Contacts of the helix formed by residues 55 - 77 (chain E) in PDB entry 1R5I
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 GLU 55 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PHE* 1.3 81.6 - - + +
56E ALA* 1.3 54.8 + - - +
57E GLN* 2.9 13.7 + - + +
58E GLY* 2.6 32.7 + - - -
204E PO4 3.8 31.4 - - - +
308G TYR 5.1 0.8 + - - -
9H LYS* 5.6 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E VAL* 4.0 8.1 - - + +
39E LYS* 3.7 20.5 - - + +
40E GLU* 3.7 30.5 - - - +
41E THR* 3.9 11.9 - - - +
54E PHE* 3.1 15.2 + - - -
55E GLU* 1.3 71.5 + - - +
57E GLN* 1.3 62.9 + - - +
59E ALA* 2.8 21.3 + - - +
60E LEU* 3.4 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LYS* 3.1 37.3 - - - +
55E GLU* 2.8 12.4 + - + +
56E ALA* 1.3 77.5 - - - +
58E GLY* 1.3 63.3 + - - +
60E LEU* 3.2 19.9 + - - +
61E ALA* 3.1 18.7 + - - +
204E PO4 4.2 4.9 - - - +
82H LYS* 3.2 25.8 + - - +
106H ILE* 5.6 0.2 - - - +
109H GLU* 4.6 11.5 - - - +
110H ILE* 4.0 9.4 - - - +
113H LYS* 3.4 40.2 - - + +
214H PO4 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PHE* 4.7 2.2 - - - -
55E GLU 2.6 17.6 + - - -
57E GLN* 1.3 73.4 - - - +
59E ALA* 1.3 61.2 + - - -
61E ALA* 3.1 12.9 + - - +
62E ASN* 3.1 10.2 + - - +
204E PO4 3.1 27.8 + - - -
310G LYS* 3.4 24.0 - - - -
214H PO4 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E PHE* 3.6 35.7 - - + -
34E VAL* 3.7 16.2 - - + -
36E MSE 3.6 20.2 - - + -
54E PHE* 4.2 3.8 - - + -
55E GLU 4.0 1.2 + - - -
56E ALA 2.8 14.9 + - - +
58E GLY* 1.3 70.7 - - - -
60E LEU* 1.3 63.9 + - - +
62E ASN* 3.1 3.1 + - - +
63E ILE* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E VAL* 5.6 0.2 - - - +
36E MSE 4.8 13.1 - - - +
39E LYS* 4.7 12.1 - - + -
56E ALA 3.4 4.0 + - - +
57E GLN* 3.2 33.9 + - - +
59E ALA* 1.3 79.1 - - - +
61E ALA* 1.3 62.3 + - - +
63E ILE* 4.7 3.1 - - - +
64E ALA* 2.9 26.2 + - - +
82H LYS* 4.1 16.2 - - + +
85H VAL* 3.9 31.6 - - + -
86H VAL* 4.9 5.2 - - + -
106H ILE* 4.1 16.2 - - + -
110H ILE* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E GLN* 3.1 9.7 + - + +
58E GLY 3.1 9.3 + - - +
60E LEU* 1.3 78.1 - - - +
62E ASN* 1.3 63.2 + - - +
64E ALA* 3.3 3.7 + - - +
65E VAL* 3.2 25.8 + - - +
310G LYS* 4.5 0.7 - - - +
14H HIS* 3.9 14.4 - - + +
78H MET* 3.9 4.1 - - + +
82H LYS* 4.0 24.4 - - - +
214H PO4 3.4 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 3.4 2.8 - - - +
11E GLU* 2.8 35.4 + - - +
22E PHE* 3.8 7.5 - - + -
58E GLY 3.1 5.7 + - - +
59E ALA 3.1 6.0 + - - +
61E ALA* 1.3 76.1 - - - +
63E ILE* 1.3 59.9 + - - +
66E ASP* 2.8 33.0 + - - +
13F PHE* 4.7 0.8 - - - -
310G LYS* 3.6 14.3 - - - +
311G GLN 2.9 23.7 + - - -
312G ASN* 3.5 6.9 - - - -
313G THR* 2.9 36.2 + - - +
14H HIS* 3.6 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLU* 4.1 6.7 - - + +
12E PHE 3.9 9.2 - - - +
13E TYR* 3.9 26.9 - - + -
20E GLY* 4.5 5.6 - - - -
21E GLU 3.3 33.2 - - - +
22E PHE* 4.2 4.0 - - + -
36E MSE 3.7 25.6 - - + -
59E ALA 2.9 25.2 + - - +
60E LEU* 4.1 2.5 - - - +
62E ASN* 1.3 70.1 - - - +
64E ALA* 1.3 56.6 + - - +
66E ASP* 2.9 16.2 + - - +
67E LYS* 2.7 33.4 + - - +
85H VAL* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU 2.9 19.7 + - - +
61E ALA 3.4 6.5 - - - +
62E ASN 3.3 0.2 - - - -
63E ILE* 1.3 78.6 - - - +
65E VAL* 1.3 59.9 + - - +
67E LYS* 3.5 4.5 + - - +
68E ALA* 3.3 18.4 + - - +
78H MET* 4.7 2.2 - - + -
81H LEU* 3.5 42.0 - - + +
82H LYS* 3.9 11.7 - - + +
85H VAL* 3.4 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ALA 3.2 11.5 + - - +
63E ILE 3.2 0.2 - - - -
64E ALA* 1.3 73.9 - - - +
66E ASP* 1.3 66.5 + - - +
68E ALA* 3.1 8.7 + - + +
69E ASN* 2.9 36.7 + - - +
313G THR* 3.2 23.8 - - + +
314G LEU 3.8 17.5 - - - -
315G LYS* 3.9 9.0 - - + +
14H HIS* 3.6 31.0 - - + -
16H VAL* 5.3 1.3 - - + -
78H MET* 4.0 13.7 - - - -
81H LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLU* 2.6 31.0 - - - +
12E PHE* 5.4 3.1 - - - -
13E TYR* 4.2 14.4 - - + +
62E ASN 2.8 23.1 + - - +
63E ILE* 2.9 20.1 + - + +
65E VAL* 1.3 76.5 - - - +
67E LYS* 1.3 63.9 + - - +
69E ASN* 3.0 7.0 + - - +
70E LEU* 2.9 21.0 + - - +
9F TRP* 3.8 29.9 + - + -
11F LEU* 3.9 6.8 - - - +
313G THR* 2.9 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.1 53.0 - - + +
15E ASN* 5.3 3.0 + - - +
18E GLN* 3.4 12.0 - - - +
63E ILE 2.7 16.0 + - - +
64E ALA 3.5 10.5 - - - +
66E ASP* 1.3 73.1 - - - +
68E ALA* 1.3 63.1 + - - +
70E LEU* 3.3 4.3 + - - +
71E GLU* 3.3 19.6 + - - +
81H LEU 5.5 0.2 - - - +
84H SER* 2.9 32.9 + - - +
85H VAL* 4.4 12.6 - - + -
88H ASP* 3.0 26.2 + - - +
91H ARG* 3.8 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA 3.3 9.8 + - - +
65E VAL* 3.1 13.4 + - + +
67E LYS* 1.3 79.8 - - - +
69E ASN* 1.3 65.0 + - - +
71E GLU* 3.1 11.7 - - - +
72E ILE* 3.1 28.5 + - + +
315G LYS* 5.4 4.0 - - + -
19H LEU* 4.6 11.9 - - + -
81H LEU* 4.3 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E VAL* 2.9 27.2 + - - +
66E ASP* 3.0 6.8 + - - +
68E ALA* 1.3 75.4 - - - +
70E LEU* 1.3 60.5 + - - +
72E ILE* 3.1 7.7 + - - +
73E MSE 2.8 31.8 + - - +
9F TRP* 3.9 24.1 - - + +
313G THR* 4.3 4.0 + - - -
314G LEU 2.9 22.4 + - - -
315G LYS* 3.4 9.0 - - - +
316G LEU* 2.6 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 3.5 24.9 - - + +
15E ASN* 3.1 34.3 - - + +
66E ASP 2.9 11.5 + - - +
67E LYS 3.7 8.3 - - - +
69E ASN* 1.3 75.6 - - - +
71E GLU* 1.3 63.7 + - - +
73E MSE 4.7 1.3 - - - -
74E THR* 2.9 42.1 + - - +
7F PHE 3.3 21.5 - - - +
8F LEU 3.7 14.6 - - - +
9F TRP* 3.4 27.9 - - + -
32F TYR* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ASN* 4.9 8.0 - - - +
67E LYS 3.3 8.5 + - - +
68E ALA* 3.1 15.0 + - - +
70E LEU* 1.3 82.3 - - - +
72E ILE* 1.3 66.4 + - + +
74E THR* 3.9 4.3 - - - -
75E LYS* 3.3 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ALA* 3.4 13.9 - - + +
69E ASN* 3.1 14.1 + - - +
71E GLU* 1.3 79.1 - - + +
73E MSE 1.3 59.7 + - - +
75E LYS* 3.1 9.3 + - - +
76E ARG* 2.8 50.4 + - + +
315G LYS* 3.9 29.6 - - + -
316G LEU* 4.0 26.7 - - + +
317G ALA 4.6 2.9 - - - +
318G THR 4.5 7.4 - - - +
19H LEU* 5.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ASN 2.8 15.5 + - - +
70E LEU 4.1 1.3 - - - +
72E ILE* 1.3 70.4 - - - +
74E THR* 1.3 68.5 + - - +
76E ARG* 3.0 18.6 + - - +
77E SER* 2.7 28.1 + - - -
9F TRP* 3.5 22.7 - - + -
32F TYR* 3.7 25.4 - - + -
37F SER* 3.6 28.9 - - - +
53F LEU* 3.6 33.0 - - - +
57F ASP* 3.6 22.9 - - - +
316G LEU* 3.3 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ASN* 5.1 2.3 + - - -
70E LEU* 2.9 33.0 + - - +
71E GLU* 3.9 4.9 - - - -
73E MSE 1.3 71.5 - - - +
75E LYS* 1.3 57.6 + - - +
77E SER* 3.0 6.2 + - - -
79E TYR* 2.7 56.7 + - + -
7F PHE* 3.4 50.5 - - + +
32F TYR* 3.4 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E GLU* 3.3 34.2 + - - +
72E ILE* 3.1 11.3 + - - +
74E THR* 1.3 79.9 - - - +
76E ARG* 1.3 57.9 + - - +
78E ASN* 2.8 22.0 + - - -
79E TYR* 2.8 42.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ILE* 2.8 31.8 + - + +
73E MSE 3.5 22.1 - - - +
75E LYS* 1.3 72.4 - - - +
77E SER* 1.3 56.2 + - - +
78E ASN* 2.9 10.9 + - - +
53F LEU* 3.6 39.1 + - + +
56F PRO* 4.1 18.7 - - - +
57F ASP* 2.7 43.2 + - - -
316G LEU* 4.2 4.8 - - - +
317G ALA* 3.5 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E MSE 2.7 16.1 + - - -
74E THR 3.0 14.0 + - - -
76E ARG* 1.3 71.7 - - - +
78E ASN* 1.3 63.4 + - - +
80E THR* 2.8 43.7 + - - -
32F TYR* 3.2 27.7 + - - -
53F LEU* 3.9 22.9 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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