Contacts of the helix formed by residues 11 - 31 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 1.3 87.8 - - - +
12A ALA* 1.3 60.9 + - - -
13A GLN 3.1 0.7 - - - -
14A ALA* 3.0 19.5 + - + +
15A ARG* 3.0 12.4 + - - +
55A LEU* 5.7 0.7 - - + -
58A LEU* 3.7 26.9 - - + -
104A ILE* 4.3 8.4 - - + +
107A ILE* 4.9 1.8 - - + +
108A ASP* 3.2 33.9 - - + +
111A PHE* 3.3 47.6 - - + -
112A TRP* 4.7 0.2 - - - +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 2.7 26.7 + - + +
11A PRO* 1.3 77.9 - - - +
13A GLN* 1.3 62.6 + - - +
15A ARG* 3.7 35.0 - - - +
16A ILE* 2.9 37.7 + - + +
108A ASP* 4.5 1.4 + - - -
12C ALA* 6.0 2.7 - - + -
16C ILE* 4.8 6.1 - - + -
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HIS* 3.9 27.2 + - - +
10A ASP 3.0 21.1 + - - +
12A ALA* 1.3 80.4 - - - +
14A ALA* 1.3 61.9 + - - +
16A ILE* 3.8 8.4 + - - +
17A GLU* 3.5 16.8 + - - +
54A HIS* 3.5 46.9 + - + +
13C GLN* 5.2 9.5 + - + +
16C ILE* 3.9 31.9 - - + +
17C GLU* 3.3 27.5 + - - +
54C HIS* 5.9 1.2 + - - -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 3.0 11.6 + - + +
13A GLN* 1.3 78.0 - - - +
15A ARG* 1.3 66.1 + - - +
17A GLU* 3.1 4.9 + - - +
18A ALA* 3.0 22.2 + - - +
51A ALA* 3.7 19.9 - - - +
54A HIS* 3.8 15.9 - - + +
55A LEU* 3.7 31.0 - - + -
58A LEU* 5.8 0.2 - - + -
104A ILE* 4.1 8.7 - - + -
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO 3.0 11.9 + - - +
12A ALA* 3.2 37.9 + - - +
14A ALA* 1.3 76.3 - - - +
16A ILE* 1.3 63.5 + - - +
18A ALA* 2.9 4.9 + - - +
19A GLU* 2.8 59.8 + - - +
101A LEU* 4.2 14.1 - - + +
104A ILE* 4.1 22.1 - - + +
108A ASP* 4.9 12.5 + - - -
10C ASP* 5.1 6.3 + - - -
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 2.9 29.0 + - + +
13A GLN* 4.1 7.2 - - - +
15A ARG* 1.3 85.4 - - - +
17A GLU* 1.3 61.2 + - - +
19A GLU* 3.4 14.3 + - - +
20A SER* 3.3 21.3 + - - -
1C HIS* 4.0 18.6 - - + +
8C VAL* 3.9 13.5 - - + +
10C ASP* 4.3 26.0 - - + +
12C ALA* 4.5 12.3 - - + -
13C GLN* 4.0 34.8 - - + +
16C ILE* 5.8 2.0 - - + -
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN 3.5 13.9 + - - +
14A ALA 3.1 7.8 + - - +
16A ILE* 1.3 74.9 - - - +
18A ALA* 1.3 66.2 + - - +
20A SER* 3.1 6.5 + - - -
21A VAL* 3.1 23.2 + - - +
47A ARG* 2.9 56.1 + - - +
50A LEU* 3.8 20.4 - - + +
51A ALA* 3.8 7.4 - - + +
54A HIS* 4.3 8.6 + - + +
7003A THJ 3.6 5.0 - - - -
1C HIS* 2.8 26.3 + - - -
13C GLN* 3.4 15.5 + - - +
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA 3.0 5.0 + - - +
15A ARG 2.9 8.2 + - - +
17A GLU* 1.3 77.7 - - - +
19A GLU* 1.3 61.2 + - - +
21A VAL* 3.2 13.3 + - - +
22A LYS* 3.1 21.5 + - - +
51A ALA* 4.2 3.3 - - + +
85A LEU* 4.4 13.2 - - + -
97A GLY* 4.9 2.4 - - - +
100A ALA* 5.0 1.3 - - + -
101A LEU* 3.6 20.0 - - + +
104A ILE* 3.6 30.3 - - + -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 2.8 45.8 + - - +
16A ILE* 3.6 12.6 - - - +
17A GLU 3.2 0.2 - - - -
18A ALA* 1.3 74.7 - - - +
20A SER* 1.3 59.6 + - - +
22A LYS* 3.4 1.9 + - - +
23A ALA* 3.0 29.3 + - - +
101A LEU* 3.9 22.9 - - + -
8C VAL* 4.0 21.8 - - + +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE 3.3 1.4 + - - -
17A GLU 3.1 9.9 + - - -
19A GLU* 1.3 76.9 - - - +
21A VAL* 1.3 60.1 + - - +
23A ALA* 3.7 1.7 - - - +
24A ILE* 2.8 38.2 + - - +
47A ARG* 4.3 15.9 - - - -
1C HIS* 2.8 34.1 - - - -
2C CYS* 4.9 0.2 - - - -
6C CYS* 3.2 22.1 - - - -
8C VAL* 3.4 12.0 - - - +
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU 3.1 17.5 + - - +
18A ALA* 3.2 14.3 + - - +
20A SER* 1.3 77.7 - - - +
22A LYS* 1.3 63.1 + - - +
24A ILE* 3.4 7.4 + - - +
25A GLN* 3.1 32.9 + - - +
44A LYS* 3.9 21.9 - - + +
47A ARG* 3.9 4.0 - - + -
48A ALA* 3.5 38.1 - - + +
85A LEU* 5.2 4.7 - - + -
88A ALA* 3.9 27.8 - - + -
97A GLY* 4.5 4.5 - - - -
100A ALA* 6.4 0.2 - - + -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ALA 3.1 14.4 + - - +
19A GLU* 4.0 3.8 - - - +
21A VAL* 1.3 75.5 - - - +
23A ALA* 1.3 67.4 + - - +
25A GLN* 3.2 11.8 + - - +
26A GLU* 3.1 43.1 + - - +
94A PRO* 3.6 34.5 - - + +
97A GLY* 4.3 4.9 - - - -
98A GLN* 2.7 36.7 + - - +
101A LEU* 4.0 16.2 - - + -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU 3.0 18.4 + - - +
20A SER 3.7 3.8 - - - +
22A LYS* 1.3 76.9 - - - +
24A ILE* 1.3 63.0 + - - +
26A GLU* 3.2 14.9 + - - +
27A LYS* 3.1 30.0 + - - +
6C CYS 3.6 23.6 - - - +
8C VAL* 4.2 9.0 - - + -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER 2.8 30.4 + - - +
21A VAL 3.7 4.5 - - - +
22A LYS 3.2 0.2 - - - -
23A ALA* 1.3 77.3 - - - +
25A GLN* 1.3 57.7 + - - +
27A LYS* 3.1 4.6 + - - +
28A MET* 2.9 31.0 + - - +
40A ALA* 3.5 35.2 - - + +
43A ILE* 3.8 28.5 - - + -
44A LYS* 3.8 24.0 - - + +
47A ARG* 4.3 6.5 - - + -
2C CYS* 4.3 7.0 - - - -
4C LEU* 3.7 22.4 - - + -
6C CYS* 4.0 8.7 - - + -
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.1 16.5 + - - +
22A LYS* 3.2 10.7 + - - +
24A ILE* 1.3 75.1 - - - +
26A GLU* 1.3 62.2 + - - +
28A MET* 3.3 9.3 + - - +
29A ALA* 3.3 17.8 + - - +
44A LYS* 3.5 14.1 - - + +
88A ALA* 3.3 14.8 + - - +
91A SER 3.2 22.2 + - - +
92A THR 3.4 23.4 - - - +
93A ASP 3.3 9.8 + - - +
94A PRO* 3.4 12.1 - - + +
96A THR* 2.8 23.6 + - - -
97A GLY* 3.2 25.6 + - - -
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.1 36.5 + - - +
23A ALA* 3.5 15.7 - - - +
24A ILE 3.2 0.2 - - - -
25A GLN* 1.3 76.3 - - - +
27A LYS* 1.3 62.1 + - + +
29A ALA* 3.2 17.9 + - - +
30A ALA* 3.5 8.0 + - - +
94A PRO* 3.5 22.7 - - + +
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.1 15.7 + - - +
24A ILE* 3.1 7.2 + - - +
26A GLU* 1.3 77.6 - - + +
28A MET* 1.3 63.9 + - - +
30A ALA* 3.0 17.2 + - - +
31A ASN* 3.2 11.4 + - - +
36A PHE* 3.7 24.2 - - + -
4C LEU* 4.1 11.7 - - + -
5C PRO* 3.5 27.0 + - - +
6C CYS* 3.7 23.7 + - - +
7C GLY* 5.2 2.0 - - - +
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Residues in contact with MET 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 2.9 21.0 + - - +
25A GLN* 3.6 11.4 - - - +
26A GLU 3.3 0.2 - - - -
27A LYS* 1.3 76.6 - - - +
29A ALA* 1.3 61.3 + - - +
31A ASN 3.3 5.7 + - - +
32A ASP* 4.9 0.3 - - - -
36A PHE* 4.0 3.8 - - + -
37A GLN* 2.9 55.8 + - - +
40A ALA* 3.4 24.7 - - + -
41A THR* 3.5 25.4 - - - +
44A LYS* 3.8 26.7 - - - +
92A THR* 3.8 18.2 - - + -
35D HIS* 3.7 14.6 - - + +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN 3.3 8.7 + - - +
26A GLU* 3.2 12.7 + - - +
27A LYS 3.1 0.8 - - - -
28A MET* 1.3 79.1 - - - +
30A ALA* 1.3 61.5 + - - +
31A ASN 3.8 0.7 + - - -
92A THR* 5.3 4.2 + - - +
94A PRO* 5.5 5.8 - - + -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU 3.5 6.8 + - - +
27A LYS* 3.0 9.6 + - - +
29A ALA* 1.3 81.0 - - + +
31A ASN* 1.3 58.9 + - + +
32A ASP 4.2 0.7 - - - -
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Residues in contact with ASN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS 3.2 5.8 + - - +
28A MET 3.3 2.7 - - - +
29A ALA 3.5 0.8 - - - -
30A ALA* 1.3 79.7 - - + +
32A ASP* 1.3 53.9 + - - +
33A ASP* 2.7 40.3 + - - +
36A PHE* 3.6 42.3 - - + +
37A GLN* 2.6 28.9 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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