Contacts of the helix formed by residues 9 - 30 (chain A) in PDB entry 2LOS
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A SER* 4.1 4.5 - - - +
7A VAL* 2.6 15.4 - - + +
8A VAL* 1.4 88.4 - - - +
10A LEU* 1.3 62.1 + - - +
11A HIS* 4.5 5.8 - - + +
12A TRP* 3.4 38.0 + - + +
13A PHE* 2.8 28.7 + - - +
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Residues in contact with LEU 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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4A THR* 5.8 11.9 - - + -
9A PRO* 1.3 70.3 - - - +
11A HIS* 1.3 61.9 + - - +
13A PHE* 2.5 43.5 + - + +
14A GLY* 2.9 3.3 + - - -
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Residues in contact with HIS 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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9A PRO* 3.5 5.7 - - + +
10A LEU* 1.3 75.5 - - - +
12A TRP* 1.3 69.1 + - + +
14A GLY* 2.7 15.7 + - - +
15A PHE* 3.0 39.7 + + - +
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Residues in contact with TRP 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 VAL* 4.5 12.1 - - + -
9A PRO* 3.4 37.9 + - + +
10A LEU 3.2 0.6 - - - -
11A HIS* 1.3 79.4 + - + +
13A PHE* 1.3 52.4 + - - +
15A PHE* 2.7 38.8 + + + +
16A GLY* 2.7 19.7 + - - -
48A ALA* 5.4 1.8 - - + -
49A GLY* 5.7 2.2 - - - -
52A ALA* 4.3 13.5 - - + -
53A TYR* 3.9 33.2 - + - -
65A PHE* 6.3 2.5 - + - -
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Residues in contact with PHE 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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4A THR 5.5 3.6 - - - -
5A SER* 5.3 8.1 - - - -
8A VAL* 4.0 28.4 - - + +
9A PRO 2.8 12.0 + - - +
10A LEU* 2.5 31.0 + - + +
12A TRP* 1.3 71.3 - - - +
14A GLY* 1.3 54.4 - - - +
16A GLY* 3.3 1.7 + - - +
17A TYR* 3.0 62.8 + + - +
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Residues in contact with GLY 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 LEU 2.9 6.4 + - - -
11A HIS* 2.7 15.6 + - - -
13A PHE* 1.3 73.3 - - - +
15A PHE* 1.3 56.4 + - - -
17A TYR* 3.7 5.5 - - - +
18A ALA* 3.0 32.2 + - - +
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Residues in contact with PHE 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 HIS* 3.0 40.9 + + - +
12A TRP* 2.7 34.8 + + + +
14A GLY* 1.3 72.9 - - - +
16A GLY* 1.3 50.1 + - - +
18A ALA* 4.3 2.8 - - - +
19A ALA* 2.6 40.1 + - - +
44A PHE* 6.2 4.0 - + - -
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Residues in contact with GLY 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 TRP* 2.7 19.9 + - - -
13A PHE* 3.8 2.2 - - - -
15A PHE* 1.3 72.9 - - - +
17A TYR* 1.3 54.5 + - - +
19A ALA* 3.6 5.9 - - - +
20A LEU* 2.7 40.7 + - - +
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Residues in contact with TYR 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 PHE* 3.0 49.6 + + - +
14A GLY* 3.7 7.2 - - - +
16A GLY* 1.3 77.4 - - - +
18A ALA* 1.3 58.3 + - - +
20A LEU* 3.0 8.8 + - - +
21A VAL* 3.0 35.0 + - + +
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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 GLY 3.0 15.0 + - - +
15A PHE* 4.3 3.1 - - - +
17A TYR* 1.3 79.4 - - - +
19A ALA* 1.3 58.4 + - - +
21A VAL* 3.3 9.3 + - - +
22A ALA* 3.0 30.3 + - - +
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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 PHE 2.6 24.9 + - - +
16A GLY* 3.6 7.4 - - - +
18A ALA* 1.3 77.7 - - - +
20A LEU* 1.3 51.2 + - - +
22A ALA* 4.2 3.5 - - - +
23A SER* 2.6 40.7 + - - +
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Residues in contact with LEU 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 GLY 2.7 18.5 + - - +
17A TYR* 3.3 7.9 - - - +
19A ALA* 1.3 76.6 - - - +
21A VAL* 1.3 59.8 + - + +
23A SER* 4.0 5.4 - - - -
24A GLY* 2.7 31.5 + - - -
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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 TYR* 3.0 23.7 + - + +
18A ALA* 3.3 10.5 + - - +
20A LEU* 1.3 77.4 - - + +
22A ALA* 1.3 59.0 - - - +
24A GLY* 4.2 0.2 - - - -
25A GLY* 2.8 26.9 + - - -
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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 ALA 3.0 16.4 + - - +
19A ALA* 4.2 3.6 - - - +
21A VAL* 1.3 75.9 - - + +
23A SER* 1.3 71.4 + - - +
25A GLY* 2.8 10.0 + - - -
26A ILE* 2.9 20.4 + - + +
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Residues in contact with SER 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 ALA 2.6 27.6 + - - -
20A LEU* 3.6 7.2 - - - -
22A ALA* 1.3 73.3 - - - +
24A GLY* 1.3 53.6 + - - +
26A ILE* 4.5 0.6 - - - +
27A ILE* 2.6 59.4 + - - +
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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 LEU* 2.7 18.3 + - - +
21A VAL 4.2 0.2 - - - -
23A SER* 1.3 74.7 + - - +
25A GLY* 1.3 54.4 + - - +
27A ILE* 3.3 11.0 - - - -
28A GLY* 2.7 31.1 + - - -
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Residues in contact with GLY 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 2.8 18.6 + - - -
22A ALA* 2.8 6.9 + - - -
24A GLY* 1.3 82.0 - - - +
26A ILE* 1.3 63.6 + - - -
29A TYR* 2.9 33.4 + - - -
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Residues in contact with ILE 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 ALA* 2.9 15.3 + - + +
23A SER* 5.8 0.2 - - - -
25A GLY* 1.3 67.3 - - - -
27A ILE* 1.3 57.1 + - - +
28A GLY 2.7 8.9 + - - -
29A TYR* 4.7 5.2 - - + +
30A VAL* 2.7 58.3 + - + +
34A SER* 4.5 13.7 - - - +
37A SER* 4.6 10.5 - - - +
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Residues in contact with ILE 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 SER* 2.6 48.0 + - - +
24A GLY* 3.3 9.2 - - - +
26A ILE* 1.3 75.6 - - - +
28A GLY* 1.3 55.5 + - - +
30A VAL* 4.8 0.9 - - - -
31A LYS* 2.6 52.0 - - - +
32A ALA* 4.6 10.1 - - + +
34A SER* 6.6 0.4 - - - -
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Residues in contact with GLY 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 GLY 2.7 23.9 + - - -
26A ILE 2.7 1.2 + - - -
27A ILE* 1.3 76.3 - - - +
29A TYR* 1.3 60.8 + - - +
30A VAL 3.0 0.7 - - - -
31A LYS* 2.6 33.0 + - - +
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Residues in contact with TYR 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 GLY* 2.9 28.6 + - - +
26A ILE* 4.2 5.2 - - + +
28A GLY* 1.3 71.7 - - - +
30A VAL* 1.3 65.8 + - + +
31A LYS* 4.7 5.2 - - - +
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Residues in contact with VAL 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 ILE* 2.7 45.1 + - + +
27A ILE* 4.8 0.7 - - - -
29A TYR* 1.3 78.1 - - + +
31A LYS* 1.3 67.9 + - - +
32A ALA* 3.0 28.9 + - - +
34A SER* 4.4 15.0 - - - +
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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