Contacts of the helix formed by residues 10 - 27 (chain A) in PDB entry 2HDZ
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 ARG 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 4.0 2.2 + - - +
9A LYS* 1.3 76.1 - - - +
11A ALA* 1.3 66.0 + - - +
12A GLU* 3.1 42.6 + - - +
13A GLU* 3.2 30.9 + - + +
14A ILE* 3.2 10.7 + - - +
16A GLN* 5.3 4.2 + - - +
57A ALA* 4.0 2.7 - - - -
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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 ARG* 1.3 72.5 - - - +
12A GLU* 1.3 63.3 + - - +
14A ILE* 3.3 6.3 + - - +
15A TRP* 3.0 19.2 + - - +
42A TRP* 3.8 17.3 - - + -
53A TRP* 3.5 39.8 - - - +
54A ILE* 3.7 16.6 - - + +
57A ALA* 3.5 9.6 - - + +
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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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10A ARG* 3.2 33.7 + - - +
11A ALA* 1.3 78.4 - - - +
13A GLU* 1.3 58.6 + - - +
15A TRP* 3.4 2.3 + - - +
16A GLN* 2.8 57.8 + - + +
39A GLU* 4.6 13.2 - - - +
42A TRP* 3.5 58.8 + - + +
43A ASN* 5.2 1.4 - - - +
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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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8A PRO 4.9 1.0 - - - +
9A LYS* 3.5 28.4 - - + +
10A ARG* 3.2 37.8 + - + +
12A GLU* 1.3 77.9 - - - +
14A ILE* 1.3 59.8 + - - +
16A GLN* 3.3 16.4 + - - +
17A GLN* 3.0 51.8 + - + +
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Residues in contact with ILE 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 LYS* 3.7 30.5 - - + +
10A ARG 3.2 10.7 + - - +
11A ALA* 3.3 6.0 + - - +
13A GLU* 1.3 71.2 - - - +
15A TRP* 1.3 64.9 + - - +
17A GLN* 3.3 12.7 + - + +
18A SER* 3.3 19.8 + - - -
53A TRP* 3.7 21.3 - - + +
56A LYS* 3.6 22.7 - - + +
57A ALA* 3.5 36.8 - - + +
60A ASP* 4.6 5.4 - - + -
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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 8.0 + - - +
12A GLU 3.7 2.5 - - - +
14A ILE* 1.3 77.0 - - - +
16A GLN* 1.3 83.8 + - + +
18A SER* 2.5 27.5 + - - -
19A VAL* 3.3 36.4 + - + +
23A TYR* 4.0 8.5 - - - -
38A MET* 3.5 41.3 - - + -
41A THR* 3.7 29.6 - - + -
42A TRP* 3.5 43.5 - + + -
45A MET* 3.8 15.3 - - + +
53A TRP* 3.4 42.5 - + + -
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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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10A ARG* 5.3 3.5 + - - +
12A GLU* 2.8 51.0 + - + +
13A GLU* 3.3 17.2 + - - +
15A TRP* 1.3 84.8 - - + +
17A GLN* 1.3 58.4 + - + +
19A VAL* 3.1 1.7 + - - +
20A ILE* 2.8 36.0 + - + +
35A LEU* 5.2 11.1 + - - +
38A MET* 3.5 33.7 - - + +
39A GLU* 5.3 4.2 - - - +
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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 LYS* 3.3 43.8 + - - +
13A GLU* 3.0 34.1 + - + +
14A ILE* 3.6 10.8 - - - +
15A TRP 3.2 0.2 - - - -
16A GLN* 1.3 76.3 - - + +
18A SER* 1.3 62.1 + - - +
19A VAL 3.4 0.5 + - - -
20A ILE* 3.6 18.9 + - + +
21A GLY 5.2 0.5 + - - -
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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 ILE 3.3 4.9 + - - -
15A TRP* 2.5 21.6 + - - -
17A GLN* 1.3 78.2 - - - +
19A VAL* 1.3 69.3 + - - +
22A ASP* 5.1 3.8 - - - +
53A TRP* 3.5 33.1 - - - -
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Residues in contact with VAL 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* 3.6 38.1 - - + +
16A GLN* 3.1 8.9 + - - +
18A SER* 1.3 94.1 - - - +
20A ILE* 1.3 67.4 + - - +
21A GLY 3.3 2.7 - - - -
22A ASP* 3.0 23.6 + - + +
23A TYR* 3.1 40.7 + - + -
38A MET* 3.9 11.4 - - + -
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Residues in contact with ILE 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* 2.8 24.6 + - + +
17A GLN* 3.6 17.7 - - - +
18A SER 3.9 0.2 - - - -
19A VAL* 1.3 72.0 - - - +
21A GLY* 1.3 65.5 + - - +
23A TYR 3.2 1.2 + - - -
24A LEU* 2.9 54.0 + - + +
34A ALA* 4.6 3.6 - - + -
35A LEU* 4.5 13.7 - - + -
38A MET* 3.5 29.8 - - + -
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Residues in contact with GLY 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 5.2 0.4 + - - -
18A SER 5.6 0.2 - - - -
19A VAL 3.3 1.2 + - - -
20A ILE* 1.3 82.7 - - - +
22A ASP* 1.3 57.6 + - - +
24A LEU* 3.8 8.2 - - - +
25A ALA* 3.0 29.5 + - - +
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Residues in contact with ASP 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 5.1 3.0 - - - +
19A VAL* 3.0 18.9 + - + +
21A GLY* 1.3 74.8 - - - +
23A TYR* 1.3 64.4 + - + +
25A ALA* 3.4 6.0 + - - +
26A ARG* 2.9 42.2 + - + +
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Residues in contact with TYR 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* 4.0 4.8 - + - -
19A VAL* 3.1 52.5 + - + -
20A ILE 3.9 4.9 - - - +
22A ASP* 1.3 78.4 - - + +
24A LEU* 1.3 58.6 + - - +
26A ARG* 4.2 32.1 + - - -
27A PHE* 2.8 44.9 + + - +
34A ALA* 3.9 10.3 - - + +
37A ALA* 3.8 30.3 - - + -
38A MET* 3.5 34.3 - - + -
41A THR* 3.3 31.6 + - - +
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Residues in contact with LEU 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 ILE* 2.9 42.9 + - + +
21A GLY* 3.8 7.0 - - - +
23A TYR* 1.3 77.7 - - - +
25A ALA* 1.3 55.4 + - - +
27A PHE* 3.5 0.6 + - - +
28A LYS* 3.1 6.9 + - - -
29A ASN* 2.7 55.2 + - + +
31A ARG* 3.8 34.3 - - + +
34A ALA* 3.7 21.3 - - + -
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Residues in contact with ALA 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 GLY 3.0 18.5 + - - +
22A ASP* 3.7 7.2 - - - +
24A LEU* 1.3 72.2 - - - +
26A ARG* 1.3 66.4 + - - +
28A LYS* 3.6 12.0 + - - +
29A ASN* 4.8 3.8 + - - +
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Residues in contact with ARG 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 ASP* 2.9 31.2 + - + +
23A TYR* 3.4 39.6 + - - +
25A ALA* 1.3 79.2 - - - +
27A PHE* 1.3 83.1 + - + +
28A LYS* 3.1 14.1 + - - +
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Residues in contact with PHE 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 TYR* 2.8 43.8 + + - +
24A LEU 5.2 0.2 - - - -
26A ARG* 1.3 88.8 - - + +
28A LYS* 1.3 72.7 + - - +
29A ASN 3.1 2.5 - - - -
30A ASP* 2.9 33.2 + - + +
33A LYS* 3.5 42.1 - - + +
34A ALA* 3.8 12.6 - - + -
37A ALA* 3.5 30.5 - - + -
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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