Contacts of the helix formed by residues 11 - 31 (chain E) in PDB entry 1Q0K
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 PRO 11 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ASP* 1.3 87.7 - - - +
12E ALA* 1.3 57.6 + - - +
13E GLN 3.1 0.4 - - - -
14E ALA* 3.1 10.3 + - + +
15E ARG* 2.9 26.9 + - - +
55E LEU* 5.9 0.4 - - + -
58E LEU* 3.8 26.0 - - + -
104E ILE* 4.5 7.4 - - + +
107E ILE* 5.0 1.8 - - + +
108E ASP* 3.6 33.0 - - + +
111E PHE* 3.4 48.2 - - + -
112E TRP* 4.5 0.7 - - - +
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Residues in contact with ALA 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 5.8 2.9 - - + -
16B ILE* 4.5 8.5 - - + -
10E ASP* 2.8 24.0 + - - +
11E PRO* 1.3 78.4 - - - +
13E GLN* 1.3 56.6 + - - +
15E ARG* 3.8 29.8 - - - +
16E ILE* 2.8 43.2 + - + +
108E ASP* 4.8 1.7 + - - -
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Residues in contact with GLN 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 5.2 8.5 + - + +
16B ILE* 3.7 32.1 - - + +
17B GLU* 3.3 27.7 + - - +
54B HIS* 6.0 0.6 + - - -
1E HIS* 3.6 32.4 + - - +
10E ASP 3.1 19.8 + - - +
12E ALA* 1.3 80.0 - - - +
14E ALA* 1.3 61.9 + - - +
16E ILE* 4.0 6.8 - - - +
17E GLU* 3.4 17.8 + - - +
54E HIS* 3.5 44.8 + - + +
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Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ASP 4.5 0.2 + - - -
11E PRO* 3.1 11.0 + - + +
13E GLN* 1.3 78.5 - - - +
15E ARG* 1.3 65.8 + - - +
17E GLU* 3.3 3.6 + - - +
18E ALA* 2.9 23.7 + - - +
51E ALA* 3.9 9.1 - - - +
54E HIS* 3.7 23.4 - - + +
55E LEU* 3.6 35.0 - - + +
58E LEU* 5.6 0.7 - - + -
104E ILE* 4.4 7.4 - - + -
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Residues in contact with ARG 15 (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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10B ASP* 4.9 7.7 + - - -
11E PRO 2.9 15.2 + - - +
12E ALA* 3.7 26.0 - - - +
14E ALA* 1.3 78.2 - - - +
16E ILE* 1.3 66.2 + - - +
18E ALA* 3.1 6.4 + - - +
19E GLU* 2.7 81.9 + - + +
101E LEU* 4.3 9.4 - - + -
104E ILE* 4.2 17.4 - - + +
105E ALA* 6.6 0.2 - - - +
108E ASP* 5.7 4.4 + - - -
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Residues in contact with ILE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B HIS* 4.0 10.8 - - + +
8B VAL* 3.9 12.8 - - + +
10B ASP* 4.0 31.2 - - + +
12B ALA* 4.3 10.3 - - + -
13B GLN* 3.8 42.6 - - + +
16B ILE* 5.6 1.8 - - + -
12E ALA* 2.8 38.9 + - + +
13E GLN* 4.0 4.9 - - - +
15E ARG* 1.3 89.1 - - - +
17E GLU* 1.3 60.6 + - - +
19E GLU* 3.5 11.0 + - - +
20E SER* 3.3 21.3 + - - -
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Residues in contact with GLU 17 (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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1B HIS* 3.1 9.2 + - - -
13B GLN* 3.0 22.8 + - - +
54B HIS* 5.5 0.3 - - - -
7002B THJ 3.8 3.8 + - - -
13E GLN 3.4 13.8 + - - +
14E ALA 3.3 7.0 + - - +
15E ARG 3.2 0.4 - - - -
16E ILE* 1.3 74.9 - - - +
18E ALA* 1.3 66.6 + - - +
20E SER* 3.1 6.7 + - - +
21E VAL* 3.1 25.7 + - - +
47E ARG* 3.0 58.5 + - - +
50E LEU* 3.9 21.3 - - + +
51E ALA* 3.8 6.7 - - + -
54E HIS* 4.1 11.6 + - + +
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Residues in contact with ALA 18 (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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14E ALA 2.9 17.0 + - - +
15E ARG 3.6 0.7 - - - +
17E GLU* 1.3 75.0 - - - +
19E GLU* 1.3 64.5 + - - +
21E VAL* 3.2 11.9 + - - +
22E LYS* 3.1 22.3 + - - +
51E ALA* 4.1 3.3 - - + +
85E LEU* 4.3 13.0 - - + -
97E GLY* 5.0 1.9 - - - +
100E ALA* 5.2 1.1 - - + -
101E LEU* 3.5 28.2 - - + +
104E ILE* 3.5 18.4 - - + -
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Residues in contact with GLU 19 (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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8B VAL* 3.9 20.2 - - + +
15E ARG* 2.7 61.9 + - - +
16E ILE* 3.7 12.8 - - - +
17E GLU 3.2 0.2 - - - -
18E ALA* 1.3 75.7 - - - +
20E SER* 1.3 58.4 + - - +
22E LYS* 3.5 3.1 + - - +
23E ALA* 2.9 29.6 + - - +
101E LEU* 3.9 22.6 - - + +
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Residues in contact with SER 20 (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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1B HIS* 2.8 34.5 - - - -
2B CYS* 4.9 0.4 - - - -
6B CYS* 3.6 13.3 - - - -
8B VAL* 3.4 16.9 - - - +
16E ILE 3.3 3.9 + - - -
17E GLU 3.1 10.6 + - - -
19E GLU* 1.3 76.5 - - - +
21E VAL* 1.3 58.9 + - - +
23E ALA* 3.7 1.8 - - - +
24E ILE* 2.8 37.4 + - - +
47E ARG* 4.3 16.6 - - - -
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Residues in contact with VAL 21 (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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17E GLU 3.1 15.6 + - - +
18E ALA* 3.2 13.7 + - - +
20E SER* 1.3 77.9 - - - +
22E LYS* 1.3 62.8 + - - +
24E ILE* 3.3 9.8 + - - +
25E GLN* 3.1 27.2 + - - +
44E LYS* 4.0 20.9 - - + +
47E ARG* 3.9 4.7 - - + -
48E ALA* 3.5 38.8 - - + +
85E LEU* 5.0 4.9 - - + -
88E ALA* 4.0 26.9 - - + -
97E GLY* 4.7 3.8 - - - -
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Residues in contact with LYS 22 (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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18E ALA 3.1 12.1 + - - +
19E GLU* 4.0 3.6 - - - +
21E VAL* 1.3 76.5 - - - +
23E ALA* 1.3 66.8 + - - +
25E GLN* 3.1 12.3 + - - +
26E GLU* 2.9 48.8 + - - +
94E PRO* 3.7 22.9 - - + +
97E GLY* 4.2 4.7 - - - -
98E GLN* 2.6 45.9 + - + +
101E LEU* 3.8 18.8 - - + +
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Residues in contact with ALA 23 (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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6B CYS 3.6 22.9 - - - +
8B VAL* 3.9 12.6 - - + -
19E GLU 2.9 19.2 + - - +
20E SER* 3.7 4.0 - - - +
22E LYS* 1.3 77.5 - - - +
24E ILE* 1.3 61.8 + - - +
26E GLU* 3.3 16.3 + - - +
27E LYS* 3.1 29.5 + - - +
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Residues in contact with ILE 24 (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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2B CYS* 4.2 4.0 - - - -
4B LEU* 3.8 16.2 - - + -
6B CYS* 4.0 11.0 - - + -
20E SER 2.8 26.2 + - - +
21E VAL* 3.5 4.5 - - - +
23E ALA* 1.3 74.3 - - - +
25E GLN* 1.3 60.5 + - - +
27E LYS* 3.1 8.6 + - - +
28E MET* 2.9 35.1 + - - +
40E ALA* 3.6 36.1 - - + +
43E ILE* 3.7 24.5 - - + -
44E LYS* 3.7 30.5 - - + +
47E ARG* 4.1 9.6 - - + -
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Residues in contact with GLN 25 (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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21E VAL* 3.1 13.8 + - - +
22E LYS* 3.5 10.7 - - - +
24E ILE* 1.3 75.8 - - - +
26E GLU* 1.3 63.9 + - - +
28E MET* 3.1 18.7 + - - +
29E ALA* 3.3 10.6 + - - +
44E LYS* 3.6 15.3 - - + -
88E ALA* 3.3 14.6 + - - +
91E SER 3.1 21.0 + - - +
92E THR 3.5 19.9 - - - +
93E ASP 3.3 10.7 + - - +
94E PRO* 3.5 13.5 - - + +
96E THR* 2.8 24.7 + - - -
97E GLY* 3.2 26.9 + - - -
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Residues in contact with GLU 26 (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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22E LYS* 2.9 44.6 + - - +
23E ALA* 3.5 18.6 - - - +
24E ILE 3.2 0.2 - - - -
25E GLN* 1.3 77.0 - - - +
27E LYS* 1.3 61.1 + - + +
29E ALA* 3.3 18.3 + - - +
30E ALA* 3.7 7.3 + - - +
94E PRO* 4.0 22.6 - - + +
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Residues in contact with LYS 27 (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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4B LEU* 4.4 10.3 - - + -
5B PRO* 3.4 27.1 - - - +
6B CYS* 3.5 22.4 - - - +
7B GLY* 4.5 2.5 - - - +
9002B SO4 5.5 2.2 + - - -
23E ALA* 3.1 13.0 + - - +
24E ILE* 3.1 8.5 + - - +
26E GLU* 1.3 77.6 - - + +
28E MET* 1.3 62.0 + - - +
30E ALA* 3.3 16.2 + - - +
31E ASN* 3.4 10.0 + - - +
36E PHE* 3.4 24.5 - - + -
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Residues in contact with MET 28 (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* 2.9 19.9 + - - +
25E GLN* 3.1 12.7 + - - +
27E LYS* 1.3 76.4 - - - +
29E ALA* 1.3 62.0 + - - +
30E ALA 3.4 0.2 + - - -
31E ASN 3.5 6.5 + - - +
32E ASP* 5.1 1.9 - - - +
36E PHE* 4.0 3.1 - - + -
37E GLN* 3.1 57.0 + - - +
40E ALA* 3.6 25.4 - - + -
41E THR* 3.6 25.1 - - - +
44E LYS* 3.7 25.4 - - - -
92E THR* 3.6 28.9 - - + -
35F HIS* 3.9 0.4 - - - +
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Residues in contact with ALA 29 (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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25E GLN 3.3 9.0 + - - +
26E GLU* 3.3 13.8 + - - +
27E LYS 3.2 0.4 - - - -
28E MET* 1.3 77.5 - - - +
30E ALA* 1.3 59.6 + - - +
92E THR 5.4 2.0 + - - +
94E PRO* 5.3 9.0 - - + -
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Residues in contact with ALA 30 (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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26E GLU 3.7 7.5 + - - +
27E LYS* 3.3 10.6 + - - +
28E MET 3.2 0.4 - - - -
29E ALA* 1.3 80.1 - - - +
31E ASN* 1.3 60.2 + - + +
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Residues in contact with ASN 31 (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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27E LYS 3.4 5.2 + - - +
28E MET 3.5 2.1 - - - +
29E ALA 3.6 1.0 - - - -
30E ALA* 1.3 81.4 - - + +
32E ASP* 1.3 53.5 + - - +
33E ASP* 2.8 33.6 + - - +
36E PHE* 3.5 43.2 - - + +
37E GLN* 2.7 29.4 + - - -
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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