Contacts of the helix formed by residues 6 - 24 (chain A) in PDB entry 1QLS
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 THR 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO* 1.3 78.8 - - + +
7A GLU* 1.3 62.8 + - - +
8A THR* 3.6 9.6 + - - +
9A GLU* 2.6 41.9 + - - +
10A ARG* 2.9 27.5 + - - +
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Residues in contact with GLU 7 (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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6A THR* 1.3 74.5 - - - +
8A THR* 1.3 65.0 + - + +
10A ARG* 2.5 46.6 + - - +
11A CYS* 2.9 29.8 + - - +
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Residues in contact with THR 8 (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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6A THR* 3.2 7.8 + - - +
7A GLU* 1.3 80.1 - - + +
9A GLU* 1.3 62.9 + - - +
11A CYS* 3.3 4.2 + - - +
12A ILE* 3.0 37.9 + - - +
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Residues in contact with GLU 9 (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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5A PRO* 3.0 17.6 - - + +
6A THR* 2.6 51.2 + - - +
8A THR* 1.3 78.8 + - - +
10A ARG* 1.3 61.9 + - - +
12A ILE* 3.3 10.3 + - + +
13A GLU* 3.0 24.1 + - - +
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Residues in contact with ARG 10 (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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5A PRO* 4.9 17.5 - - + +
6A THR 2.9 16.9 + - - +
7A GLU* 2.5 42.2 + - - +
9A GLU* 1.3 78.0 - - - +
11A CYS* 1.3 83.1 + - - +
13A GLU* 3.3 10.8 + - + +
14A SER* 2.9 51.7 + - - +
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Residues in contact with CYS 11 (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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7A GLU* 2.9 18.5 + - - +
8A THR* 4.1 3.4 - - - +
10A ARG* 1.3 106.4 - - - +
12A ILE* 1.3 64.1 + - - +
14A SER* 3.4 6.8 + - - -
15A LEU* 2.9 31.4 + - + +
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Residues in contact with ILE 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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8A THR* 3.0 33.5 + - - +
9A GLU* 3.7 9.6 - - + +
11A CYS* 1.3 75.1 - - - +
13A GLU* 1.3 64.3 + - - +
15A LEU* 3.3 10.8 + - + +
16A ILE* 3.3 36.0 + - + +
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Residues in contact with GLU 13 (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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9A GLU 3.0 17.8 + - - +
10A ARG* 3.5 11.1 - - - +
12A ILE* 1.3 81.5 - - - +
14A SER* 1.3 58.2 + - - +
16A ILE* 3.3 12.4 + - + +
17A ALA* 2.9 27.9 + - + +
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Residues in contact with SER 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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10A ARG* 2.9 38.3 + - - +
11A CYS* 3.7 10.5 - - - -
13A GLU* 1.3 69.1 - - - +
15A LEU* 1.3 59.3 + - - +
17A ALA* 3.1 6.8 + - - -
18A ILE* 2.7 54.2 + - - +
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Residues in contact with LEU 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 CYS* 2.9 24.6 + - + +
12A ILE* 3.7 9.2 - - + +
13A GLU 3.2 0.4 - - - -
14A SER* 1.3 78.7 - - - +
16A ILE* 1.3 57.6 + - - +
18A ILE* 3.7 14.0 - - + +
19A PHE* 2.9 30.5 + - - +
75A PHE* 3.8 6.8 - - + -
78A PHE* 4.0 7.8 - - + -
79A LEU* 3.8 29.6 - - + -
82A ILE* 4.2 34.1 - - + -
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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
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12A ILE* 3.3 27.5 + - + +
13A GLU* 3.5 11.7 - - + +
14A SER 3.2 0.4 - - - -
15A LEU* 1.3 78.0 - - - +
17A ALA* 1.3 63.6 + - - +
19A PHE* 3.4 0.7 + - - +
20A GLN* 3.1 37.0 + - + +
75A PHE* 3.8 27.8 - - + -
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Residues in contact with ALA 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 GLU* 2.9 16.8 + - + +
14A SER* 3.1 10.7 + - - +
16A ILE* 1.3 75.0 - - - +
18A ILE* 1.3 67.6 + - + +
20A GLN* 3.3 5.0 + - - +
21A LYS* 2.9 26.2 + - - +
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Residues in contact with ILE 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 SER* 2.7 40.9 + - - +
15A LEU* 3.7 14.8 - - + +
17A ALA* 1.3 74.1 - - + +
19A PHE* 1.3 65.2 + - - +
21A LYS* 3.7 4.0 - - - +
22A HIS* 3.0 38.2 + - + +
40A PHE* 3.8 29.8 - - + -
44A GLU* 4.6 16.6 - - + +
78A PHE* 3.9 10.3 - - + -
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Residues in contact with PHE 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 LEU 2.9 13.3 + - - +
16A ILE 3.7 2.2 - - - +
18A ILE* 1.3 79.8 - - - +
20A GLN* 1.3 80.1 + - - +
22A HIS* 3.6 1.0 - - - +
23A ALA* 2.6 54.5 + - + +
29A ASN 4.0 0.2 - - - -
30A THR* 3.6 23.8 - - - -
32A ILE* 3.5 32.0 - - + +
73A LEU 3.9 4.5 - - - -
74A ASP 3.7 7.9 - - - -
75A PHE* 3.4 59.0 - + + -
78A PHE* 3.7 23.1 - + + -
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Residues in contact with GLN 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* 3.1 28.4 + - + +
17A ALA* 3.9 5.4 - - - +
18A ILE 3.2 0.2 - - - -
19A PHE* 1.3 100.8 - - - +
21A LYS* 1.3 57.7 + - - +
23A ALA* 4.3 1.1 - - - +
24A GLY* 2.8 28.9 + - - -
29A ASN* 2.7 39.6 + - + +
30A THR* 4.5 4.0 - - - +
75A PHE* 5.2 1.4 - - - -
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Residues in contact with LYS 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 ALA 2.9 17.7 + - - +
18A ILE* 3.7 5.8 - - - +
20A GLN* 1.3 77.6 - - - +
22A HIS* 1.3 86.4 + - + +
24A GLY* 3.7 4.2 + - - -
25A ARG* 3.4 30.1 + - - +
44A GLU* 4.7 8.9 + - - -
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Residues in contact with HIS 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 ILE* 3.0 30.9 + - + +
19A PHE 4.0 1.6 - - - +
21A LYS* 1.3 100.3 + - + +
23A ALA* 1.4 65.6 + - - +
24A GLY 3.5 0.2 + - - -
25A ARG* 3.5 32.2 + - - +
32A ILE* 4.2 17.0 - - + -
36A GLU* 3.2 30.2 - - - +
39A ILE* 4.7 0.4 - - + -
40A PHE* 3.7 36.0 - + + -
43A THR* 4.0 10.0 + - - -
44A GLU* 3.7 31.6 - - + +
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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 PHE* 2.6 36.9 + - + +
20A GLN* 4.2 1.6 - - - +
22A HIS* 1.4 76.3 - - - +
24A GLY* 1.3 56.0 + - - +
25A ARG 3.3 0.4 + - - -
26A ASP* 3.8 0.7 - - - +
28A ASN 3.3 5.7 - - - +
29A ASN* 3.5 22.2 - - - +
31A LYS 3.5 19.7 - - - +
32A ILE* 3.8 9.1 - - + +
36A GLU* 3.2 2.5 - - - +
101A CA 2.5 24.2 - - - -
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Residues in contact with GLY 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 GLN 2.8 17.7 + - - -
21A LYS 3.7 3.1 + - - -
22A HIS 3.3 1.0 - - - -
23A ALA* 1.3 74.6 - - - +
25A ARG* 1.3 64.1 + - - +
26A ASP 3.5 8.0 - - - +
29A ASN* 3.8 17.2 - - - +
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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