Contacts of the helix formed by residues 60 - 79 (chain E) in PDB entry 1S5E
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 60 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ILE* 3.4 17.5 - - - +
59E ASP* 1.3 78.4 - - - +
61E GLN* 1.3 59.6 + - - +
63E LYS* 2.8 39.8 + - - +
64E ALA 4.2 0.3 + - - -
34F LYS* 4.6 1.9 + - - +
36F GLU* 2.7 34.5 + - - +
52F VAL* 6.3 0.2 - - - -
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Residues in contact with GLN 61 (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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56E GLN 4.1 3.0 + - - +
57E HIS* 3.2 30.7 - - + -
58E ILE* 2.9 38.6 + - + +
60E SER* 1.3 77.8 + - - +
62E LYS* 1.3 64.4 + - - +
63E LYS 3.3 0.2 - - - -
64E ALA* 3.0 4.5 + - - +
65E ILE* 2.9 28.8 + - + +
88E TRP* 4.3 8.7 - - - -
31F LEU* 3.0 33.9 + - - +
32F ALA* 3.9 3.0 - - - +
33F GLY* 3.3 29.1 - - - +
36F GLU* 3.7 7.9 - - - +
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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
----------------------------------------------------------
53E PRO* 4.0 30.4 - - + +
54E GLY 4.4 9.6 - - - +
57E HIS* 4.4 20.6 - - + -
58E ILE 4.4 4.7 - - - +
59E ASP* 3.1 34.9 + - + +
61E GLN* 1.3 79.4 - - - +
63E LYS* 1.3 62.4 + - - +
65E ILE* 3.4 8.3 + - + +
66E GLU* 3.3 25.7 + - - +
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Residues in contact with LYS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 4.7 8.3 - - + +
236A ILE* 5.5 15.0 - - - +
59E ASP 4.4 1.0 + - - -
60E SER* 2.8 43.6 + - - +
62E LYS* 1.3 80.8 - - - +
64E ALA* 1.3 61.6 + - + +
66E GLU* 3.5 8.0 + - - +
67E ARG* 3.1 25.7 + - - +
36F GLU* 4.5 10.1 - - - +
53F PRO* 4.2 23.2 - - - +
66F GLU* 3.7 37.4 - - + +
69F LYS* 4.6 4.5 - - - +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E SER 4.5 0.4 - - - +
61E GLN 3.0 7.2 + - - +
63E LYS* 1.3 81.9 - - + +
65E ILE* 1.3 60.4 + - - +
67E ARG* 3.7 10.2 - - - +
68E MET* 2.8 31.2 + - - +
29F GLU* 5.1 0.7 - - - +
30F SER 4.1 6.7 - - - +
31F LEU* 3.4 32.3 - - + +
36F GLU* 4.1 20.2 - - + -
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Residues in contact with ILE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E VAL* 3.8 19.8 - - + +
51E GLU* 3.9 11.7 - - + +
53E PRO* 4.4 14.6 - - + -
57E HIS* 3.7 46.0 - - + +
61E GLN* 2.9 22.9 + - + +
62E LYS* 3.4 12.1 + - - +
64E ALA* 1.3 76.1 - - - +
66E GLU* 1.3 74.0 + - - +
68E MET* 3.2 2.9 + - - +
69E LYS* 3.1 30.5 + - - +
31F LEU* 4.1 23.1 - - + -
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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
----------------------------------------------------------
232A THR* 5.5 4.5 - - + -
235A ARG* 5.8 3.1 - - - +
236A ILE* 6.0 6.5 - - - -
63D LYS* 4.4 21.4 - - + +
64D ALA* 6.0 0.2 - - - -
67D ARG* 3.0 40.6 + - - +
53E PRO* 4.4 9.5 - - - +
62E LYS 3.3 14.6 + - - +
63E LYS* 3.8 9.0 - - - +
64E ALA 3.3 0.4 - - - -
65E ILE* 1.3 82.9 - - - +
67E ARG* 1.3 64.1 + - - +
69E LYS* 2.8 29.4 + - - +
70E ASP* 3.2 15.5 + - - +
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Residues in contact with ARG 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 3.4 24.8 + - + +
63E LYS 3.1 15.7 + - - +
64E ALA* 3.7 12.9 - - - +
65E ILE 3.3 0.2 - - - -
66E GLU* 1.3 76.1 - - - +
68E MET* 1.3 58.0 + - - +
70E ASP* 3.1 10.8 + - - +
71E THR* 2.9 28.6 + - - -
29F GLU* 3.3 32.9 + - - +
66F GLU* 2.9 51.7 + - - +
69F LYS* 3.5 28.0 + - - +
70F ASP* 2.7 37.3 + - - +
73F ARG* 3.7 12.9 - - - +
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Residues in contact with MET 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E VAL* 3.9 18.6 - - + -
64E ALA 2.8 18.2 + - - +
65E ILE 3.7 4.3 - - - +
66E GLU 3.2 0.4 - - - -
67E ARG* 1.3 77.2 - - - +
69E LYS* 1.3 56.1 + - - +
71E THR* 3.1 3.8 + - - -
72E LEU* 2.9 42.4 + - + +
96E ILE* 4.0 15.9 - - + -
97E ALA 4.1 2.2 - - - +
98E ALA* 3.9 16.6 - - - -
99E ILE* 3.7 23.3 - - + -
29F GLU* 3.7 40.2 - - + +
31F LEU* 3.7 30.3 - - + +
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 6.2 1.8 - - - +
67D ARG* 3.6 30.1 - - - +
27E TYR* 3.7 7.5 + - - +
29E GLU* 6.2 0.4 - - + -
36E GLU* 4.2 19.4 + - - +
37E MET* 4.6 4.7 - - - -
38E ALA* 4.0 31.6 - - + +
50E VAL* 3.9 18.2 - - + -
51E GLU 5.4 0.6 + - - +
53E PRO* 5.0 2.8 - - - +
65E ILE* 3.1 25.2 + - - +
66E GLU* 2.8 40.4 + - - +
67E ARG 3.3 0.2 - - - -
68E MET* 1.3 75.8 - - - +
70E ASP* 1.3 62.6 + - - +
72E LEU* 3.4 8.7 + - - +
73E ARG* 3.1 22.3 + - - +
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Residues in contact with ASP 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 4.2 8.1 - - + +
232A THR* 4.5 6.6 + - - +
235A ARG* 3.2 29.7 + - - -
67D ARG* 2.3 34.7 + - - +
66E GLU 3.2 10.6 + - - +
67E ARG* 3.1 9.9 + - - +
69E LYS* 1.3 75.0 - - - +
71E THR* 1.3 59.9 + - - +
73E ARG* 3.2 25.5 + - - +
74E ILE* 2.9 38.6 + - + +
73F ARG* 3.9 13.2 - - - +
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Residues in contact with THR 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E ARG 2.9 6.4 + - - -
68E MET* 3.4 9.9 - - - -
70E ASP* 1.3 75.5 - - - +
72E LEU* 1.3 58.5 + - - +
74E ILE* 3.4 3.0 + - - +
75E ALA* 2.9 29.0 + - + +
99E ILE* 4.2 26.5 - - + -
101E MET* 4.6 16.3 - - + +
27F TYR* 5.1 1.1 - - + -
29F GLU* 2.7 31.8 + - - +
73F ARG* 2.8 34.7 + - - +
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Residues in contact with LEU 72 (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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24E ILE* 3.7 7.6 - - + +
27E TYR* 4.1 12.0 - - + -
38E ALA* 5.1 5.6 - - + +
40E ILE* 4.2 32.1 - - + -
50E VAL* 3.6 31.9 - - + -
68E MET* 2.9 27.7 + - + +
69E LYS* 3.8 5.8 - - - +
71E THR* 1.3 75.0 - - + +
73E ARG* 1.3 59.4 + - - +
75E ALA* 3.5 4.4 + - - +
76E TYR* 2.9 29.8 + - - +
85E LEU* 5.1 0.2 - - + -
96E ILE* 3.7 18.6 - - + -
99E ILE* 3.8 28.0 - - + -
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Residues in contact with ARG 73 (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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227A GLN* 4.8 4.4 + - - -
230A ILE* 4.2 16.0 - - - +
235A ARG* 4.2 7.3 - - - +
67D ARG* 3.7 29.3 + - - +
70D ASP* 3.7 17.9 + - - +
71D THR* 2.9 44.5 + - - +
74D ILE* 4.2 14.3 - - - +
101D MET* 4.9 2.5 - - + -
27E TYR* 3.7 26.1 - - + +
29E GLU* 4.1 2.1 + - - -
69E LYS 3.1 14.2 + - - +
70E ASP* 3.4 32.2 + - - +
72E LEU* 1.3 72.3 - - - +
74E ILE* 1.3 65.8 + - - +
76E TYR* 3.3 2.9 + - - +
77E LEU* 3.0 36.9 + - + +
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Residues in contact with ILE 74 (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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227A GLN* 3.5 33.2 - - + +
230A ILE* 3.9 19.7 - - + -
70E ASP* 2.9 22.9 + - + +
71E THR* 3.6 3.8 - - - +
73E ARG* 1.3 78.4 - - + +
75E ALA* 1.3 56.5 + - - +
77E LEU* 3.3 1.4 + - - +
78E THR* 2.8 40.0 + - + +
73F ARG* 3.5 40.8 - - + +
74F ILE* 4.3 14.1 - - + -
77F LEU* 3.6 28.7 - - + -
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Residues in contact with ALA 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 3.9 16.8 + - + -
71E THR 2.9 18.8 + - - +
72E LEU* 3.7 5.2 - - - +
74E ILE* 1.3 76.4 - - - +
76E TYR* 1.3 64.1 + - - +
78E THR* 3.2 6.8 + - - -
79E GLU* 3.1 4.9 + - - -
80E ALA* 3.1 35.3 + - + +
82E VAL* 5.3 2.0 - - + -
99E ILE* 5.2 6.1 - - + -
101E MET* 4.3 22.2 - - + -
77F LEU* 5.6 1.3 - - + -
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Residues in contact with TYR 76 (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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80D ALA* 5.1 4.0 - - + -
81D LYS 4.7 2.4 + - - -
101D MET* 3.7 25.9 - - + +
102D ALA* 3.1 31.7 + - - -
103D ASN* 3.8 14.0 + - - -
24E ILE* 3.6 40.3 - - + +
25E PHE 3.6 21.8 - - - -
26E SER* 3.9 4.5 - - - -
27E TYR* 3.7 22.4 - - + -
72E LEU 2.9 18.9 + - - +
73E ARG 3.6 3.8 - - - +
74E ILE 3.3 0.2 - - - -
75E ALA* 1.3 75.9 - - - +
77E LEU* 1.3 84.4 + - + +
79E GLU* 3.2 18.1 + - - +
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Residues in contact with LEU 77 (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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219A LYS* 4.1 9.0 - - - +
223A PHE* 3.5 18.9 - - - -
227A GLN* 3.8 18.2 - - - +
71D THR 5.6 0.2 - - - +
74D ILE* 3.7 35.9 - - + -
75D ALA* 4.9 2.0 - - - +
78D THR* 3.9 13.9 - - + +
80D ALA* 3.5 32.1 - - + -
101D MET* 4.3 9.4 - - + -
73E ARG* 3.0 32.0 + - + +
74E ILE 4.0 2.7 - - - +
76E TYR* 1.3 94.1 - - + +
78E THR* 1.3 59.7 + - - +
79E GLU* 3.3 1.9 + - - +
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Residues in contact with THR 78 (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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216A SER 3.5 3.5 - - - +
219A LYS* 4.2 7.4 - - - -
220A ARG* 3.4 32.4 + - - +
223A PHE* 3.9 2.9 - - + -
224A SER* 3.3 32.1 + - - +
227A GLN* 3.5 21.3 - - - +
74E ILE* 2.8 24.4 + - + +
75E ALA* 3.2 8.1 + - - -
77E LEU* 1.3 77.4 - - - +
79E GLU* 1.3 71.0 + - - +
80E ALA* 3.2 14.1 + - - +
77F LEU* 4.4 3.8 - - - +
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Residues in contact with GLU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP 4.5 1.7 - - - +
215A GLN* 4.5 0.9 - - - +
216A SER* 2.4 53.1 + - - +
219A LYS* 3.0 37.4 + - + +
220A ARG* 5.4 0.5 - - - +
103D ASN* 4.3 10.9 - - - +
23E LYS* 3.8 36.8 - - + +
24E ILE 6.0 0.4 - - - -
75E ALA 3.1 7.0 + - - -
76E TYR* 3.2 12.1 + - - +
77E LEU 4.5 1.3 - - - +
78E THR* 1.3 81.5 - - - +
80E ALA* 1.3 63.9 + - - +
81E LYS 3.6 1.9 + - - -
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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