Contacts of the helix formed by residues 64 - 83 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 3.5 23.5 + - - +
62A LEU* 3.4 1.0 - - - +
63A GLU* 1.3 76.0 - - - +
65A LYS* 1.3 56.4 + - - +
66A PHE* 2.9 19.9 + - - +
67A GLU* 2.7 56.4 + - + +
68A ASN* 2.8 35.6 + - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU 5.2 0.7 - - - +
63A GLU 3.2 9.8 + - - +
64A ASP* 1.3 73.6 + - - +
66A PHE* 1.3 60.0 + - + +
68A ASN* 3.6 10.9 + - + +
69A MET* 3.1 32.3 + - - +
522A THR* 3.6 26.8 + - + +
523A ASP* 3.4 29.7 - - + +
524A LEU 4.4 11.0 + - - -
525A PRO* 4.7 18.4 - - + -
41B ASP* 4.5 4.7 - - - +
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 3.5 43.3 - - - -
7A LYS* 3.6 42.2 - - + -
12A ALA* 6.2 0.4 - - - -
15A LYS* 3.8 31.2 - - + +
16A MET* 4.6 0.3 - - - -
64A ASP* 2.9 11.6 + - - +
65A LYS* 1.3 74.8 - - + +
67A GLU* 1.3 65.4 + - - +
68A ASN 3.1 1.1 - - - -
69A MET* 2.9 16.5 + - - +
70A GLY* 3.0 11.1 + - - -
520A MET* 3.8 44.4 - - + +
522A THR* 3.3 24.7 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 3.3 38.2 - - + +
18A ARG* 2.7 40.7 + - + +
19A GLY* 3.3 14.6 + - - +
22A VAL* 5.4 1.9 - - - +
62A LEU* 3.6 24.9 - - + +
64A ASP* 2.7 37.2 + - + +
66A PHE* 1.3 72.8 - - - +
68A ASN* 1.3 61.9 + - - +
70A GLY 3.3 1.4 + - - +
71A ALA 3.0 19.2 + - - -
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 3.3 18.2 + - - +
62A LEU* 3.1 47.6 + - - +
64A ASP 2.8 11.9 + - - +
65A LYS* 3.6 12.7 + - + +
67A GLU* 1.3 78.1 - - - +
69A MET* 1.3 55.3 + - - +
71A ALA* 3.3 2.2 + - - +
72A GLN* 2.7 60.7 + - - +
41B ASP* 4.8 10.9 + - - -
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Residues in contact with MET 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS 3.1 21.0 + - - +
66A PHE* 2.9 13.9 + - - +
68A ASN* 1.3 79.5 - - - +
70A GLY* 1.3 61.9 + - - +
72A GLN* 3.5 0.8 + - - -
73A MET* 3.1 30.8 + - + +
520A MET* 3.6 24.7 - - + -
521A VAL 3.6 17.9 - - - +
522A THR* 3.6 13.2 - - - -
39B VAL* 3.4 37.0 - - + +
41B ASP* 3.5 39.5 - - + +
47B PRO* 3.8 11.6 - - + +
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 3.8 26.2 - - - +
20A VAL* 3.6 14.4 - - - +
66A PHE 3.0 11.4 + - - -
67A GLU 3.3 3.3 + - - -
68A ASN 3.2 0.2 - - - -
69A MET* 1.3 76.4 - - - +
71A ALA* 1.3 61.4 + - - +
73A MET* 3.1 26.5 + - - +
74A VAL 3.3 9.5 + - - -
514A MET* 4.4 0.5 - - - +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 3.5 22.2 - - - +
20A VAL 4.0 2.0 - - - +
23A LEU* 3.5 15.5 - - + +
60A ILE* 4.3 12.1 - - + +
61A GLU* 6.2 0.2 - - - -
62A LEU* 4.2 11.4 - - + -
67A GLU 3.0 14.1 + - - +
68A ASN* 3.8 2.9 - - - +
70A GLY* 1.3 74.3 - - - +
72A GLN* 1.3 59.1 + - + +
74A VAL* 3.0 13.8 - - - +
75A LYS* 2.8 30.0 + - - +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ILE 3.4 8.6 - - - +
61A GLU* 4.0 10.4 - - - +
68A ASN* 2.7 52.7 + - - +
69A MET* 3.9 4.3 - - - +
71A ALA* 1.3 72.7 - - + +
73A MET* 1.3 59.2 + - - +
75A LYS* 3.0 54.7 + - - +
76A GLU* 4.0 3.5 + - - +
45B GLY 5.5 2.4 + - - -
46B ALA* 4.0 20.2 - - - +
47B PRO* 4.0 17.0 - - + -
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Residues in contact with MET 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 4.2 19.5 - - + -
69A MET* 3.1 32.2 + - + +
70A GLY* 3.1 13.8 + - - +
71A ALA 3.0 0.8 - - - -
72A GLN* 1.3 76.3 - - - +
74A VAL* 1.3 64.0 + - - +
75A LYS 3.2 0.2 - - - -
76A GLU* 3.3 24.2 - - - +
77A VAL 4.2 1.0 + - - -
510A VAL* 4.8 5.0 - - - +
514A MET* 3.8 25.5 - - + +
520A MET* 5.2 2.0 - - + -
39B VAL* 4.1 26.7 - - + -
46B ALA* 5.4 0.9 - - + -
47B PRO* 3.9 21.5 - - + +
49B ILE* 4.0 28.5 - - + -
387B VAL* 5.8 4.9 - - + -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.7 42.6 - - + +
23A LEU* 4.0 21.0 - - + +
24A ALA* 6.2 0.4 - - + -
70A GLY 3.7 0.9 - - - +
71A ALA* 3.0 30.1 - - - +
73A MET* 1.3 72.1 - - - +
75A LYS* 1.3 60.7 + - - +
76A GLU 2.9 6.1 - - - -
77A VAL* 2.8 35.5 - - + +
78A ALA* 3.7 3.3 + - - +
93A THR* 5.0 2.9 + - + -
96A ALA* 5.1 8.7 - - + -
100A ILE* 3.7 19.1 - - + -
510A VAL* 5.3 1.3 - - + -
514A MET* 3.9 9.6 - - + -
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Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.7 13.7 - - + -
54A VAL* 5.6 0.3 - - - +
57A ALA* 3.4 18.5 - - + +
58A ARG* 3.0 38.8 + - + -
60A ILE 3.0 30.0 + - - -
61A GLU* 5.1 2.0 + - - +
71A ALA 2.8 16.9 + - - +
72A GLN* 3.0 37.3 + - - +
73A MET 3.2 0.2 - - - -
74A VAL* 1.3 77.0 - - - +
76A GLU* 1.3 59.5 + - - +
78A ALA* 3.7 6.5 + - - +
79A SER* 3.3 21.6 + - - -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN 4.0 4.2 + - - +
73A MET* 3.3 17.6 + - - +
74A VAL 2.9 0.4 - - - -
75A LYS* 1.3 79.0 - - - +
77A VAL* 1.3 59.3 + - - +
79A SER* 3.7 5.7 - - - -
80A LYS* 2.8 38.3 + - + +
510A VAL* 4.7 7.0 - - + -
46B ALA* 4.3 13.3 - - + +
385B THR* 4.0 4.8 - - - -
386B GLU* 3.7 15.6 + - - +
387B VAL* 3.1 52.7 + - - +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET 4.2 0.8 + - - -
74A VAL* 2.8 30.6 + - + +
76A GLU* 1.3 77.6 - - - +
78A ALA* 1.3 63.8 + - - +
80A LYS* 4.8 2.9 - - - -
81A ALA* 3.3 22.5 + - - +
92A ALA* 4.6 8.3 - - + +
93A THR* 4.2 11.2 - - + +
96A ALA* 4.1 17.7 - - + -
506A TYR* 3.4 11.4 - - + +
507A ALA* 3.2 44.4 - - + +
510A VAL* 3.6 18.7 - - + +
385B THR* 6.1 0.9 - - - -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 5.7 0.7 - - + -
27A VAL* 6.3 0.4 - - + -
53A GLY 5.6 0.2 - - - -
54A VAL* 3.7 13.3 - - + +
57A ALA* 4.0 24.0 - - + -
74A VAL 3.7 3.5 + - - +
75A LYS 4.0 7.6 - - - +
76A GLU 3.3 0.2 - - - -
77A VAL* 1.3 81.9 - - - +
79A SER* 1.3 61.6 + - - +
81A ALA* 3.6 5.3 + - - +
82A ASN 3.2 16.1 + - - -
89A THR* 3.7 18.7 - - - +
93A THR* 3.3 24.2 - - - +
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.9 13.0 - - - -
58A ARG* 3.9 23.8 + - - +
75A LYS* 3.3 17.1 + - - -
76A GLU* 3.2 9.0 + - - -
78A ALA* 1.3 77.7 - - - +
80A LYS* 1.3 64.1 + - - +
81A ALA 3.2 1.8 - - - -
82A ASN* 3.3 2.8 + - - +
83A ASP* 3.1 35.0 + - - +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 2.8 28.0 + - + +
77A VAL* 4.4 1.3 - - - +
79A SER* 1.3 73.8 - - - +
81A ALA* 1.3 60.9 + - - +
83A ASP* 3.4 19.6 + - + +
84A ALA* 3.3 13.0 + - - +
506A TYR* 3.3 47.6 + - + +
384B ALA 4.3 11.9 + - - -
385B THR* 4.4 18.8 - - + +
386B GLU* 5.6 2.9 - - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL 3.3 17.6 + - - +
78A ALA 3.6 6.3 - - - +
79A SER 3.2 0.4 - - - -
80A LYS* 1.3 76.4 - - - +
82A ASN* 1.3 55.3 + - - +
84A ALA* 3.0 3.3 + - - +
85A ALA* 2.8 35.3 + - + +
86A GLY 3.7 1.9 + - - -
87A ASP 5.5 1.8 - - - +
88A GLY 5.3 1.3 - - - +
89A THR* 4.3 13.5 - - + +
92A ALA* 4.4 18.4 - - + -
502A SER* 5.5 2.2 - - - -
503A ALA* 5.1 4.9 - - + +
506A TYR* 3.5 18.5 - - + -
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASP* 5.1 2.9 - - - +
54A VAL* 3.7 25.8 - - + +
58A ARG* 3.8 22.4 - - - +
78A ALA 3.2 11.7 + - - +
79A SER* 3.3 8.3 + - - +
81A ALA* 1.3 79.0 - - - +
83A ASP* 1.3 65.6 + - - +
84A ALA 3.0 1.4 + - - -
85A ALA 4.0 1.2 + - - -
86A GLY* 3.4 35.9 + - - +
89A THR* 3.8 12.3 - - + +
398A ASP* 5.5 0.2 - - - +
401A HIS* 5.3 2.9 - - - -
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 4.3 8.7 + - - -
79A SER* 3.1 23.0 + - - +
80A LYS* 3.7 26.2 - - + +
81A ALA 3.2 0.2 - - - -
82A ASN* 1.3 87.1 + - - +
84A ALA* 1.3 59.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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