + - - +
61E ILE* 1.3 75.2 - - - +
63E ARG* 1.3 62.4 + - - +
65E THR* 3.2 11.0 + - - -
66E GLU* 3.1 19.2 + - - +
93E MET* 3.1 37.7 + - - +
94E LEU* 3.4 26.4 + - + +
95E SER 3.3 19.8 + - - -
96E ASP* 4.4 1.8 - - - +
98E GLU 4.6 2.6 + - - -
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Residues in contact with ARG 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E HIS 2.9 12.9 + - - +
60E TYR* 3.3 15.9 - - + +
62E LYS* 1.3 77.0 - - - +
64E LEU* 1.3 71.3 + - + +
66E GLU* 2.6 44.0 + - - +
67E SER* 3.3 13.4 + - - -
94E LEU* 5.1 7.6 - - - +
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Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E TYR* 2.9 63.3 + - + +
61E ILE* 2.9 9.8 + - + +
63E ARG* 1.3 84.4 - - + +
65E THR* 1.3 57.2 + - - +
67E SER* 3.5 3.3 + - - +
68E ALA* 3.0 28.1 + - - +
108E LEU* 3.9 11.4 - - + -
111E GLU* 3.5 18.9 - - + +
112E MET* 3.8 30.7 - - + -
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Residues in contact with THR 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 3.5 10.5 - - + -
61E ILE 2.8 15.9 + - - -
62E LYS* 3.3 10.8 - - - -
63E ARG 3.2 0.2 - - - -
64E LEU* 1.3 75.8 - - - +
66E GLU* 1.3 58.8 + - - +
68E ALA* 3.4 4.8 + - + +
69E ALA* 2.8 28.2 + - - +
89E TYR* 4.3 4.3 - - - +
93E MET* 3.4 22.0 - - + -
104E GLU* 3.6 31.6 - - + -
107E MET* 4.6 5.6 - - + +
108E LEU* 3.4 25.4 - - + +
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Residues in contact with GLU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E LYS 3.1 12.2 + - - +
63E ARG* 2.6 51.4 + - - +
65E THR* 1.3 75.1 - - - +
67E SER* 1.3 61.3 + - - +
69E ALA* 3.3 3.3 + - - +
70E ARG* 3.1 44.5 + - - +
90E LEU* 3.7 21.7 - - + +
93E MET* 3.6 12.5 - - + +
94E LEU* 3.9 22.7 - - + +
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Residues in contact with SER 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ARG* 3.3 10.9 + - - -
64E LEU* 3.8 5.4 - - - -
65E THR 3.3 0.4 - - - -
66E GLU* 1.3 78.7 - - - +
68E ALA* 1.3 64.1 + - - +
70E ARG* 3.5 7.0 + - - +
71E LYS* 3.3 30.1 + - - +
111E GLU* 2.9 25.6 + - - -
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Residues in contact with ALA 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E LEU 3.0 13.8 + - - +
65E THR* 3.6 8.7 - - - +
67E SER* 1.3 74.9 - - - +
69E ALA* 1.3 52.4 + - - +
71E LYS* 3.1 2.5 + - - +
72E TYR* 2.8 44.0 + - + +
107E MET* 3.6 26.2 - - + +
108E LEU* 4.4 0.7 - - - +
111E GLU* 3.4 36.4 + - + -
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Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR 2.8 18.3 + - - +
66E GLU 3.4 5.8 - - - +
67E SER 3.2 0.2 - - - -
68E ALA* 1.3 70.5 - - - +
70E ARG* 1.3 56.9 + - - +
71E LYS 2.7 14.5 + - - -
73E TYR* 2.6 35.1 + - + +
74E GLN 4.5 0.3 + - - -
86E LEU* 4.2 1.6 - - + +
89E TYR* 3.9 19.7 - - + -
90E LEU* 3.5 20.9 - - + -
93E MET* 5.3 0.2 - - + -
107E MET* 3.8 14.8 - - + -
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Residues in contact with ARG 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E GLU* 3.1 33.5 + - - +
67E SER* 3.5 7.4 + - - +
69E ALA* 1.3 77.8 - - - +
71E LYS* 1.3 58.1 + - - +
74E GLN* 5.1 5.5 - - - +
86E LEU* 4.2 27.0 - - + +
87E GLU* 4.6 19.8 + - - +
90E LEU* 3.4 31.5 - - + +
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Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E SER* 3.3 15.7 + - - +
68E ALA 3.1 8.7 + - - +
69E ALA 2.7 4.9 + - - -
70E ARG* 1.3 78.0 - - - +
72E TYR* 1.3 92.9 + - + +
74E GLN* 5.6 2.0 - - - +
75E GLU* 6.1 0.5 - - - +
111E GLU* 3.1 24.9 + - - -
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Residues in contact with TYR 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ALA* 2.8 30.0 + - + +
69E ALA 2.8 4.2 + - - -
71E LYS* 1.3 105.5 - - + +
73E TYR* 1.3 65.1 + - - +
74E GLN* 3.1 3.8 - - - -
75E GLU* 2.8 21.2 + - + +
76E GLU* 3.2 24.5 + - - +
107E MET* 4.1 16.4 - - + -
110E LYS* 3.7 51.2 + - + +
111E GLU* 4.1 13.1 - - - -
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Residues in contact with TYR 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ALA* 2.6 32.1 + - + +
72E TYR* 1.3 72.6 - - - +
74E GLN* 1.3 73.3 + - - +
76E GLU* 3.5 4.2 + - - -
79E ALA* 3.4 44.1 + - + +
82E VAL* 3.8 15.5 - - + +
84E LEU 2.7 26.0 + - - -
85E SER* 4.8 0.2 - - - -
86E LEU* 3.6 43.5 - - + -
89E TYR* 3.5 45.0 - + + +
103E LEU* 4.2 6.3 - - + -
107E MET* 3.8 13.8 - - - -
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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