Contacts of the helix formed by residues 11 - 31 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASP* 1.3 89.3 - - - +
12D ALA* 1.3 59.5 + - - +
13D GLN 3.1 0.4 - - - -
14D ALA* 3.0 19.3 + - + +
15D ARG* 3.0 13.4 + - - +
55D LEU* 5.9 0.7 - - + -
58D LEU* 3.9 25.3 - - + -
104D ILE* 4.3 9.4 - - + +
107D ILE* 5.0 1.6 - - + +
108D ASP* 3.5 34.8 - - + +
111D PHE* 3.4 45.8 - - + -
112D TRP* 4.8 0.9 - - - +
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASP* 2.8 24.5 + - + +
11D PRO* 1.3 75.7 - - - +
13D GLN* 1.3 66.1 + - - +
15D ARG* 3.6 31.2 - - - +
16D ILE* 2.9 37.8 + - + +
108D ASP* 5.0 1.0 + - - -
12F ALA* 6.0 2.5 - - + -
16F ILE* 4.6 6.7 - - + -
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D HIS* 3.8 31.4 + - - +
10D ASP 3.0 21.3 + - - +
12D ALA* 1.3 77.7 - - - +
14D ALA* 1.3 61.8 + - - +
16D ILE* 4.0 7.7 + - - +
17D GLU* 3.6 16.5 + - - +
54D HIS* 3.2 45.4 + - + +
7004D THJ 5.3 0.2 + - - -
13F GLN* 5.4 9.4 + - + +
16F ILE* 3.9 32.8 - - + +
17F GLU* 3.4 25.1 + - - +
54F HIS* 6.1 0.2 + - - -
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASP 4.5 0.2 + - - -
11D PRO* 3.0 12.1 + - + +
13D GLN* 1.3 79.7 - - - +
15D ARG* 1.3 59.2 + - - +
17D GLU* 3.4 3.8 + - - +
18D ALA* 3.0 28.6 + - - +
51D ALA* 3.9 8.3 - - - +
54D HIS* 3.8 22.5 - - + +
55D LEU* 3.7 34.1 - - + -
58D LEU* 5.7 0.9 - - + -
104D ILE* 4.1 8.9 - - + +
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Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO 3.0 12.1 + - - +
12D ALA* 3.2 30.9 + - - +
14D ALA* 1.3 74.7 - - - +
16D ILE* 1.3 68.4 + - - +
18D ALA* 3.0 7.6 + - - +
19D GLU* 2.6 73.2 + - + +
101D LEU* 4.4 7.9 - - + -
104D ILE* 4.2 16.7 - - + +
108D ASP* 6.3 0.6 - - - -
10F ASP* 5.2 7.1 + - - -
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Residues in contact with ILE 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA* 2.9 26.2 + - + +
13D GLN* 4.2 6.5 - - - +
15D ARG* 1.3 89.6 - - - +
17D GLU* 1.3 62.8 + - - +
19D GLU* 3.3 14.3 + - - +
20D SER* 3.2 20.6 + - - -
1F HIS* 4.0 17.9 - - + +
8F VAL* 4.0 12.6 - - + +
10F ASP* 4.2 29.4 - - + +
12F ALA* 4.6 8.1 - - + -
13F GLN* 3.9 34.8 - - + +
16F ILE* 6.0 1.8 - - + -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLN 3.6 14.5 + - - +
14D ALA 3.4 7.2 + - - +
15D ARG 3.2 0.4 - - - -
16D ILE* 1.3 76.2 - - - +
18D ALA* 1.3 64.8 + - - +
20D SER* 3.0 15.6 + - - -
21D VAL* 3.2 14.2 + - - +
47D ARG* 3.1 59.8 + - - +
50D LEU* 4.0 20.0 - - + +
51D ALA* 4.1 6.7 - - + -
54D HIS* 4.0 8.8 + - + +
7006D THJ 3.7 3.1 + - - -
1F HIS* 2.9 23.2 + - - -
13F GLN* 3.1 17.7 + - - +
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA 3.0 18.1 + - - +
15D ARG 3.5 4.0 - - - +
17D GLU* 1.3 77.1 - - - +
19D GLU* 1.3 62.9 + - - +
21D VAL* 3.1 21.6 + - - +
22D LYS* 3.1 13.7 + - - +
51D ALA* 4.3 3.7 - - + +
85D LEU* 4.4 12.8 - - + -
97D GLY 5.0 2.0 - - - +
100D ALA* 5.2 1.1 - - + -
101D LEU* 3.5 24.5 - - + +
104D ILE* 3.6 17.9 - - + -
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG* 2.6 54.0 + - + +
16D ILE* 3.4 12.8 - - - +
17D GLU 3.1 0.2 - - - -
18D ALA* 1.3 74.4 - - - +
20D SER* 1.3 56.5 + - - +
22D LYS* 3.3 3.0 + - - +
23D ALA* 2.9 29.5 + - - +
101D LEU* 3.9 21.8 - - + -
8F VAL* 3.8 23.6 - - + +
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Residues in contact with SER 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE 3.2 1.2 + - - -
17D GLU 3.0 11.7 + - - -
19D GLU* 1.3 76.0 - - - +
21D VAL* 1.3 59.6 + - - +
23D ALA* 3.7 1.0 - - - +
24D ILE* 2.8 38.6 + - - +
47D ARG* 4.1 17.0 - - - -
1F HIS* 2.8 34.5 + - - -
2F CYS* 5.0 0.2 - - - -
6F CYS* 3.4 20.9 - - - -
8F VAL* 3.6 11.6 - - - +
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU 3.5 13.2 - - - +
18D ALA* 3.1 14.3 + - + +
20D SER* 1.3 78.1 - - - +
22D LYS* 1.3 59.9 + - - +
24D ILE* 3.7 4.9 - - - +
25D GLN* 3.0 35.5 + - - +
44D LYS* 3.9 24.8 - - + +
47D ARG* 4.0 4.7 - - + -
48D ALA* 3.6 37.2 - - + +
85D LEU* 5.0 4.7 - - + -
88D ALA* 3.9 27.6 - - + -
97D GLY* 4.5 4.3 - - - -
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Residues in contact with LYS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA 3.1 8.6 + - - +
19D GLU* 3.9 5.8 - - - +
21D VAL* 1.3 76.8 - - - +
23D ALA* 1.3 67.3 + - - +
25D GLN* 3.1 12.2 + - - +
26D GLU* 3.0 47.9 + - - +
94D PRO* 3.7 27.8 - - + +
97D GLY* 4.4 4.9 - - - -
98D GLN* 2.8 34.2 + - - +
101D LEU* 3.8 19.1 - - + -
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLU 2.9 17.9 + - - +
20D SER* 3.7 4.0 - - - +
22D LYS* 1.3 77.3 - - - +
24D ILE* 1.3 62.0 + - - +
26D GLU* 3.5 13.1 + - - +
27D LYS* 3.1 30.8 + - - +
6F CYS 3.5 23.1 - - - +
8F VAL* 3.9 12.3 - - + -
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Residues in contact with ILE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D SER 2.8 30.2 + - - +
21D VAL 3.7 4.3 - - - +
23D ALA* 1.3 75.0 - - - +
25D GLN* 1.3 60.9 + - - +
27D LYS* 3.2 7.7 + - - +
28D MET* 2.8 36.8 + - + +
40D ALA* 3.6 34.8 - - + +
43D ILE* 3.7 31.0 - - + -
44D LYS* 3.9 22.2 - - + -
47D ARG* 4.1 6.3 - - + -
2F CYS* 4.3 5.4 - - - -
4F LEU* 3.8 17.3 - - + -
6F CYS* 4.1 9.4 - - + -
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Residues in contact with GLN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 3.0 23.6 + - - +
22D LYS* 3.1 7.2 + - - +
24D ILE* 1.3 75.9 - - - +
26D GLU* 1.3 57.8 + - - +
28D MET* 2.9 25.4 + - - +
29D ALA* 3.0 11.4 + - - +
44D LYS* 3.5 17.1 - - + +
88D ALA* 3.4 11.9 + - - +
91D SER 3.0 22.0 + - - +
92D THR 3.7 17.4 - - - +
93D ASP 3.5 5.2 + - - -
94D PRO* 3.4 16.9 - - + +
96D THR* 2.7 24.5 + - - -
97D GLY* 3.1 26.7 + - - +
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 3.0 44.9 + - - +
23D ALA* 3.7 14.1 - - - +
25D GLN* 1.3 75.8 - - - +
27D LYS* 1.3 64.4 + - + +
29D ALA* 3.2 13.9 + - - +
30D ALA* 3.4 12.1 + - - +
94D PRO* 3.7 21.9 - - + +
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA* 3.1 19.1 + - - +
24D ILE 3.6 6.7 - - - +
26D GLU* 1.3 77.5 - - + +
28D MET* 1.3 60.9 + - - +
30D ALA* 3.3 5.3 + - - +
31D ASN* 3.1 22.5 + - - +
36D PHE* 3.5 24.2 - - + -
4F LEU* 4.4 11.4 - - + -
5F PRO* 3.6 24.1 + - - +
6F CYS* 3.3 29.6 + - - -
7F GLY* 4.9 3.0 - - - +
9006F SO4 6.0 0.4 + - - -
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Residues in contact with MET 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B HIS* 4.4 0.4 - - - +
24D ILE* 2.8 25.5 + - - +
25D GLN* 2.9 13.9 + - - +
27D LYS* 1.3 78.1 - - - +
29D ALA* 1.3 59.1 + - - +
31D ASN 3.4 4.5 - - - +
32D ASP* 3.8 4.9 - - - +
36D PHE* 3.9 3.1 - - + -
37D GLN* 3.0 61.1 + - - +
40D ALA* 3.6 26.2 - - + -
41D THR* 3.3 26.9 - - - +
44D LYS* 3.8 26.7 - - - -
92D THR* 4.0 25.6 - - + -
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLN 3.0 10.7 + - - +
26D GLU* 3.2 11.8 + - - +
28D MET* 1.3 77.6 - - - +
30D ALA* 1.3 60.2 + - - +
32D ASP* 3.9 11.7 - - - +
92D THR* 5.2 4.4 + - - +
94D PRO* 5.1 9.4 - - + -
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU 3.4 8.6 + - - +
27D LYS* 3.3 8.8 + - - +
28D MET 3.3 0.2 - - - -
29D ALA* 1.3 80.5 - - + +
31D ASN* 1.3 59.5 + - + +
32D ASP* 4.1 4.4 + - - +
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Residues in contact with ASN 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LYS 3.1 14.1 + - - +
28D MET 3.4 1.4 - - - +
30D ALA* 1.3 79.2 - - + +
32D ASP* 1.3 56.6 + - - +
33D ASP* 3.0 24.1 + - - +
36D PHE* 3.4 40.3 - - + +
37D GLN* 2.7 26.5 + - - -
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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
------------------------------------------------------------
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