Contacts of the helix formed by residues 15 - 30 (chain A) in PDB entry 3ZHP
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 1.4 66.5 + - - +
17A ILE* 3.5 8.4 - - - +
18A VAL* 3.6 34.2 - - - +
19A LYS* 3.7 8.5 + - - +
68A GLN* 5.7 8.4 - - + +
69A LEU* 4.6 15.6 - - - +
72A GLU* 4.6 11.8 - - + +
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA* 1.4 79.5 - - - +
17A ILE* 1.3 67.6 + - + +
18A VAL 3.6 0.2 + - - -
19A LYS* 3.7 13.8 + - - +
20A ILE* 3.4 17.6 - - + +
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Residues in contact with ILE 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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15A ALA 3.5 5.6 - - - +
16A GLU* 1.3 80.3 - - + +
18A VAL* 1.4 65.3 + - + +
20A ILE* 3.2 16.2 + - + +
21A LEU* 3.1 20.4 + - - +
45A SER* 3.4 42.3 + - - +
48A ALA* 4.5 14.6 - - + -
49A MET* 3.9 16.4 - - + -
52A ILE* 3.9 27.6 - - + -
69A LEU* 5.7 1.6 - - + -
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Residues in contact with VAL 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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15A ALA* 3.6 22.7 - - - +
16A GLU 3.4 0.4 - - - -
17A ILE* 1.4 75.8 - - - +
19A LYS* 1.4 56.6 + - - +
21A LEU* 3.4 2.8 + - - +
22A LYS* 2.9 53.5 + - + +
49A MET* 3.9 22.2 - - + -
69A LEU* 4.2 9.4 - - + +
72A GLU* 3.8 43.5 - - + +
73A LEU* 5.1 2.9 - - + +
76A SER* 4.3 3.6 - - - +
78A LEU* 4.3 9.1 - - + +
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Residues in contact with LYS 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 ALA 3.7 6.3 + - - +
16A GLU* 3.7 12.3 + - - +
17A ILE 3.3 0.4 - - - -
18A VAL* 1.4 76.5 - - - +
20A ILE* 1.4 63.3 + - + +
22A LYS* 3.8 10.1 + - - +
23A ASP* 3.6 20.8 + - - +
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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 GLU* 3.4 21.8 - - + +
17A ILE* 3.2 16.7 + - + +
19A LYS* 1.4 73.4 - - + +
21A LEU* 1.4 58.9 + - - +
22A LYS 3.5 0.2 + - - -
23A ASP* 3.5 4.4 + - - +
24A ASN* 3.1 51.0 + - - +
41A GLU* 5.1 5.2 - - + -
45A SER* 4.2 13.9 - - - +
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Residues in contact with LEU 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 ILE 3.1 16.0 + - - +
18A VAL* 3.8 4.3 - - - +
20A ILE* 1.4 73.7 - - - +
22A LYS* 1.4 66.0 + - - +
24A ASN* 4.6 3.4 - - - -
25A LEU* 3.1 45.6 + - + +
42A VAL* 3.6 46.7 - - + +
45A SER* 3.8 12.5 + - - -
46A LEU* 4.0 17.7 - - + -
49A MET* 3.8 28.5 - - + -
78A LEU* 3.8 17.9 - - + -
82A LEU* 4.7 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 VAL* 2.9 32.4 + - + +
19A LYS* 3.9 9.2 - - - +
20A ILE 3.4 0.2 - - - -
21A LEU* 1.4 76.9 - - - +
23A ASP* 1.4 61.5 + - - +
25A LEU* 3.7 3.1 + - - +
26A ALA* 3.6 17.8 + - - +
76A SER* 3.7 28.0 - - - +
78A LEU* 3.7 26.1 - - + +
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Residues in contact with ASP 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 LYS 3.6 12.7 + - - +
20A ILE* 3.5 4.6 + - - +
21A LEU 3.4 0.2 - - - -
22A LYS* 1.4 75.8 - - - +
24A ASN* 1.4 65.1 + - - +
26A ALA* 3.3 16.9 + - - +
27A ILE* 3.3 24.0 + - + +
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Residues in contact with ASN 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* 3.1 37.3 + - - +
21A LEU* 4.1 2.5 - - - +
22A LYS 3.5 0.2 - - - -
23A ASP* 1.4 74.0 - - - +
25A LEU* 1.4 60.0 + - - +
27A ILE* 3.3 18.7 + - - +
28A LEU* 3.0 25.6 + - - +
38A ALA* 3.4 29.4 - - - +
41A GLU* 3.5 26.0 - - + +
42A VAL* 3.7 18.7 - - + +
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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 LEU* 3.1 35.6 + - + +
22A LYS 4.0 4.5 - - - +
23A ASP 3.3 0.2 - - - -
24A ASN* 1.4 74.3 - - - +
26A ALA* 1.4 54.2 + - - +
28A LEU* 3.3 10.6 + - + +
29A GLU* 2.8 38.1 + - - +
42A VAL* 4.2 23.1 - - + -
78A LEU* 3.8 24.0 - - + -
81A THR* 4.7 10.1 - - - +
82A LEU* 4.0 17.0 - - + -
85A ASP* 4.7 19.9 - - + +
89A ILE* 4.5 19.7 - - + -
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Residues in contact with ALA 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 3.6 10.4 + - - +
23A ASP* 3.3 13.1 + - - +
25A LEU* 1.4 76.3 - - - +
27A ILE* 1.4 62.4 + - + +
29A GLU* 3.4 22.2 - - - +
30A LYS* 3.8 5.9 + - - +
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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 ASP* 3.3 21.5 + - + +
24A ASN* 3.5 23.1 - - - +
25A LEU 3.3 0.4 - - - -
26A ALA* 1.4 77.0 - - + +
28A LEU* 1.4 60.6 + - - +
30A LYS* 3.4 23.0 + - - +
32A ASP* 5.6 1.0 - - - +
34A LYS* 5.1 6.5 - - + +
35A THR* 4.1 13.0 - - - +
38A ALA* 4.2 16.2 - - + -
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Residues in contact with LEU 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 ASN 3.0 9.2 + - - +
25A LEU* 3.3 15.7 + - + +
27A ILE* 1.4 74.9 - - - +
29A GLU* 1.4 61.6 + - - +
30A LYS 3.2 9.8 - - - +
35A THR* 4.0 20.7 - - - +
38A ALA* 4.1 2.5 - - + -
39A SER* 3.5 41.7 - - - +
42A VAL* 3.8 25.4 - - + -
85A ASP* 6.5 0.4 - - + -
88A LEU* 3.5 49.9 - - + +
89A ILE* 5.8 3.4 - - + -
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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 LEU 2.8 19.0 + - - +
26A ALA* 3.4 17.5 - - - +
27A ILE 3.3 0.8 - - - -
28A LEU* 1.4 75.1 - - - +
30A LYS* 1.4 60.8 + - - +
31A GLN* 3.7 2.3 + - - -
85A ASP* 3.4 32.5 - - - +
88A LEU* 4.2 12.6 - - - +
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Residues in contact with LYS 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 ALA 3.8 5.0 + - - +
27A ILE* 3.4 19.3 + - - +
28A LEU 3.2 12.5 - - - +
29A GLU* 1.4 77.6 - - - +
31A GLN* 1.3 57.6 + - - +
32A ASP* 3.0 25.8 + - + +
35A THR* 4.2 2.8 - - - -
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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