Contacts of the helix formed by residues 56 - 78 (chain A) in PDB entry 4P5K
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 ALA 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.7 23.3 - - + +
39A LYS 3.7 23.6 - - - +
40A GLU* 4.4 0.4 - - - -
41A THR* 4.0 22.0 - - - +
54A PHE* 3.0 6.2 + - - -
55A GLU* 1.3 71.5 - - - +
57A GLN* 1.3 62.1 + - + +
58A GLY 2.9 0.2 - - - -
59A GLY* 2.8 20.5 + - - -
60A LEU* 3.4 11.6 + - + +
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Residues in contact with GLN 57 (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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55A GLU* 3.0 31.3 + - + +
56A ALA* 1.3 83.3 + - + +
58A GLY* 1.3 62.4 + - - +
60A LEU* 3.1 19.4 + - + +
61A ALA* 2.9 29.1 + - + +
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Residues in contact with GLY 58 (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 PHE* 4.3 2.7 - - - -
55A GLU* 2.8 14.7 + - - +
57A GLN* 1.3 79.2 - - - +
59A GLY* 1.3 54.7 + - - +
61A ALA* 4.2 4.6 - - - +
62A ASN* 2.7 36.8 + - - -
-21B THR* 4.0 20.4 - - - -
-19B LEU* 4.4 3.4 - - - +
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Residues in contact with GLY 59 (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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22A PHE* 3.8 32.4 - - - -
34A VAL* 4.2 7.4 - - - -
36A LEU* 5.0 0.7 - - - -
54A PHE* 4.0 4.2 - - - -
56A ALA 2.8 10.4 + - - -
58A GLY* 1.3 78.2 - - - +
60A LEU* 1.3 62.4 + - - -
61A ALA 3.4 0.2 - - - -
62A ASN 3.5 0.9 + - - -
63A ILE* 3.1 29.7 + - - +
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Residues in contact with LEU 60 (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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34A VAL* 4.8 4.7 - - + +
36A LEU* 4.4 27.4 - - + +
39A LYS* 4.0 37.2 - - + -
56A ALA* 3.4 9.3 + - + +
57A GLN* 3.1 28.9 + - + +
59A GLY* 1.3 72.1 - - - +
61A ALA* 1.3 66.7 + - - +
63A ILE* 3.2 10.5 + - - +
64A ALA* 3.1 22.2 + - - +
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Residues in contact with ALA 61 (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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57A GLN 2.9 16.7 + - - +
58A GLY* 4.2 2.0 - - - +
60A LEU* 1.3 76.7 - - - +
62A ASN* 1.3 55.5 + - - +
63A ILE 3.2 0.2 + - - -
64A ALA* 3.3 8.1 + - - +
65A ILE* 3.0 36.2 + - + +
-19B LEU* 4.0 22.2 - - + -
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Residues in contact with ASN 62 (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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22A PHE* 3.6 32.7 - - + -
58A GLY 2.7 24.2 + - - +
59A GLY 3.5 1.8 + - - +
60A LEU 3.4 0.4 - - - -
61A ALA* 1.3 77.5 - - - +
63A ILE* 1.3 58.5 + - - +
65A ILE* 3.6 7.9 - - - +
66A LEU* 3.0 33.7 + - + +
-21B THR* 4.2 2.8 - - - +
-20B GLN 3.3 17.6 + - - +
-19B LEU* 3.3 12.5 - - - +
-18B PHE* 3.0 46.2 + - + +
13B GLN* 5.4 0.2 + - - -
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Residues in contact with ILE 63 (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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11A ALA* 4.4 7.4 - - + -
12A PHE 4.6 8.5 - - - +
13A VAL* 4.1 11.2 - - + +
19A THR* 6.2 2.2 - - + -
20A GLY* 5.3 1.8 - - - -
21A GLU 4.0 23.3 - - - +
22A PHE* 4.1 11.9 - - + -
36A LEU* 4.0 32.8 - - + -
59A GLY 3.1 15.5 + - - +
60A LEU* 3.2 8.9 + - - +
61A ALA 3.1 0.8 - - - -
62A ASN* 1.3 77.4 - - - +
64A ALA* 1.3 68.1 + - - +
65A ILE 3.0 0.9 - - - -
66A LEU* 2.9 18.5 + - + +
67A ASN* 3.0 28.2 + - - +
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Residues in contact with ALA 64 (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 LEU 3.1 9.5 + - - +
61A ALA* 3.6 10.8 - - - +
63A ILE* 1.3 79.5 - - - +
65A ILE* 1.3 62.2 + - + +
67A ASN* 3.3 12.3 + - - +
68A ASN* 3.3 28.2 + - - +
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Residues in contact with ILE 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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61A ALA* 3.0 22.8 + - + +
62A ASN* 3.6 7.2 - - - +
63A ILE 3.0 0.2 - - - -
64A ALA* 1.3 76.1 - - + +
66A LEU* 1.3 57.8 + - - +
68A ASN* 3.4 11.7 + - - +
69A ASN* 3.2 26.6 + - - +
-19B LEU* 4.1 28.9 - - + -
-18B PHE* 3.5 32.3 - - + +
-17B HIS 3.4 23.8 - - - +
-16B THR* 3.7 19.3 - - + +
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Residues in contact with LEU 66 (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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11A ALA* 3.6 44.2 - - + +
12A PHE* 4.1 10.8 - - - +
13A VAL* 3.7 15.0 - - + +
62A ASN 3.0 21.6 + - - +
63A ILE* 2.9 12.0 + - + +
65A ILE* 1.3 75.3 - - - +
67A ASN* 1.3 52.4 + - - +
69A ASN* 3.2 9.6 + - - +
70A LEU* 2.7 32.9 + - - +
-18B PHE* 4.2 27.6 - - + -
9B PHE* 3.6 34.2 - - + +
11B GLY 4.6 5.2 - - - +
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Residues in contact with ASN 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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13A VAL* 3.4 21.6 - - - +
14A GLN 5.3 0.9 + - - +
19A THR* 5.1 3.7 - - - +
63A ILE* 3.0 36.4 + - - +
64A ALA* 3.3 11.8 + - - +
66A LEU* 1.3 71.5 - - - +
68A ASN* 1.3 61.4 + - - +
70A LEU* 3.1 10.7 + - - +
71A ASN* 2.4 43.2 + - - +
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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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64A ALA* 3.3 15.9 + - - +
65A ILE* 3.6 3.1 - - - +
67A ASN* 1.3 78.2 - - - +
69A ASN* 1.3 59.2 + - - +
71A ASN* 3.3 9.8 + - - +
72A THR* 2.8 34.8 + - - +
-16B THR* 3.4 32.1 - - + +
-15B ILE 5.6 1.1 - - - +
-12B GLY* 5.0 5.1 - - - -
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Residues in contact with ASN 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 ILE* 3.2 16.5 + - - +
66A LEU* 3.2 10.4 + - - +
68A ASN* 1.3 78.6 - - - +
70A LEU* 1.3 60.4 + - - +
72A THR* 4.3 3.6 - - - -
73A LEU* 3.2 29.7 + - - +
-17B HIS 2.8 19.8 + - - +
-16B THR* 3.6 6.5 - - - +
-15B ILE* 3.2 43.5 + - + +
9B PHE* 3.5 35.0 - - + -
28B TYR* 4.4 4.2 - - - -
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Residues in contact with LEU 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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13A VAL* 3.5 24.5 - - + +
14A GLN* 3.9 10.8 - - - -
15A THR* 4.4 4.3 - - + +
66A LEU 2.7 17.7 + - - +
67A ASN* 3.1 14.8 + - - +
69A ASN* 1.3 70.1 - - - +
71A ASN* 1.3 57.1 + - - +
73A LEU* 2.9 3.2 + - - -
74A ILE* 2.8 49.8 + - + +
7B TYR* 3.7 24.7 - - + +
8B LEU 3.6 36.3 - - - +
9B PHE* 3.6 6.5 - - + +
30B TYR* 4.2 6.7 - - + -
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Residues in contact with ASN 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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67A ASN* 2.4 35.3 + - - +
68A ASN* 3.6 12.5 + - - +
70A LEU* 1.3 75.8 - - - +
72A THR* 1.3 57.4 + - - +
74A ILE* 3.2 14.2 + - - +
75A GLN* 3.0 38.7 + - + +
-12B GLY* 5.5 5.6 - - - -
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Residues in contact with THR 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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68A ASN 2.8 20.0 + - - -
69A ASN* 3.8 7.6 - - - -
70A LEU 3.2 0.2 - - - -
71A ASN* 1.3 75.6 - - - +
73A LEU* 1.3 60.7 + - + +
75A GLN* 4.1 4.6 - - - +
76A ARG* 3.3 34.2 + - - +
-15B ILE* 4.1 20.7 + - + -
-14B THR 4.1 5.8 - - - +
-13B GLY* 3.3 36.1 - - - +
-12B GLY* 2.9 20.9 + - - +
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Residues in contact with LEU 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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69A ASN 3.2 24.0 + - - +
70A LEU 2.9 3.2 + - - +
72A THR* 1.3 87.6 - - + +
74A ILE* 1.3 56.6 + - - +
75A GLN 3.3 0.4 - - - -
76A ARG* 3.9 17.9 - - + +
77A SER* 2.7 39.2 + - - -
-15B ILE* 4.0 19.7 - - + -
9B PHE* 4.0 11.9 - - + -
30B TYR* 3.6 30.3 - - + -
35B PHE* 3.4 36.8 - - + -
51B LEU* 4.1 15.5 - - + -
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Residues in contact with ILE 74 (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 THR* 5.1 3.8 - - + -
70A LEU* 2.8 43.9 + - + +
71A ASN* 3.7 14.4 - - - +
73A LEU* 1.3 75.0 - - - +
75A GLN* 1.3 70.9 + - - +
77A SER* 3.2 6.0 + - - -
79A HIS* 3.0 63.0 + - + +
7B TYR* 3.7 41.7 - - + -
30B TYR* 4.1 4.0 - - - +
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Residues in contact with GLN 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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71A ASN* 3.0 23.8 + - + +
72A THR* 4.1 5.8 - - - +
74A ILE* 1.3 95.4 - - - +
76A ARG* 1.3 65.0 + - + +
78A ASN* 3.3 13.3 + - - +
79A HIS* 3.9 16.1 + - - -
-13B GLY 5.0 10.5 - - - +
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Residues in contact with ARG 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 THR* 3.3 29.0 + - - +
73A LEU* 4.5 16.2 - - + +
74A ILE 3.5 0.2 - - - -
75A GLN* 1.3 81.9 - - + +
77A SER* 1.3 62.5 + - - +
78A ASN* 3.1 8.9 + - - +
-15B ILE* 3.4 30.5 - - - +
-14B THR 4.4 4.0 + - - -
-13B GLY* 6.2 0.7 - - - -
35B PHE* 4.6 2.2 - - - -
51B LEU* 2.5 50.8 + - + +
54B PRO* 3.9 25.0 - - - +
55B ASP* 2.5 26.2 + - - -
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Residues in contact with SER 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 LEU* 2.7 23.7 + - - -
74A ILE 3.2 1.0 + - - -
76A ARG* 1.3 77.4 - - - +
78A ASN* 1.3 64.2 + - - +
79A HIS 3.1 5.2 + - - -
80A THR* 3.1 38.0 + - - -
30B TYR* 3.2 25.9 + - - -
51B LEU* 4.5 16.2 - - - -
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Residues in contact with ASN 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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75A GLN 3.3 10.6 + - - +
76A ARG 3.1 12.4 + - - +
77A SER* 1.3 80.5 - - - +
79A HIS* 1.3 73.9 + - - +
80A THR* 4.8 1.2 + - - +
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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