Contacts of the helix formed by residues 24 - 37 (chain A) in PDB entry 1Z2M
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 SER 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A SER* 4.2 10.1 + - - -
23A MET* 1.3 75.0 - - - +
25A VAL* 1.3 65.3 + - - +
26A SER* 3.7 8.9 + - - -
27A GLU* 3.1 33.2 + - - +
28A LEU 3.1 9.9 + - - -
56A ASP 6.2 0.4 - - - -
58A VAL 5.9 0.2 - - - -
59A PRO* 5.2 6.3 - - - -
60A LEU* 3.4 15.7 - - - +
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Residues in contact with VAL 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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24A SER* 1.3 74.5 - - - +
26A SER* 1.3 64.0 + - - +
28A LEU* 3.2 7.5 + - + +
29A LYS* 3.1 46.8 + - + +
45A LEU* 5.4 0.4 - - + -
54A LEU* 4.3 21.5 - - + -
55A GLN 3.1 29.2 - - - +
56A ASP* 4.1 23.3 + - + +
58A VAL 4.0 4.3 + - - +
60A LEU* 3.2 21.9 - - + +
63A GLN* 4.0 6.5 - - - +
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Residues in contact with SER 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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24A SER* 3.1 9.9 + - - -
25A VAL* 1.3 79.2 - - - +
27A GLU* 1.3 63.6 + - - +
29A LYS* 3.1 10.2 + - - +
30A ALA* 2.9 22.6 + - - +
56A ASP 5.8 0.2 + - - -
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Residues in contact with GLU 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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19A LEU* 3.3 26.3 - - + +
20A SER 3.9 3.6 + - - -
21A SER* 3.5 26.6 + - - -
22A SER* 3.0 29.1 + - - -
23A MET 3.1 10.5 + - - -
24A SER* 3.1 11.9 + - - +
26A SER* 1.3 77.9 - - - +
28A LEU* 1.3 63.5 + - - +
30A ALA* 3.1 9.6 + - - +
31A GLN* 3.1 29.0 + - + +
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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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5A LEU* 4.0 31.2 - - + -
7A VAL* 4.7 6.5 - - + -
17A VAL* 4.3 17.3 - - + -
19A LEU* 4.1 6.3 - - + +
24A SER 3.1 11.6 + - - +
25A VAL* 3.3 10.5 - - - +
26A SER 3.1 0.2 - - - -
27A GLU* 1.3 76.3 - - - +
29A LYS* 1.3 59.0 + - + +
31A GLN* 2.9 24.1 + - - +
32A ILE* 3.1 28.6 + - + +
45A LEU* 4.2 12.1 - - + -
54A LEU* 4.0 26.7 - - + -
60A LEU* 4.1 14.8 - - + -
65A LEU* 5.3 0.2 - - + -
71A VAL* 4.6 10.5 - - + -
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Residues in contact with LYS 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 VAL* 3.1 28.5 + - + +
26A SER* 3.1 8.7 + - - +
28A LEU* 1.3 80.4 - - - +
30A ALA* 1.3 56.5 + - - +
32A ILE* 3.1 1.1 + - - -
33A THR* 2.9 34.0 + - - -
40A ALA* 3.9 39.7 + - + +
41A PHE* 5.7 1.2 - - - +
43A GLN* 3.2 37.6 + - - +
45A LEU* 4.0 21.1 - - + -
56A ASP* 3.6 20.6 + - - -
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Residues in contact with ALA 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 SER 2.9 14.2 + - - +
27A GLU* 3.3 13.9 - - - +
28A LEU 3.1 0.2 - - - -
29A LYS* 1.3 76.7 - - - +
31A GLN* 1.3 63.8 + - - +
33A THR* 3.6 8.0 + - - -
34A GLN* 3.1 31.4 + - + +
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Residues in contact with GLN 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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17A VAL* 3.3 38.8 - - + +
18A SER* 3.7 20.8 + - - +
19A LEU* 4.5 2.7 - - + +
27A GLU* 3.2 20.2 + - - +
28A LEU* 2.9 9.1 + - - +
30A ALA* 1.3 83.6 + - - +
32A ILE* 1.3 65.6 + - - +
34A GLN* 3.0 17.9 + - - +
35A LYS* 2.9 23.2 + - - +
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Residues in contact with ILE 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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7A VAL* 3.6 39.7 - - + -
15A PHE* 4.0 7.6 - - + -
17A VAL* 4.6 1.3 - - + -
28A LEU* 3.1 23.7 + - + +
29A LYS* 3.4 2.0 - - - +
31A GLN* 1.3 76.1 - - - +
33A THR* 1.3 57.9 + - - +
35A LYS* 3.0 6.7 + - - +
36A ILE* 2.8 48.0 + - + +
38A VAL* 5.4 0.4 - - + +
43A GLN* 3.1 35.9 - - + +
45A LEU* 5.1 7.0 - - + -
73A LEU* 3.6 24.7 - - + -
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Residues in contact with THR 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 LYS 2.9 17.1 + - - -
30A ALA* 3.8 8.0 - - - -
32A ILE* 1.3 76.8 - - - +
34A GLN* 1.3 59.2 + - - +
37A GLY* 2.7 34.5 + - - -
38A VAL 2.6 33.9 + - - +
39A HIS* 4.7 8.7 - - + +
40A ALA* 3.8 8.4 + - - +
43A GLN* 3.1 4.7 + - - -
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Residues in contact with GLN 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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30A ALA* 3.1 24.2 + - + +
31A GLN* 3.0 25.4 + - - +
33A THR* 1.3 79.9 - - - +
35A LYS* 1.3 57.2 + - - +
37A GLY 4.7 0.3 + - - -
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Residues in contact with LYS 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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15A PHE* 3.6 55.7 - - + +
16A GLN 5.4 1.8 - - - +
17A VAL* 5.6 1.3 - - + -
31A GLN 2.9 10.9 + - - +
32A ILE 3.6 5.6 - - - +
34A GLN* 1.3 80.7 - - + +
36A ILE* 1.3 67.8 + - + +
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Residues in contact with ILE 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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9A MET* 4.8 12.3 - - + -
15A PHE* 4.4 11.0 - - + -
32A ILE* 2.8 40.2 + - + +
35A LYS* 1.3 90.1 - - + +
37A GLY* 1.3 62.5 + - - +
38A VAL* 3.3 28.4 + - + +
73A LEU* 4.0 15.5 - - + -
75A VAL* 4.3 8.7 - - + -
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Residues in contact with GLY 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 THR* 2.7 32.7 + - - -
34A GLN 4.5 0.2 - - - -
35A LYS 3.6 0.8 - - - -
36A ILE* 1.3 73.9 - - - +
38A VAL* 1.3 60.1 + - - +
39A HIS* 4.0 5.2 + - - -
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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