Contacts of the helix formed by residues 10 - 29 (chain A) in PDB entry 2QIB
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 GLY 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A MSE 1.3 77.4 - - - +
11A VAL* 1.3 55.2 + - - -
12A GLU 3.5 2.9 - - - -
13A GLU* 3.4 12.1 + - - +
14A ARG* 2.8 33.3 + - - +
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Residues in contact with VAL 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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10A GLY* 1.3 71.0 - - - -
12A GLU* 1.3 71.5 + - + +
14A ARG 3.3 1.2 + - - -
15A ARG* 2.9 31.7 + - - +
52A HIS* 5.7 6.5 - - + +
53A TYR* 3.3 34.5 - - + +
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Residues in contact with GLU 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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11A VAL* 1.3 80.1 - - + +
13A GLU* 1.3 64.9 - - - +
15A ARG* 2.0 48.6 + - - +
16A GLN* 3.0 34.7 + - + +
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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 MSE 3.3 34.7 - - + +
10A GLY* 3.4 15.4 + - - +
12A GLU* 1.3 78.5 - - - +
14A ARG* 1.3 56.8 + - - +
16A GLN* 3.3 5.5 + - - +
17A GLN* 2.8 29.5 + - + +
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Residues in contact with ARG 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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9A MSE 3.5 47.8 + - + +
10A GLY 2.8 15.9 + - - +
11A VAL 3.6 0.4 - - - +
13A GLU* 1.3 77.2 - - - +
15A ARG* 1.3 62.8 + - - +
17A GLN* 2.9 30.6 + - - +
18A LEU* 2.9 26.2 + - + +
43A ALA 3.4 8.5 + - - -
44A GLY 5.0 1.8 + - - -
45A ILE* 3.3 38.3 - - - +
49A LEU* 4.9 6.9 - - + +
53A TYR* 3.3 41.7 - - + +
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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 VAL* 2.9 24.0 + - - +
12A GLU* 2.0 54.1 + - - +
13A GLU 3.3 0.2 - - - -
14A ARG* 1.3 76.5 - - - +
16A GLN* 1.3 70.9 + - - +
18A LEU* 3.3 5.1 + - - +
19A ILE* 3.0 37.0 + - + +
53A TYR* 3.8 32.4 + - + -
54A PHE* 4.0 21.7 - - + -
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Residues in contact with GLN 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 GLU* 3.0 24.5 + - + +
13A GLU* 3.9 4.0 - - - +
15A ARG* 1.3 89.3 - - - +
17A GLN* 1.3 64.1 + - - +
19A ILE* 3.4 21.7 + - - +
20A GLY* 3.0 10.0 + - - -
67A ARG* 2.9 47.6 + - - +
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Residues in contact with GLN 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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9A MSE 4.0 18.2 - - + +
13A GLU* 2.8 22.4 + - + +
14A ARG* 2.9 41.4 + - - +
16A GLN* 1.3 71.9 - - - +
18A LEU* 1.3 58.9 + - - +
20A GLY* 3.1 3.2 + - - -
21A VAL* 2.9 34.4 + - + +
42A ALA 4.9 0.5 - - - +
43A ALA* 3.1 38.5 - - - +
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Residues in contact with LEU 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 ARG* 2.9 17.0 + - + +
15A ARG 3.5 4.7 - - - +
17A GLN* 1.3 74.6 - - - +
19A ILE* 1.3 60.4 + - - +
21A VAL* 3.3 4.0 + - - +
22A ALA* 2.9 30.1 + - - +
39A ILE* 3.9 23.6 - - + +
43A ALA* 3.5 28.7 - - + -
45A ILE* 3.7 22.2 - - + -
50A VAL* 4.1 15.7 - - + +
53A TYR* 3.7 41.7 - - + -
54A PHE* 4.3 10.5 - - + -
60A LEU* 4.1 4.3 - - + +
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Residues in contact with ILE 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* 3.0 18.1 + - + +
16A GLN* 3.7 30.3 - - - +
17A GLN 3.3 0.4 - - - -
18A LEU* 1.3 74.2 - - - +
20A GLY* 1.3 52.7 + - - +
22A ALA* 3.4 2.1 + - - +
23A LEU* 2.8 32.9 + - - +
54A PHE* 3.5 26.5 - - + -
60A LEU* 4.2 6.3 - - + -
63A ALA* 3.6 39.0 - - + +
64A ALA* 3.9 4.7 - - - +
67A ARG* 3.7 28.9 - - + +
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Residues in contact with GLY 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 GLN 3.0 12.0 + - - -
17A GLN* 3.1 3.8 + - - -
19A ILE* 1.3 74.4 - - - +
21A VAL* 1.3 59.3 + - - +
23A LEU* 3.3 5.0 + - - +
24A ASP* 2.9 28.9 + - - +
67A ARG* 3.3 22.1 - - - +
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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 GLN* 2.9 28.7 + - + +
18A LEU* 3.7 5.8 - - - +
20A GLY* 1.3 74.2 - - - +
22A ALA* 1.3 65.4 + - - +
24A ASP* 3.2 9.0 + - - +
25A LEU* 3.0 25.0 + - + +
39A ILE* 3.6 24.7 - - + +
42A ALA* 3.5 33.0 - - + +
43A ALA* 4.1 21.5 - - + +
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Residues in contact with ALA 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 LEU 2.9 17.0 + - - +
19A ILE 3.5 4.7 - - - +
21A VAL* 1.3 77.9 - - - +
23A LEU* 1.3 57.8 + - - +
25A LEU* 3.3 1.6 + - - +
26A PHE* 2.8 49.9 + - + -
39A ILE* 4.2 12.3 - - + -
60A LEU* 3.6 33.0 - - + -
64A ALA* 4.3 4.9 - - + -
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Residues in contact with LEU 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 ILE 2.8 22.1 + - - +
20A GLY* 3.6 7.0 - - - +
22A ALA* 1.3 73.0 - - - +
24A ASP* 1.3 56.5 + - - +
26A PHE* 4.7 0.7 - - - -
27A SER* 2.7 51.0 + - - +
64A ALA* 3.7 28.4 - - + +
67A ARG* 3.9 26.9 - - + +
68A ALA* 4.0 18.2 - - + +
102A HIS* 4.2 12.3 - - + +
701A P6G 3.6 22.9 - - - +
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Residues in contact with ASP 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 GLY 2.9 15.0 + - - +
21A VAL* 3.2 12.1 + - - +
23A LEU* 1.3 78.4 - - - +
25A LEU* 1.3 70.6 + - - +
27A SER* 3.5 4.6 - - - -
28A ARG* 3.2 60.2 + - - +
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Residues in contact with LEU 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* 3.0 19.3 + - + +
22A ALA* 4.0 2.2 - - - +
24A ASP* 1.3 88.3 - - - +
26A PHE* 1.3 57.8 + - - +
28A ARG* 3.1 24.2 + - - +
29A ARG* 3.2 32.5 + - - +
34A VAL* 3.5 29.2 - - + +
38A GLU* 3.8 40.2 - - + +
39A ILE* 3.9 16.2 - - + -
42A ALA* 4.5 10.5 - - + -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 2.8 36.8 + - + +
23A LEU 4.2 0.2 - - - +
25A LEU* 1.3 70.8 - - - +
27A SER* 1.3 58.5 + - - +
29A ARG 3.4 9.8 - - - +
31A PRO* 3.9 23.9 - - + +
34A VAL* 3.6 30.5 - - + -
39A ILE* 4.1 18.6 - - + -
57A LYS* 4.1 21.1 - - + -
60A LEU* 4.5 1.1 - - + -
61A TYR* 3.6 51.2 - + + -
64A ALA* 4.4 1.1 - - + -
105A GLY* 3.1 23.4 - - - -
701A P6G 3.4 29.3 - - - +
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Residues in contact with SER 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 LEU* 2.7 30.1 + - - +
24A ASP* 3.5 7.8 - - - -
26A PHE* 1.3 79.8 - - - +
28A ARG* 1.3 58.6 + - - +
101A GLU 4.0 12.6 - - - -
102A HIS* 2.9 38.8 - - - +
104A PRO* 3.1 14.4 - - - +
105A GLY* 3.0 22.5 + - - +
701A P6G 4.1 2.0 - - - -
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Residues in contact with ARG 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 ASP* 3.2 47.0 + - - +
25A LEU* 3.1 18.2 + - - +
27A SER* 1.3 80.8 - - - +
29A ARG* 1.3 75.5 + - + +
104A PRO* 3.3 20.0 - - - +
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Residues in contact with ARG 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 LEU* 3.2 37.2 + - - +
26A PHE* 3.4 21.4 - - - +
27A SER 3.5 1.0 - - - -
28A ARG* 1.3 95.4 - - + +
30A SER* 1.3 72.7 + - - +
31A PRO* 3.6 1.6 - - - +
33A GLU* 2.8 39.1 + - + +
34A VAL* 4.0 12.5 - - + +
38A GLU* 2.9 34.4 + - - +
104A PRO* 4.1 9.4 - - - -
105A GLY* 4.3 1.4 - - - -
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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
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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