Contacts of the helix formed by residues 9 - 23 (chain A) in PDB entry 2HZA
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 ASP 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 1.3 76.2 - - - +
10A ASP* 1.3 66.5 + - - +
11A ASP* 3.9 9.5 - - + +
12A LEU* 3.1 33.0 + - - +
13A LEU* 3.1 19.8 + - - +
1B MSE 3.1 31.1 - - + +
33B ARG* 4.4 1.6 - - - -
37B ARG* 3.4 25.7 + - - -
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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
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9A ASP* 1.3 72.0 - - - +
11A ASP* 1.3 65.0 + - - +
13A LEU* 3.2 8.6 + - - +
14A GLU* 3.0 24.2 + - - +
1B MSE 3.6 26.6 + - - +
2B GLN* 4.2 11.5 + - - +
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Residues in contact with ASP 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 ASP* 3.4 9.9 + - + +
10A ASP* 1.3 78.4 - - - +
12A LEU* 1.3 63.4 + - - +
14A GLU* 3.2 7.2 + - - +
15A THR* 3.1 25.3 + - - -
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Residues in contact with LEU 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 LEU* 3.5 32.8 - - + -
9A ASP* 3.1 31.7 + - - +
11A ASP* 1.3 79.1 - - - +
13A LEU* 1.3 56.7 + - - +
15A THR* 3.1 9.3 + - + -
16A LEU* 2.9 27.2 + - + +
33B ARG* 4.3 13.2 - - + +
36B LEU* 4.8 6.3 - - + -
37B ARG* 3.9 36.8 - - - +
40B LEU* 4.0 21.8 - - + -
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Residues in contact with LEU 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 LEU* 4.1 19.0 - - + +
9A ASP 3.1 12.5 + - - +
10A ASP* 3.8 8.7 - - - +
12A LEU* 1.3 73.7 - - - +
14A GLU* 1.3 61.8 + - - +
16A LEU* 3.6 11.8 - - + +
17A ASP* 2.9 39.9 + - - +
28A ARG* 3.8 37.0 - - - +
2B GLN* 3.5 44.2 - - + +
4B VAL* 4.0 21.1 - - + -
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Residues in contact with GLU 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 3.0 13.8 + - - +
11A ASP* 3.5 10.3 - - - +
13A LEU* 1.3 77.3 - - - +
15A THR* 1.3 58.4 + - - +
17A ASP* 3.2 8.2 + - - +
18A SER* 2.8 31.6 + - - -
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Residues in contact with THR 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 ASP 3.1 13.9 + - - -
12A LEU* 3.1 11.8 + - + -
14A GLU* 1.3 74.0 - - - +
16A LEU* 1.3 66.7 + - - +
17A ASP 3.1 0.2 + - - -
18A SER* 3.2 4.1 + - - -
19A LEU* 2.9 43.8 + - + +
40B LEU* 3.4 25.6 - - + +
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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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8A LEU* 4.6 6.7 - - + -
12A LEU* 2.9 14.6 + - + +
13A LEU* 3.6 19.5 - - + +
15A THR* 1.3 75.7 - - - +
17A ASP* 1.3 57.8 + - - +
19A LEU* 4.2 0.2 - - - +
20A SER* 2.6 49.8 + - - +
28A ARG* 4.3 19.3 - - + -
31A ALA* 4.3 13.2 - - + -
32A ILE* 3.7 35.4 - - + -
35A ILE* 4.5 9.4 - - + -
36B LEU* 4.8 7.0 - - + -
40B LEU* 3.5 28.2 - - + +
201B 3CM 5.0 1.1 - - + -
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Residues in contact with ASP 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 LEU* 2.9 23.5 + - - +
14A GLU* 3.4 8.9 - - - +
16A LEU* 1.3 76.5 - - - +
18A SER* 1.3 63.4 + - - +
20A SER* 3.2 5.6 + - - -
21A GLN* 3.0 24.9 + - - +
28A ARG* 3.0 51.8 + - - +
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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 GLU 2.8 19.2 + - - -
15A THR* 3.9 4.0 - - - -
17A ASP* 1.3 73.1 - - - +
19A LEU* 1.3 67.8 + - - +
21A GLN* 3.3 7.4 + - - +
22A ARG* 3.2 22.3 + - - +
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Residues in contact with LEU 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 THR* 2.9 42.9 + - + +
16A LEU 4.2 0.7 - - - +
18A SER* 1.3 76.6 - - - +
20A SER* 1.3 62.9 + - - +
22A ARG* 3.4 7.5 + - + +
23A ARG* 3.2 28.3 + - + +
40B LEU* 3.7 35.4 - - + +
43B GLU* 4.5 29.6 - - + +
201B 3CM 3.8 15.5 - - + -
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Residues in contact with SER 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* 2.6 30.3 + - - +
17A ASP* 3.4 6.1 - - - -
19A LEU* 1.3 77.7 - - - +
21A GLN* 1.3 60.6 + - - +
23A ARG* 3.2 4.3 + - - +
24A GLY 3.2 4.5 + - - -
25A TYR* 2.8 41.7 + - - +
27A ASN 5.6 3.1 - - - -
28A ARG* 5.7 1.6 - - - -
31A ALA* 3.5 14.4 - - - +
201B 3CM 3.5 23.9 - - - +
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Residues in contact with GLN 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 ASP 3.0 15.9 + - - +
18A SER* 3.9 6.9 - - - +
20A SER* 1.3 74.4 - - - +
22A ARG* 1.3 68.3 + - - +
24A GLY* 3.1 12.0 + - - -
25A TYR 3.8 11.2 + - - +
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Residues in contact with ARG 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 3.2 10.7 + - - +
19A LEU* 3.7 12.1 - - + +
21A GLN* 1.3 79.4 - - - +
23A ARG* 1.3 62.0 + - + +
24A GLY 3.3 3.5 + - - -
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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 LEU 3.2 17.8 + - - +
20A SER 3.8 3.4 - - - +
21A GLN 3.1 0.8 - - - -
22A ARG* 1.3 80.4 - - + +
24A GLY* 1.3 60.1 + - - +
25A TYR* 3.4 23.0 + - + -
43B GLU* 3.1 39.9 + - - +
201B 3CM 3.6 52.1 + - + +
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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