Contacts of the helix formed by residues 64 - 85 (chain B) in PDB entry 4PKO
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 ASP 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS* 3.2 30.0 + - - +
62B LEU* 3.5 1.7 - - - +
63B GLU* 1.3 74.9 - - - +
65B LYS* 1.3 54.3 + - - +
66B PHE* 2.9 28.8 + - - +
67B GLU* 3.1 30.1 + - + +
68B ASN* 2.7 34.5 + - - +
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 5.7 0.9 - - - +
63B GLU 3.2 8.6 + - - +
64B ASP* 1.3 73.3 + - - +
66B PHE* 1.3 58.3 + - + +
68B ASN* 3.5 15.7 + - + +
69B MET* 3.0 33.5 + - - +
522B THR* 3.4 29.8 + - + +
523B ASP* 3.7 36.1 + - - +
524B LEU 4.7 5.1 + - - -
525B PRO* 5.7 8.3 - - + +
41C ASP* 4.4 7.9 + - - +
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASP* 3.6 35.2 - - - -
7B LYS* 3.5 45.1 - - + -
12B ALA* 6.1 0.7 - - - -
15B LYS* 3.6 30.4 - - + +
16B MET* 4.3 0.7 - - - -
64B ASP* 2.9 12.4 + - - +
65B LYS* 1.3 75.8 - - + +
67B GLU* 1.3 65.6 + - - +
69B MET* 3.1 16.0 + - - +
70B GLY* 3.1 10.0 + - - -
520B MET* 3.5 51.9 - - + +
522B THR* 3.4 24.0 - - + -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 3.0 44.7 + - + +
18B ARG* 2.9 39.5 + - + +
19B GLY* 3.2 21.8 + - - +
22B VAL* 5.6 1.6 - - - +
62B LEU* 4.2 14.8 - - + +
64B ASP* 3.1 30.0 + - + +
66B PHE* 1.3 78.2 - - - +
68B ASN* 1.3 62.9 + - - +
70B GLY 3.1 2.4 + - - -
71B ALA* 3.1 19.2 + - - +
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 3.6 15.8 + - - +
62B LEU* 3.3 45.7 + - - +
64B ASP 2.7 15.2 + - - +
65B LYS* 3.5 19.0 + - + +
67B GLU* 1.3 74.2 - - - +
69B MET* 1.3 58.9 + - - +
71B ALA* 3.2 3.8 + - - +
72B GLN* 2.9 51.9 + - - +
41C ASP* 4.6 12.5 + - - -
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Residues in contact with MET 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS 3.0 23.0 + - - +
66B PHE* 3.3 13.0 - - - +
68B ASN* 1.3 76.6 - - - +
70B GLY* 1.3 62.4 + - - +
72B GLN* 3.5 1.3 + - - -
73B MET* 3.1 31.9 + - + +
520B MET* 3.4 26.5 - - + -
521B VAL 3.8 8.1 - - - +
522B THR* 4.0 9.6 - - - -
39C VAL* 3.2 45.3 - - + +
41C ASP* 3.4 44.0 - - + +
47C PRO* 3.7 13.8 - - + +
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B MET* 3.7 34.9 - - - +
20B VAL* 3.7 10.9 - - - +
66B PHE 3.1 8.3 + - - -
67B GLU 3.1 3.8 + - - -
69B MET* 1.3 78.4 - - - +
71B ALA* 1.3 62.1 + - - +
73B MET* 3.1 16.8 + - - +
74B VAL* 3.2 14.2 + - - +
514B MET* 4.2 0.5 - - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.5 23.3 - - - +
23B LEU* 3.8 15.2 - - + +
60B ILE* 4.4 11.4 - - + +
61B GLU* 6.3 0.2 - - - -
62B LEU* 4.2 11.2 - - + -
67B GLU 3.1 10.1 + - - +
68B ASN* 3.8 6.3 - - - +
70B GLY* 1.3 74.6 - - - +
72B GLN* 1.3 54.3 + - + +
74B VAL* 3.0 11.4 - - - +
75B LYS* 2.6 39.4 + - - +
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ILE 3.6 6.8 - - - +
61B GLU* 4.5 7.4 - - - +
68B ASN* 2.9 41.7 + - - +
69B MET 3.8 1.3 - - - +
71B ALA* 1.3 77.3 - - + +
73B MET* 1.3 60.5 + - - +
75B LYS* 2.7 53.9 + - - +
76B GLU* 3.9 3.8 + - - +
45C GLY 5.1 4.6 + - - +
46C ALA* 3.7 22.1 - - - +
47C PRO* 3.8 20.9 - - + -
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Residues in contact with MET 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 4.1 20.6 - - + -
69B MET* 3.1 29.8 + - + +
70B GLY* 3.1 13.6 + - - +
71B ALA 3.1 1.0 - - - -
72B GLN* 1.3 76.3 - - - +
74B VAL* 1.3 58.2 + - - +
75B LYS 3.3 0.2 - - - -
76B GLU* 3.2 27.4 - - - +
510B VAL* 4.0 7.6 - - - +
514B MET* 3.7 29.3 - - + +
520B MET* 5.1 1.3 - - + -
39C VAL* 4.0 22.9 - - + -
46C ALA* 5.0 0.9 - - + -
47C PRO* 3.9 17.5 - - + +
49C ILE* 3.5 39.0 - - + -
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.7 22.7 - - + -
23B LEU* 4.0 19.7 - - + +
70B GLY 3.2 8.9 + - - +
71B ALA* 3.0 25.4 - - - +
73B MET* 1.3 73.5 - - - +
75B LYS* 1.3 62.4 + - - +
76B GLU 2.8 5.4 - - - -
77B VAL* 2.9 33.2 - - + +
78B ALA* 3.6 2.4 + - - +
93B THR* 6.4 0.7 - - + -
96B ALA* 5.0 8.7 - - + -
100B ILE* 3.5 20.0 - - + -
510B VAL* 4.9 1.1 - - + -
514B MET* 3.4 28.9 - - + -
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.4 11.7 - - + -
54B VAL* 5.6 0.2 - - - +
57B ALA* 3.2 32.7 - - + +
58B ARG* 3.3 26.9 + - + +
60B ILE* 3.0 20.3 + - - +
61B GLU* 5.3 0.8 - - - +
71B ALA 2.6 22.5 + - - +
72B GLN* 2.7 47.7 + - - +
73B MET 3.3 0.2 - - - -
74B VAL* 1.3 72.8 - - - +
76B GLU* 1.3 57.1 + - - +
78B ALA* 3.6 6.7 + - - +
79B SER* 3.2 24.0 + - - -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN 3.9 4.6 + - - +
73B MET* 3.2 19.5 + - - +
74B VAL 2.8 0.2 - - - -
75B LYS* 1.3 76.7 - - - +
77B VAL* 1.3 59.9 + - - +
78B ALA 3.2 1.3 - - - -
79B SER* 3.1 7.5 + - - -
80B LYS* 2.8 41.5 + - + +
510B VAL* 4.4 16.8 - - + +
46C ALA* 4.1 18.9 - - + +
47C PRO 5.5 0.9 - - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B MET 4.2 1.2 + - - -
74B VAL* 2.9 27.5 + - + +
76B GLU* 1.3 77.8 - - - +
78B ALA* 1.3 64.4 + - - +
80B LYS* 3.6 5.8 + - - +
81B ALA* 3.2 22.2 + - - +
92B ALA* 4.2 9.2 - - + +
93B THR* 4.5 12.6 - - + +
96B ALA* 3.8 18.6 - - + -
506B TYR* 3.3 9.3 - - + +
507B ALA* 3.1 45.1 - - + +
510B VAL* 3.5 19.6 - - + +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 5.3 0.2 - - + -
53B GLY 5.6 0.9 - - - -
54B VAL* 3.4 20.7 - - + +
57B ALA* 3.8 24.2 - - + -
74B VAL 4.4 4.3 - - - +
75B LYS* 3.6 9.1 + - - +
76B GLU 3.2 0.2 - - - -
77B VAL* 1.3 83.9 - - - +
79B SER* 1.3 60.3 + - - +
81B ALA* 3.5 3.7 + - - +
82B ASN 3.3 15.9 + - - -
89B THR* 3.9 11.0 - - - +
93B THR* 3.4 23.3 - - - +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B VAL* 3.8 13.0 - - - +
58B ARG* 3.8 20.3 + - - +
75B LYS* 3.2 18.1 + - - -
76B GLU* 3.1 12.0 + - - -
78B ALA* 1.3 76.9 - - - +
80B LYS* 1.3 59.1 + - - +
82B ASN* 3.3 2.8 + - - +
83B ASP* 2.9 45.1 + - - +
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLU* 2.8 29.1 + - + +
77B VAL* 4.1 2.7 - - - +
79B SER* 1.3 75.3 - - - +
81B ALA* 1.3 65.5 + - - +
83B ASP* 4.2 14.9 - - + +
84B ALA* 3.1 26.4 + - + +
506B TYR* 3.3 54.3 + - + +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL 3.2 17.9 + - - +
78B ALA 3.7 1.1 - - - +
79B SER 3.3 0.4 - - - -
80B LYS* 1.3 76.8 - - - +
82B ASN* 1.3 57.6 + - - +
84B ALA* 3.8 0.6 - - - +
85B ALA* 2.8 32.4 + - - +
86B GLY 3.3 3.8 + - - -
87B ASP 4.6 1.1 - - - +
88B GLY 3.9 9.4 - - - +
89B THR* 3.6 29.8 - - - +
92B ALA* 4.0 9.4 - - + -
502B SER* 5.5 2.9 - - - -
503B ALA* 5.2 3.6 - - - +
506B TYR* 3.9 10.5 - - + -
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASP* 4.9 4.5 - - - +
54B VAL* 3.5 26.9 - - + +
58B ARG* 3.6 28.5 - - - +
78B ALA 3.3 2.0 + - - -
79B SER 3.3 7.7 + - - +
80B LYS 3.3 0.4 - - - -
81B ALA* 1.3 80.3 - - - +
83B ASP* 1.3 61.0 + - - +
84B ALA 3.1 0.2 - - - -
85B ALA 4.0 0.5 - - - -
86B GLY* 3.3 36.4 + - - +
89B THR* 3.5 17.5 - - + +
401B HIS* 5.2 4.9 + - - -
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG* 3.4 19.4 + - - -
79B SER* 2.9 35.4 + - - +
80B LYS* 4.0 20.2 - - + +
81B ALA 3.3 0.4 - - - -
82B ASN* 1.3 78.7 + - - +
84B ALA* 1.3 58.4 + - - +
359B ASP* 5.5 2.8 - - - +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LYS* 3.1 18.3 + - + +
81B ALA 3.8 1.3 - - - +
83B ASP* 1.3 81.1 - - - +
85B ALA* 1.3 63.5 + - - +
498B LYS* 3.5 24.2 + - - +
502B SER* 4.3 12.3 - - - +
506B TYR* 3.7 24.2 - - + +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 2.8 10.8 + - + +
82B ASN 4.0 0.9 - - - -
84B ALA* 1.3 79.3 - - + +
86B GLY* 1.3 57.9 + - - +
87B ASP* 3.0 24.7 - - - +
401B HIS* 3.0 26.9 - - - +
405B ALA* 5.3 2.9 - - + +
498B LYS* 4.8 10.9 + - + +
499B VAL* 3.9 29.6 - - + +
502B SER* 5.3 4.9 - - - -
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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