Contacts of the helix formed by residues 24 - 37 (chain A) in PDB entry 3ZYQ
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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.5 28.7 + - - +
15A ALA* 4.2 16.4 + - - -
20A LEU* 4.1 23.0 - - + +
22A GLU 3.3 3.0 + - - -
23A THR* 1.3 72.1 - - - +
25A TRP* 1.3 61.2 + - - +
26A GLU* 3.5 9.7 + - - +
27A SER* 2.7 35.2 + - - -
28A ILE* 3.1 23.2 + - - +
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Residues in contact with TRP 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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22A GLU* 6.1 0.9 - - - -
23A THR* 3.2 40.3 + - + +
24A ASP* 1.3 72.2 - - - +
26A GLU* 1.3 65.5 + - - +
28A ILE* 4.4 14.6 - - + -
29A LEU* 2.9 48.6 + - + +
66A GLU* 5.7 4.7 - - + -
69A GLU* 6.1 4.0 - - - -
70A SER* 3.4 26.5 - - - -
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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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14A LYS* 6.1 2.2 - - - +
24A ASP* 3.2 7.9 + - - +
25A TRP* 1.3 78.8 - - - +
27A SER* 1.3 62.5 + - - +
29A LEU* 4.0 3.2 - - - +
30A GLN* 3.1 50.4 + - - +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 31.9 - - - +
14A LYS* 3.6 19.9 + - - +
15A ALA* 4.2 4.7 - - - -
24A ASP* 2.7 32.3 + - - -
26A GLU* 1.3 75.9 - - - +
28A ILE* 1.3 66.4 + - - +
30A GLN* 3.3 10.2 + - - +
31A ILE* 3.0 27.5 + - - +
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Residues in contact with ILE 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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15A ALA* 4.3 8.5 - - + +
23A THR* 3.5 31.6 - - + -
24A ASP 3.1 13.7 + - - +
25A TRP* 3.9 15.9 - - + +
27A SER* 1.3 74.8 - - - +
29A LEU* 1.3 61.0 + - + +
31A ILE* 3.2 10.7 + - - +
32A CYS* 2.9 28.4 + - - -
63A TYR 5.3 0.4 - - - +
66A GLU* 4.4 6.7 - - + +
67A VAL* 4.0 41.1 - - + +
70A SER* 3.3 33.2 - - - +
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Residues in contact with LEU 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 TRP* 2.9 41.4 + - + +
26A GLU* 4.2 3.6 - - - +
28A ILE* 1.3 80.5 - - + +
30A GLN* 1.3 57.5 + - + +
32A CYS* 3.3 10.8 + - + +
33A ASP* 3.0 38.5 + - - +
70A SER* 5.6 0.2 - - - -
74A ASN* 3.9 23.3 - - - +
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Residues in contact with GLN 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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7A THR* 5.1 3.6 - - - +
10A ARG* 5.0 5.3 - - - +
11A LEU* 3.7 35.0 - - + +
26A GLU* 3.1 44.4 + - - +
27A SER* 3.7 5.5 + - - +
29A LEU* 1.3 75.0 - - + +
31A ILE* 1.3 64.2 + - - +
33A ASP* 3.3 10.0 + - - +
34A LEU* 3.0 27.8 + - + +
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Residues in contact with ILE 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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8A PHE* 3.8 28.3 - - + -
11A LEU* 3.8 19.7 - - + +
12A LEU* 3.8 34.8 - - + +
15A ALA* 4.6 4.3 - - + -
27A SER 3.0 21.6 + - - +
28A ILE* 3.2 8.9 + - - +
30A GLN* 1.3 75.6 - - - +
32A CYS* 1.3 62.8 + - - +
34A LEU* 3.2 10.1 + - - +
35A ILE* 3.2 25.0 + - + +
49A ILE* 5.1 0.7 - - + -
67A VAL* 4.4 18.4 - - + -
71A VAL* 3.9 22.9 - - + -
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Residues in contact with CYS 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 ILE* 2.9 19.6 + - - -
29A LEU* 3.6 13.9 - - + +
31A ILE* 1.3 76.9 - - - +
33A ASP* 1.3 60.6 + - - +
35A ILE 3.3 1.0 + - - -
36A ARG* 2.9 35.7 + - + +
70A SER* 3.6 37.5 - - - -
71A VAL* 3.9 11.4 - - - -
74A ASN* 3.7 21.5 - - + +
75A CYS* 3.5 15.9 - - - -
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Residues in contact with ASP 33 (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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29A LEU* 3.0 25.2 + - - +
30A GLN* 3.6 8.9 - - - +
31A ILE 3.2 0.2 - - - -
32A CYS* 1.3 78.6 - - - +
34A LEU* 1.3 58.4 + - + +
36A ARG* 3.0 30.1 + - - +
37A GLN* 2.8 52.3 + - - +
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Residues in contact with LEU 34 (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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7A THR* 4.4 9.6 - - + -
8A PHE* 4.0 25.1 - - + +
11A LEU* 3.8 24.5 - - + -
30A GLN* 3.0 19.7 + - + +
31A ILE* 3.2 9.2 + - - +
33A ASP* 1.3 77.9 - - + +
35A ILE* 1.3 59.9 + - - +
37A GLN* 3.6 7.6 + - - +
38A GLY 3.2 2.1 + - - -
39A ASP* 2.8 53.4 + - + +
40A THR* 3.3 21.3 + - - +
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Residues in contact with ILE 35 (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 PHE* 5.3 0.4 - - + -
31A ILE* 3.2 20.7 + - + +
32A CYS 3.8 4.7 - - - +
33A ASP 3.2 0.2 - - - -
34A LEU* 1.3 76.7 - - + +
36A ARG* 1.3 66.2 + - - +
38A GLY* 3.1 13.0 + - - -
40A THR* 3.7 21.6 - - + +
42A ALA* 4.3 6.7 - - + +
45A ALA* 3.6 31.6 - - + -
46A VAL* 5.7 0.2 - - + -
49A ILE* 5.4 0.2 - - + -
71A VAL* 3.9 31.0 - - + -
75A CYS* 4.0 9.6 - - + -
78A THR* 4.2 14.7 - - + +
79A VAL* 3.7 26.7 - - + -
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Residues in contact with ARG 36 (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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32A CYS* 2.9 18.4 + - - +
33A ASP* 3.0 36.9 + - - +
35A ILE* 1.3 76.8 - - - +
37A GLN* 1.3 72.8 + - - +
38A GLY 3.5 0.7 + - - -
74A ASN* 3.2 29.8 - - - +
75A CYS* 3.9 16.8 - - - +
156A ARG* 6.0 3.6 - - - +
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Residues in contact with GLN 37 (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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33A ASP* 2.8 41.8 + - - +
34A LEU* 4.2 6.1 - - - +
36A ARG* 1.3 86.1 + - - +
38A GLY* 1.3 59.9 + - - +
39A ASP* 2.7 38.5 + - - +
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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