Contacts of the helix formed by residues 3 - 24 (chain E) in PDB entry 5IYB
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 3 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.4 25.5 - - + +
2E ASP* 1.3 79.2 - - - +
4E GLU* 1.3 69.6 + - - +
5E GLU* 3.1 29.2 + - - +
6E GLU* 3.1 20.3 + - - +
7E THR* 4.1 2.3 + - - -
49E SER* 3.9 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 4 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ASP* 1.3 73.1 + - - +
5E GLU* 1.3 64.6 + - - +
6E GLU 3.0 2.5 - - - -
7E THR* 2.9 29.8 + - - +
8E TYR* 3.4 4.7 + - - +
37E LEU* 5.8 1.0 - - - +
41E LYS* 4.5 21.7 + - - +
48E PRO 6.4 0.4 - - - -
49E SER* 4.4 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160A ARG* 4.7 13.2 + - - -
1349A GLU* 5.7 3.3 - - - +
1350A LYS* 5.5 9.0 - - + -
1E MET* 3.7 13.7 - - + +
3E ASP* 3.1 18.2 + - - +
4E GLU* 1.3 77.5 - - - +
6E GLU* 1.3 62.1 + - - +
8E TYR* 3.1 28.2 + - + +
9E ARG* 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.6 36.5 - - + +
3E ASP 3.1 14.4 + - - +
4E GLU 3.0 0.4 - - - -
5E GLU* 1.3 79.8 - - - +
7E THR* 1.3 56.7 + - - +
9E ARG* 3.0 30.6 + - - +
10E LEU* 2.9 39.7 + - + +
54E ARG* 5.9 4.7 - - - +
55E ARG* 3.3 23.8 + - - +
107E GLN* 4.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ASP 4.4 1.4 + - - -
4E GLU* 3.1 21.1 + - - -
6E GLU* 1.3 79.7 - - - +
8E TYR* 1.3 51.8 + - - +
10E LEU* 3.1 7.7 + - - +
11E TRP* 2.6 36.6 + - - +
37E LEU* 4.0 13.2 - - + -
40E PHE* 3.9 8.7 - - + -
41E LYS* 4.0 21.6 + - + -
46E ASP* 3.4 42.2 + - + +
49E SER* 5.3 3.8 + - - -
54E ARG* 5.7 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1348A SER 5.7 4.5 - - - -
1350A LYS* 3.9 46.4 - - + +
1351A ASP 5.4 0.5 + - - -
4E GLU 3.4 3.4 + - - +
5E GLU* 3.1 22.8 + - + +
7E THR* 1.3 78.6 - - - +
9E ARG* 1.3 56.7 + - + +
11E TRP* 3.4 27.2 - + - +
12E LYS* 2.7 52.3 + - + +
37E LEU* 3.7 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E GLU 3.2 7.4 + - - +
6E GLU* 3.0 33.5 + - - +
8E TYR* 1.3 83.7 - - + +
10E LEU* 1.3 58.8 + - + +
12E LYS* 3.3 5.6 + - - +
13E ILE* 2.9 38.8 + - + +
107E GLN* 4.5 12.7 + - - +
132E GLN* 3.4 33.9 + - - +
133E GLN* 5.0 4.4 - - - +
136E LEU* 3.6 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLU* 2.9 31.3 + - + +
7E THR* 3.6 7.9 - - - +
9E ARG* 1.3 72.7 - - + +
11E TRP* 1.3 67.2 + - - +
13E ILE* 3.2 21.6 - - + +
14E ARG* 3.1 24.4 + - - +
40E PHE* 4.9 8.3 - - + -
46E ASP* 4.1 10.3 - - - +
54E ARG* 3.5 44.4 - - + +
55E ARG* 3.6 33.9 - - + +
58E LEU* 4.5 11.6 - - + +
132E GLN* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E THR 2.6 21.2 + - - +
8E TYR* 3.4 38.8 - + - +
10E LEU* 1.3 73.4 - - - +
12E LYS* 1.3 72.8 + - + +
14E ARG* 3.3 8.5 + - + +
15E LYS* 3.0 51.8 + - + +
35E GLN* 3.0 29.4 + - + +
36E THR* 3.2 14.6 + - + -
37E LEU* 3.2 38.4 - - + -
40E PHE* 3.5 37.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354A PRO* 6.5 1.8 - - - -
8E TYR* 2.7 40.6 + - + +
9E ARG* 3.7 6.3 - - - +
11E TRP* 1.3 85.7 - - + +
13E ILE* 1.3 62.4 + - + +
15E LYS* 3.1 17.5 + - + +
16E THR* 3.1 40.7 + - - +
19E GLN* 5.0 6.7 + - - -
136E LEU* 3.2 34.1 - - + +
137E ILE* 4.3 9.5 - - - +
138E ASN* 4.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ARG* 2.9 21.6 + - + +
10E LEU* 3.2 32.3 - - + +
12E LYS* 1.3 73.2 - - - +
14E ARG* 1.3 68.2 + - + +
16E THR* 3.9 0.7 - - - -
17E ILE* 3.1 32.3 + - + +
58E LEU* 5.7 2.5 - - + -
76E PHE* 5.4 14.8 - - + -
105E VAL* 5.0 7.4 - - + -
132E GLN* 4.2 32.8 - - + +
135E LEU* 3.7 25.1 - - + +
136E LEU* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU 3.1 19.3 + - - +
11E TRP* 3.3 9.9 - - + +
13E ILE* 1.3 76.8 - - - +
15E LYS* 1.3 68.8 + - + +
17E ILE* 3.3 15.2 - - - +
18E MET* 3.2 49.3 + - + +
32E GLU* 3.2 21.1 + - - +
35E GLN* 5.7 5.3 - - - +
40E PHE* 4.9 15.0 - - + -
58E LEU* 2.5 55.0 + - + +
60E VAL* 3.7 24.0 - - - +
76E PHE* 4.2 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E TRP* 3.0 49.2 + - + +
12E LYS* 3.1 19.0 + - + +
14E ARG* 1.3 79.6 - - + +
16E THR* 1.3 63.2 + - - +
18E MET* 3.4 7.5 + - + +
19E GLN* 3.0 32.5 + - + +
32E GLU 2.7 21.5 + - - +
33E LEU* 2.4 33.8 + - - +
34E ASP 3.8 0.4 - - - -
35E GLN* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LYS* 3.1 25.5 + - - -
13E ILE 3.5 2.9 + - - -
14E ARG 3.3 0.2 - - - -
15E LYS* 1.3 77.0 - - - +
17E ILE* 1.3 57.8 + - - +
19E GLN* 3.2 11.4 + - - +
20E LEU* 2.9 26.3 + - - +
135E LEU* 2.9 39.3 + - + +
137E ILE 3.1 26.6 + - - +
138E ASN* 4.2 16.0 + - + +
182E TYR* 4.1 7.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ILE* 3.1 20.7 + - + +
14E ARG* 3.3 19.5 - - - +
16E THR* 1.3 76.4 - - - +
18E MET* 1.3 87.9 + - + +
20E LEU* 3.3 9.1 + - + +
21E CYS* 2.9 39.0 + - - -
60E VAL* 4.7 4.9 - - + -
74E VAL* 4.3 15.3 - - + -
76E PHE* 4.2 22.7 - - + -
103E LEU* 5.4 8.7 - - + -
105E VAL* 4.6 11.0 - - + -
130E PHE* 5.7 0.2 - - + -
135E LEU* 3.9 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ARG* 3.2 45.8 + - + +
15E LYS* 3.6 7.9 - - + +
17E ILE* 1.3 79.5 - - + +
19E GLN* 1.3 59.7 + - - +
21E CYS* 3.4 4.7 + - - +
22E HIS* 3.0 28.6 + - - +
28E VAL* 4.5 23.4 - - + +
32E GLU* 3.1 44.2 - - + +
33E LEU* 4.4 15.7 - - + +
60E VAL* 4.1 22.0 - - + -
62E VAL* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LYS* 5.0 5.4 + - - -
15E LYS* 3.0 22.0 + - - +
16E THR* 3.6 10.4 - - - +
18E MET* 1.3 75.0 - - - +
20E LEU* 1.3 57.3 + - - +
22E HIS* 3.3 7.5 + - - +
23E ASP* 2.8 30.1 + - - +
33E LEU* 4.4 15.0 - - + -
138E ASN* 3.1 31.2 + - - +
141E GLU* 3.1 23.2 + - - +
182E TYR* 4.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E THR 2.9 12.4 + - - +
17E ILE* 3.5 12.1 - - + +
19E GLN* 1.3 74.2 - - - +
21E CYS* 1.3 71.6 + - - +
23E ASP* 3.2 3.9 + - - +
24E ARG* 2.9 56.2 + - - +
72E MET* 4.9 0.4 - - + -
103E LEU* 4.1 15.9 - - + -
130E PHE* 3.6 26.5 - - + -
135E LEU* 4.7 7.6 - - + -
182E TYR* 3.3 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ILE* 2.9 28.0 + - - +
18E MET* 3.7 8.3 - - - +
19E GLN 3.4 0.2 - - - -
20E LEU* 1.3 81.4 - - - +
22E HIS* 1.3 62.0 + - - +
24E ARG* 3.2 7.6 + - - -
25E GLY 3.5 0.2 + - - -
26E TYR* 3.1 36.2 + - + +
28E VAL* 4.5 12.8 - - + -
62E VAL* 4.0 21.3 - - + -
72E MET* 3.5 26.5 - - + -
74E VAL* 4.2 12.1 - - - -
103E LEU* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E MET 3.0 19.1 + - - +
19E GLN* 3.4 9.2 - - - +
20E LEU 3.2 0.2 - - - -
21E CYS* 1.3 76.0 - - - +
23E ASP* 1.3 63.2 + - + +
25E GLY* 3.0 20.6 + - - -
26E TYR 3.8 12.8 + - - +
28E VAL* 3.5 25.2 + - + +
30E GLN* 3.9 20.6 - - - -
33E LEU* 3.9 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E GLN 2.8 17.7 + - - +
20E LEU* 3.2 7.6 + - - +
22E HIS* 1.3 78.6 - - + +
24E ARG* 1.3 59.4 + - + +
25E GLY* 3.0 6.4 + - - -
140E THR* 4.9 4.8 - - - +
182E TYR* 4.4 8.4 - - + +
183E PHE* 3.0 38.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 2.9 37.0 + - + +
21E CYS 3.2 9.4 + - - +
23E ASP* 1.3 76.3 - - - +
25E GLY* 1.3 57.7 + - - +
26E TYR* 3.6 26.5 - - + -
65E ASN* 4.3 8.7 + - - +
72E MET* 3.7 22.9 - - - +
101E ARG* 4.5 8.3 - - - +
103E LEU* 4.7 1.8 - - - +
128E GLU* 3.0 35.0 + - - -
130E PHE* 4.3 4.2 - - - -
181E ARG 3.8 3.2 + - - -
182E TYR 3.3 9.5 + - - +
183E PHE* 2.8 38.8 + - + +
184E GLY* 3.2 13.1 - - - +
----------------------------------------------------------
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