Contacts of the helix formed by residues 9 - 32 (chain A) in PDB entry 1B54
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 GLU 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A TYR* 4.3 11.1 - - - +
8A ASP* 1.3 75.3 - - - +
10A ASP* 1.3 65.7 + - - +
12A LYS* 3.4 28.4 + - - +
13A THR* 3.1 28.8 + - - +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP* 2.9 15.1 + - - +
9A GLU* 1.3 79.7 - - - +
11A ARG* 1.3 60.1 + - - +
13A THR* 3.7 6.4 + - - -
14A GLN* 3.2 23.1 + - - +
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 6.0 0.2 - - + -
8A ASP* 3.0 24.2 + - + +
9A GLU 3.3 0.2 - - - -
10A ASP* 1.3 75.3 - - - +
12A LYS* 1.3 59.8 + - - +
14A GLN* 3.6 34.2 + - - +
15A LEU* 2.8 55.4 + - - +
18A GLN* 4.3 1.2 - - - +
51A LYS* 5.2 0.8 - - - +
55A ASP* 2.8 35.4 + - - +
58A ILE* 3.7 16.6 - - + -
245A PHE* 3.1 35.3 + - - +
246A GLY 4.7 0.6 - - - -
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Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.9 28.9 - - + +
8A ASP 3.2 13.5 + - - +
9A GLU* 3.5 46.4 + - - +
10A ASP 3.3 0.2 - - - -
11A ARG* 1.3 77.7 - - - +
13A THR* 1.3 69.9 + - - +
15A LEU* 3.8 0.9 - - - +
16A ILE* 3.1 45.2 + - + +
58A ILE* 3.7 15.2 - - + +
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Residues in contact with THR 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 3.1 15.0 + - - -
10A ASP* 4.0 8.3 + - - -
12A LYS* 1.3 88.7 + - - +
14A GLN* 1.3 57.1 + - - +
16A ILE* 4.4 4.2 - - - +
17A ALA* 3.2 28.0 + - + +
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Residues in contact with GLN 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 ASP 3.2 14.7 + - - +
11A ARG* 3.6 28.8 + - - +
12A LYS 3.1 0.6 - - - -
13A THR* 1.3 79.3 - - - +
15A LEU* 1.3 64.0 + - - +
17A ALA* 3.7 4.0 - - - +
18A GLN* 2.9 56.3 + - - +
246A GLY 3.8 16.4 + - - -
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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 ARG* 2.8 41.8 + - - +
12A LYS 3.9 2.2 - - - +
14A GLN* 1.3 70.4 - - - +
16A ILE* 1.3 62.5 + - - +
18A GLN* 3.4 0.9 + - - +
19A TYR* 2.9 30.3 + - - +
55A ASP* 3.3 46.4 - - + +
58A ILE* 3.8 14.1 - - + -
59A LEU* 3.6 15.3 - - + -
244A ILE* 3.0 41.1 - - + +
245A PHE* 3.9 9.4 - - + -
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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 LYS* 3.1 39.8 + - + +
13A THR* 4.4 4.0 - - - +
15A LEU* 1.3 76.2 - - - +
17A ALA* 1.3 60.5 + - - +
19A TYR* 3.7 1.1 - - - +
20A GLU* 2.9 33.8 + - + +
58A ILE* 4.3 9.2 - - + +
59A LEU* 4.2 12.3 - - + -
62A HIS* 3.6 56.1 - - + +
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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 THR* 3.2 21.3 + - + +
14A GLN* 3.7 6.3 - - - +
15A LEU 3.2 0.6 - - - -
16A ILE* 1.3 82.0 - - - +
18A GLN* 1.3 60.9 + - + +
20A GLU* 3.9 4.4 - - - +
21A SER* 3.1 25.3 + - - -
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Residues in contact with GLN 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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11A ARG* 4.3 3.2 - - - +
14A GLN* 2.9 48.8 + - - +
15A LEU 3.9 0.4 - - - +
17A ALA* 1.3 76.4 - - + +
19A TYR* 1.3 60.7 + - - +
21A SER* 2.7 23.0 + - - +
22A VAL* 3.1 16.4 - - - +
243A ASP 4.0 12.2 + - - +
244A ILE* 3.1 25.9 + - - +
245A PHE 3.9 1.4 - - - -
246A GLY* 3.5 31.6 - - - +
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Residues in contact with TYR 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 19.7 + - - +
16A ILE 3.7 1.8 - - - +
18A GLN* 1.3 74.5 - - - +
20A GLU* 1.3 87.8 + - + +
22A VAL* 3.1 5.4 + - - +
23A ARG* 2.9 52.8 + - - +
44A LEU* 3.7 17.6 + - + +
46A VAL* 3.7 31.0 - - + -
59A LEU* 4.1 11.0 - - + -
62A HIS* 3.9 19.1 - + - -
64A VAL* 3.7 22.1 - - + +
244A ILE* 3.9 27.1 - - + +
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Residues in contact with GLU 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* 2.9 25.8 + - + +
17A ALA* 3.9 4.9 - - - +
19A TYR* 1.3 88.6 - - + +
21A SER* 1.3 57.0 + - - +
23A ARG* 3.1 36.7 + - - +
24A GLU* 2.8 45.6 + - + +
62A HIS* 2.5 34.3 + - + +
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Residues in contact with SER 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 3.1 12.9 + - - -
18A GLN* 2.7 28.1 + - - +
20A GLU* 1.3 76.9 - - - +
22A VAL* 1.3 62.0 + - - +
24A GLU* 3.6 8.1 + - - +
25A VAL* 3.2 28.6 + - - +
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Residues in contact with VAL 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 GLN 3.1 14.8 - - - +
19A TYR 3.1 7.5 + - - +
21A SER* 1.3 78.1 + - - +
23A ARG* 1.3 59.3 + - - +
25A VAL* 3.3 7.2 + - - +
26A VAL* 3.1 33.0 + - + +
44A LEU* 4.0 16.2 - - + -
227A PHE* 4.7 6.5 - - + -
240A ILE* 4.0 31.9 - - + -
243A ASP* 3.8 24.9 - - + +
244A ILE* 3.8 18.8 - - + -
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Residues in contact with ARG 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 TYR* 2.9 38.4 + - + +
20A GLU* 3.1 34.5 + - - +
22A VAL* 1.3 79.5 - - - +
24A GLU* 1.3 68.4 + - - +
26A VAL* 3.8 3.8 - - + +
27A ASN* 3.1 48.1 + - - +
44A LEU* 3.8 21.7 - - + +
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Residues in contact with GLU 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 GLU* 2.8 49.8 + - + +
21A SER* 3.8 9.0 - - - +
22A VAL 3.2 0.2 - - - -
23A ARG* 1.3 91.6 + - - +
25A VAL* 1.3 62.1 + - + +
27A ASN* 3.8 8.1 + - - +
28A ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 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 SER 3.2 15.0 - - - +
22A VAL* 3.3 9.5 + - - +
24A GLU* 1.3 75.0 - - + +
26A VAL* 1.3 60.8 + - - +
28A ALA* 3.8 5.7 - - + +
29A GLU* 2.9 36.2 + - + +
227A PHE* 3.9 13.2 - - + -
228A ARG* 3.7 38.1 - - - +
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Residues in contact with VAL 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 VAL* 3.1 23.8 + - + +
23A ARG* 3.8 7.0 - - + +
24A GLU 3.3 0.2 - - - -
25A VAL* 1.3 76.7 - - - +
27A ASN* 1.3 63.7 + - - +
30A ALA* 3.0 27.9 + - + +
42A ILE* 4.2 25.4 - - + +
44A LEU* 4.3 20.9 - - + -
227A PHE* 4.0 22.0 - - + -
231A ILE* 3.6 21.9 - - + +
238A VAL* 4.4 13.5 - - + -
240A ILE* 4.8 0.2 - - + -
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Residues in contact with ASN 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 ARG* 3.1 46.8 + - - +
24A GLU* 3.8 9.5 + - - +
26A VAL* 1.3 86.3 - - - +
28A ALA* 1.3 58.4 + - - +
30A ALA* 3.5 5.8 + - - +
31A LYS* 2.9 36.5 + - - +
41A LYS* 5.4 7.9 - - - +
42A ILE 5.1 6.6 + - - +
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Residues in contact with ALA 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 GLU 2.9 18.5 + - - +
25A VAL* 3.8 7.9 - - + +
27A ASN* 1.3 74.5 - - - +
29A GLU* 1.3 65.7 + - + +
31A LYS* 3.6 7.8 + - - +
32A ASN* 3.4 25.8 + - - +
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Residues in contact with GLU 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 VAL* 2.9 30.1 + - + +
26A VAL 3.7 2.2 - - - +
28A ALA* 1.3 77.6 - - + +
30A ALA* 1.3 62.4 + - - +
32A ASN* 3.1 21.4 + - - +
33A VAL* 3.5 10.6 - - - +
228A ARG* 3.0 37.8 + - + +
231A ILE* 3.6 22.2 - - + +
232A ARG* 3.0 45.3 + - - +
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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 VAL* 3.0 17.3 + - + +
27A ASN* 3.7 7.9 - - - +
29A GLU* 1.3 72.6 - - - +
31A LYS* 1.3 57.6 + - - +
32A ASN 2.9 10.4 + - - -
33A VAL* 3.1 21.5 + - - +
40A SER 4.6 11.0 - - - +
42A ILE* 3.8 28.5 - - + +
231A ILE* 3.6 8.0 - - - +
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Residues in contact with LYS 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 ASN* 2.9 22.8 + - - +
28A ALA* 3.9 7.6 - - - +
29A GLU 3.4 0.2 - - - -
30A ALA* 1.3 74.8 - - - +
32A ASN* 1.3 60.1 + - - +
33A VAL 3.3 7.2 + - - +
41A LYS* 5.5 6.9 - - - +
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Residues in contact with ASN 32 (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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28A ALA 3.4 13.1 + - - +
29A GLU* 3.1 17.0 + - - +
30A ALA 2.9 1.8 + - - -
31A LYS* 1.3 80.8 + - - +
33A VAL* 1.3 61.6 + - + +
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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