Contacts of the helix formed by residues 10 - 26 (chain A) in PDB entry 1QRV
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 SER 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PRO 3.9 2.2 + - - -
9A LEU* 1.3 77.9 - - - +
11A ALA* 1.3 64.7 + - - +
12A TYR* 3.6 7.9 + - - +
13A MET* 3.2 28.7 + - - +
14A LEU* 3.0 21.8 + - - +
56A ALA* 3.9 3.4 - - - -
6C A 4.8 2.6 + - - -
7C T 3.9 40.2 + - - -
8C C 5.2 9.2 - - - -
15D T 5.9 0.2 + - - -
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Residues in contact with ALA 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 SER* 1.3 74.7 - - - +
12A TYR* 1.3 58.1 + - - +
14A LEU* 3.4 3.6 + - - +
15A TRP* 3.0 28.9 + - - +
43A TRP* 3.7 19.1 - - + -
52A TRP* 3.6 28.9 - - - +
53A GLU* 4.0 14.1 - - + +
56A ALA* 3.5 17.3 - - + +
7C T 5.8 1.1 - - - +
8C C 5.6 1.0 + - - -
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Residues in contact with TYR 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 SER* 3.2 6.1 + - - +
11A ALA* 1.3 80.6 - - - +
13A MET* 1.3 88.0 + - + +
15A TRP* 3.3 12.6 + + - +
16A LEU* 2.9 42.5 + - + +
36A ALA 3.9 1.4 + - - -
39A GLY 3.8 10.4 - - - -
40A GLY 3.9 5.9 + - - -
43A TRP* 3.3 53.5 - + + -
5C T 2.8 31.3 + - + -
6C A 3.0 51.8 - + - +
7C T 4.3 4.0 + - - +
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Residues in contact with MET 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 LEU* 4.0 22.9 - - + -
10A SER* 3.2 20.5 + - - +
12A TYR* 1.3 99.6 - - + +
14A LEU* 1.3 66.3 + - - +
16A LEU* 4.4 5.2 - - + +
17A ASN* 2.9 33.1 + - - +
5C T 4.2 0.7 - - - +
6C A 3.4 31.2 - - + +
15D T 3.7 17.3 - - - +
16D A 3.8 53.8 - - + +
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Residues in contact with LEU 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 LEU* 3.8 31.0 - - + +
10A SER 3.0 17.3 + - - +
11A ALA 3.7 3.6 - - - +
13A MET* 1.3 76.8 - - - +
15A TRP* 1.3 64.1 + - - +
17A ASN* 3.9 4.3 - - + +
18A SER* 3.1 23.7 + - - -
52A TRP* 3.9 16.4 - - + +
55A LYS* 3.6 17.3 - - + +
56A ALA* 3.6 37.7 - - + +
59A ALA* 4.6 7.2 - - + -
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Residues in contact with TRP 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 ALA 3.0 17.2 + - - +
12A TYR* 3.6 13.9 - + - +
14A LEU* 1.3 79.5 - - - +
16A LEU* 1.3 75.5 + - + +
18A SER* 2.7 22.6 + - - -
19A ALA* 2.9 35.2 + - + +
23A ILE* 4.1 10.8 - - + -
39A GLY* 3.4 31.9 - - - -
42A LEU* 3.4 36.3 - - + -
43A TRP* 3.6 31.0 - + + -
46A MET* 3.5 15.9 - - + +
52A TRP* 3.4 38.5 - + + -
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Residues in contact with LEU 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 TYR* 2.9 48.4 + - + +
13A MET* 3.9 8.1 - - + +
14A LEU 3.3 0.2 - - - -
15A TRP* 1.3 82.8 - - + +
17A ASN* 1.3 62.3 + - - +
19A ALA* 3.0 0.8 + - - +
20A ARG* 2.7 59.1 + - - +
23A ILE* 4.1 23.8 - - + -
35A VAL* 4.3 19.7 - - + +
36A ALA* 5.1 5.4 - - - -
39A GLY* 4.7 1.3 - - - -
5C T 3.9 11.0 - - - +
16D A 4.0 10.8 - - + +
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Residues in contact with ASN 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 LEU* 3.3 26.0 - - - +
13A MET* 2.9 29.0 + - - +
14A LEU* 3.9 4.5 - - + +
16A LEU* 1.3 77.9 - - - +
18A SER* 1.3 60.2 + - - +
20A ARG* 3.8 24.4 + - - +
21A GLU* 5.0 2.3 + - - +
16D A 3.1 42.8 + - - +
17D T 5.0 0.8 - - - -
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Residues in contact with SER 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 LEU 3.1 13.1 + - - -
15A TRP* 2.7 18.4 + - - -
16A LEU 3.1 0.2 - - - -
17A ASN* 1.3 78.7 - - - +
19A ALA* 1.3 60.8 + - - +
21A GLU* 5.1 3.2 + - - +
22A SER* 5.2 3.5 + - - -
52A TRP* 3.3 28.6 - - - -
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Residues in contact with ALA 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 TRP* 2.9 48.4 + - + +
16A LEU 4.0 1.3 - - - +
18A SER* 1.3 80.3 - - - +
20A ARG* 1.3 64.4 + - - +
21A GLU 3.4 1.3 - - - -
22A SER* 2.9 12.4 + - - -
23A ILE* 2.9 30.5 + - + +
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Residues in contact with ARG 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 LEU* 2.7 44.9 + - + +
17A ASN* 3.9 15.1 - - - +
18A SER 3.6 0.8 - - - -
19A ALA* 1.3 69.9 - - - +
21A GLU* 1.3 72.2 + - + +
23A ILE* 3.1 7.9 + - - +
24A LYS* 2.8 47.0 + - + +
32A VAL* 4.6 7.3 + - - +
35A VAL* 3.3 29.6 - - + +
36A ALA* 5.9 0.6 - - - +
16D A 3.4 27.1 + - - -
17D T 3.2 60.6 + - - -
18D C 4.8 1.8 + - - -
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Residues in contact with GLU 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 ASN 5.0 3.2 + - - +
18A SER 5.1 2.4 + - - +
19A ALA 3.4 0.6 - - - -
20A ARG* 1.3 92.7 - - + +
22A SER* 1.3 61.3 + - - +
24A LYS* 3.6 32.3 + - - +
25A ARG* 3.1 45.0 + - - +
18D C 5.0 2.4 + - - -
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Residues in contact with SER 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 SER 5.2 2.8 + - - -
19A ALA* 2.9 18.6 + - - -
21A GLU* 1.3 76.1 - - - +
23A ILE* 1.3 67.2 + - - +
25A ARG* 3.1 22.6 + - - +
26A GLU* 3.0 41.9 + - - +
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Residues in contact with ILE 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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15A TRP* 4.1 25.6 - - + -
16A LEU* 4.1 15.5 - - + -
19A ALA* 2.9 26.3 + - + +
20A ARG* 3.5 7.0 - - - +
22A SER* 1.3 78.4 + - - +
24A LYS* 1.3 61.9 + - - +
26A GLU* 3.3 5.5 + - - -
27A ASN* 2.5 42.4 + - - +
30A ILE* 4.1 12.8 - - + -
35A VAL* 4.2 13.0 - - + +
38A ARG* 3.9 18.6 - - + -
39A GLY* 4.6 6.1 - - - -
42A LEU* 4.3 16.4 - - + -
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Residues in contact with LYS 24 (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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20A ARG* 2.8 33.4 + - + +
21A GLU* 3.6 31.6 + - - +
22A SER 3.1 0.2 - - - -
23A ILE* 1.3 77.5 - - - +
25A ARG* 1.3 59.5 + - - +
27A ASN 3.0 22.0 - - - +
28A PRO* 3.6 5.0 - - - +
29A GLY 4.6 0.9 + - - -
30A ILE* 3.6 26.9 - - + +
32A VAL* 6.6 0.2 - - + -
35A VAL* 4.0 13.0 - - + -
18D C 3.4 23.9 + - - +
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Residues in contact with ARG 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 GLU* 3.1 27.4 + - - +
22A SER* 3.2 40.0 - - - +
24A LYS* 1.3 76.0 - - - +
26A GLU* 1.3 62.5 + - + +
27A ASN 3.2 1.9 + - - -
28A PRO* 4.1 13.4 - - - +
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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 SER* 3.0 33.1 + - - +
23A ILE* 3.7 3.0 - - - +
24A LYS 3.2 0.2 - - - -
25A ARG* 1.3 80.6 - - + +
27A ASN* 1.3 76.8 + - - +
28A PRO* 3.9 5.1 - - - +
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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