Contacts of the helix formed by residues 11 - 26 (chain A) in PDB entry 1HRZ
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 ALA 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A MET 3.9 1.4 + - - -
10A ASN* 1.3 70.8 - - - +
12A PHE* 1.3 61.4 + - - +
14A VAL* 3.4 24.3 - - - +
15A TRP* 3.6 19.9 + - + -
54A PHE* 5.3 2.2 - - + -
55A PHE* 4.7 22.9 - - + -
58A ALA* 5.3 11.7 - - + -
13C G 5.3 12.2 + - - +
14C T 6.5 0.9 - - - -
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Residues in contact with PHE 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 ASN* 2.6 9.8 + - + +
11A ALA* 1.3 72.1 - - - +
13A ILE* 1.3 77.2 + - + +
14A VAL 2.9 4.9 + - - -
15A TRP* 3.1 31.8 + + + +
16A SER* 3.5 6.0 + - - -
39A LEU* 4.9 15.0 - - + -
43A TRP* 3.5 37.0 - + - -
6B A 4.6 5.8 - + - -
11C T 3.6 28.0 - + + -
12C T 2.7 55.4 - + - +
13C G 4.0 20.7 + - - +
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Residues in contact with ILE 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 MET* 4.4 18.2 - - + -
10A ASN* 2.8 23.4 + - + +
12A PHE* 1.3 90.2 - - + +
14A VAL* 1.3 63.9 + - - +
16A SER* 3.0 19.8 + - - -
17A ARG* 3.3 19.7 + - - +
5B A 3.2 37.9 - - + +
6B A 3.4 52.0 - - + +
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Residues in contact with VAL 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 MET* 4.8 14.1 - - + +
10A ASN 2.9 19.5 + - - +
11A ALA* 3.4 19.1 - - - +
12A PHE 2.9 0.2 - - - -
13A ILE* 1.3 79.1 - - - +
15A TRP* 1.3 65.8 + - - +
17A ARG* 3.2 22.3 + - + +
18A ASP* 3.5 10.9 + - - +
54A PHE* 3.7 43.1 - - + -
58A ALA* 6.0 4.9 - - + -
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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* 3.6 19.3 - - + -
12A PHE* 3.1 25.9 + + + +
14A VAL* 1.3 80.6 - - - +
16A SER* 1.3 60.4 + - - +
18A ASP* 5.4 0.9 - - - -
19A GLN* 2.4 57.3 + - + +
39A LEU* 5.0 2.0 - - + -
43A TRP* 2.9 54.9 - + + -
46A LEU* 3.6 30.7 - - + +
50A GLU* 5.1 3.4 - - + +
51A LYS* 5.5 2.9 - - + +
54A PHE* 3.1 39.9 - + - -
55A PHE* 4.0 25.5 - + - -
12C T 6.0 0.2 - - - -
13C G 5.4 9.4 - - - -
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Residues in contact with SER 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 PHE* 3.5 6.4 + - - -
13A ILE* 3.0 22.1 + - - -
15A TRP* 1.3 76.6 - - - +
17A ARG* 1.3 85.2 + - - +
19A GLN* 4.7 0.2 - - - -
20A ARG* 2.8 51.6 + - - +
39A LEU* 5.3 12.1 - - - +
6B A 4.7 8.6 + - - -
7B A 4.2 3.5 + - - -
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Residues in contact with ARG 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 MET* 5.7 9.3 - - + +
13A ILE* 3.4 18.3 + - + +
14A VAL* 3.4 11.7 - - + +
16A SER* 1.3 96.1 + - - +
18A ASP* 1.3 71.5 + - - +
20A ARG* 3.5 7.7 - - - +
21A ARG* 3.5 16.8 + - - +
6B A 3.0 50.3 + - - -
7B A 2.5 40.3 + - - -
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Residues in contact with ASP 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 VAL* 3.6 18.3 - - - +
15A TRP* 3.2 2.3 + - - +
17A ARG* 1.3 80.6 - - - +
19A GLN* 1.3 71.8 + - - +
21A ARG* 2.8 25.2 + - - +
22A LYS* 3.5 2.9 + - - +
54A PHE* 5.0 14.1 - - + +
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Residues in contact with GLN 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* 2.4 55.6 + - + +
16A SER* 4.7 0.2 - - - -
18A ASP* 1.3 73.3 - - - +
20A ARG* 1.3 62.1 + - - +
22A LYS* 3.0 42.4 + - - +
23A MET* 3.5 3.5 + - - +
39A LEU* 3.6 27.4 - - + -
42A GLN* 3.5 23.0 + - - +
43A TRP* 5.0 2.8 - - + -
47A THR* 5.0 0.4 + - - -
50A GLU* 3.8 29.0 - - - +
54A PHE* 5.4 1.8 - - - -
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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 SER* 2.8 51.3 + - - +
17A ARG* 3.5 9.2 - - - +
19A GLN* 1.3 73.6 - - - +
21A ARG* 1.3 74.8 + - - +
22A LYS 2.9 0.7 + - - -
23A MET* 2.9 11.0 + - + +
24A ALA* 2.7 28.1 + - + +
35A ILE* 4.3 24.3 - - + +
39A LEU* 5.7 3.8 - - + +
7B A 3.5 42.7 + - - -
8B C 2.8 54.8 + - - -
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Residues in contact with ARG 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 ARG 3.5 11.4 + - - +
18A ASP* 2.8 17.3 + - - +
20A ARG* 1.3 88.0 - - - +
22A LYS* 1.3 61.0 + - - +
24A ALA* 4.3 11.6 - - - +
25A LEU* 3.0 52.1 + - + +
8B C 5.6 3.8 + - - -
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Residues in contact with LYS 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 ASP 3.5 2.9 + - - +
19A GLN* 3.0 31.5 + - - +
20A ARG 2.9 0.4 - - - -
21A ARG* 1.3 80.9 - - - +
23A MET* 1.3 84.5 + - - +
25A LEU* 3.1 20.4 + - + +
26A GLU* 3.3 28.2 + - - +
42A GLN* 5.7 4.9 - - - +
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Residues in contact with MET 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 GLN 3.5 2.1 + - - +
20A ARG* 2.9 14.8 + - + +
22A LYS* 1.3 93.4 - - - +
24A ALA* 1.3 59.3 + - - +
26A GLU* 5.6 0.4 - - - -
27A ASN* 2.7 59.8 + - + +
30A MET* 3.2 41.3 - - + -
35A ILE* 4.6 22.4 - - + -
38A GLN* 4.6 26.9 - - + +
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Residues in contact with ALA 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 ARG* 2.7 29.0 + - + +
21A ARG* 3.7 18.2 - - - +
23A MET* 1.3 72.7 - - - +
25A LEU* 1.3 59.4 + - - +
27A ASN 4.2 1.1 - - - -
28A PRO* 2.9 43.5 - - + +
8B C 5.4 10.3 - - - +
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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 ARG* 3.0 44.7 + - + +
22A LYS* 3.1 10.1 + - + +
24A ALA* 1.3 81.6 - - - +
26A GLU* 1.3 65.7 + - + +
28A PRO* 3.3 9.9 - - - +
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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 LYS* 3.3 26.4 + - - +
23A MET* 5.6 0.4 - - - -
25A LEU* 1.3 85.7 - - + +
27A ASN* 1.3 76.0 + - - +
28A PRO* 3.3 4.4 - - - +
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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