Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 1Z6T
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 LYS 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP 4.6 1.8 - - - +
20A ILE* 1.3 72.8 - - - +
22A THR* 1.3 63.9 + - - +
23A SER* 3.5 3.4 - - - +
24A TYR 4.8 0.9 + - - -
25A ILE* 3.6 21.0 + - - +
49A GLN* 3.6 36.1 - - + +
80A TYR* 2.9 19.6 + - - +
397A THR* 4.4 3.0 + - - -
408A THR* 4.3 6.8 - - - +
412A GLU* 2.3 44.9 + - - +
431A LYS* 3.1 26.8 + - - +
433A PHE* 3.6 40.4 - - + +
478A GLU* 5.8 2.4 + - - -
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Residues in contact with THR 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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20A ILE* 4.0 5.6 + - + +
21A LYS* 1.3 74.2 - - - +
23A SER* 1.3 67.7 + - - +
24A TYR 3.5 0.4 - - - -
25A ILE* 3.3 7.4 + - - +
26A MET* 2.9 41.2 + - - +
43A VAL* 4.0 3.7 - - + +
49A GLN 5.1 0.8 + - - +
52A ARG* 3.5 32.9 + - - +
53A ALA* 3.7 34.3 - - + +
56A LEU* 3.8 20.4 - - + -
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Residues in contact with SER 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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21A LYS* 3.5 2.2 - - - +
22A THR* 1.3 82.9 + - - +
24A TYR* 1.3 82.0 + - - +
26A MET* 3.2 13.6 + - - +
27A ASP* 3.1 28.2 + - - +
44A ARG* 6.6 0.2 - - - -
52A ARG* 5.9 3.4 - - - -
412A GLU* 6.0 1.0 - - - +
413A ASP* 5.5 6.7 - - - -
416A GLN* 3.6 18.8 - - - -
433A PHE* 4.2 8.5 - - - -
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Residues in contact with TYR 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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21A LYS 4.8 1.2 + - - -
22A THR 3.5 0.2 - - - -
23A SER* 1.3 100.0 + - - +
25A ILE* 1.3 66.1 + - - +
27A ASP* 3.3 19.1 + - + +
28A HIS* 3.2 29.6 + + + +
78A GLU* 3.4 23.8 - - + +
412A GLU* 5.2 0.8 + - + -
416A GLN* 3.2 34.0 + - + +
419A VAL* 3.9 20.5 - - + +
420A ASN* 5.8 0.2 - - - -
426A CYS* 3.6 25.3 - - + +
428A ARG* 3.5 34.8 - - + +
433A PHE* 3.5 35.8 - + + -
435A TYR* 4.3 5.6 + - - -
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Residues in contact with ILE 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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20A ILE* 3.9 16.8 - - + -
21A LYS 3.6 18.3 + - - +
22A THR* 3.3 9.2 + - - +
24A TYR* 1.3 79.4 - - - +
26A MET* 1.3 62.0 + - - +
28A HIS* 3.3 5.3 + - - +
29A MET* 3.2 23.5 + - - +
56A LEU* 4.1 11.7 - - + -
71A PHE* 3.8 27.8 - - + -
74A ALA* 3.7 19.9 - - + +
75A LEU* 3.6 28.7 - - + -
78A GLU* 4.2 16.7 - - + +
80A TYR* 4.0 11.4 - - + -
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Residues in contact with MET 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 THR* 2.9 34.0 + - - +
23A SER* 3.2 8.9 + - - +
25A ILE* 1.3 70.5 - - - +
27A ASP* 1.3 61.9 + - - +
29A MET* 4.4 2.2 - - - -
30A ILE* 2.8 43.5 + - + +
35A LEU* 3.7 22.2 - - + -
40A GLU* 3.7 34.5 - - + +
43A VAL* 3.6 43.5 - - + -
44A ARG* 4.8 8.5 - - + +
52A ARG* 6.2 0.4 - - - -
56A LEU* 4.0 18.8 - - + -
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Residues in contact with ASP 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 SER 3.1 16.7 + - - +
24A TYR* 3.3 24.6 + - + +
26A MET* 1.3 76.4 - - - +
28A HIS* 1.3 65.6 + - + +
30A ILE* 3.6 9.8 + - - +
31A SER* 3.1 22.9 + - - -
40A GLU* 4.5 11.1 - - - +
416A GLN* 3.4 19.8 + - - +
420A ASN* 5.4 6.0 + - - +
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Residues in contact with HIS 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 TYR* 3.2 16.5 + - + -
25A ILE 3.5 5.2 - - - +
26A MET 3.2 0.4 - - - -
27A ASP* 1.3 80.0 - - + +
29A MET* 1.3 59.5 + - - +
31A SER* 3.2 6.6 + - - -
32A ASP* 2.9 40.6 + - - +
70A SER* 4.8 0.4 - - - +
74A ALA* 3.8 26.2 - - + +
77A HIS* 3.1 37.0 + + - -
78A GLU* 2.3 42.8 + - + -
428A ARG* 4.2 7.9 - - - -
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Residues in contact with MET 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 ILE* 3.2 20.9 + - - +
26A MET* 3.8 2.9 - - - +
28A HIS* 1.3 72.7 - - - +
30A ILE* 1.3 64.6 + - - +
32A ASP* 3.5 2.1 + - - +
33A GLY 3.2 3.1 + - - -
34A PHE* 3.1 36.2 + - + +
35A LEU* 3.5 20.1 + - + -
56A LEU* 5.0 7.2 - - - -
60A ILE* 3.7 23.1 - - + -
63A LYS* 5.8 0.2 - - + -
67A SER* 3.6 33.0 - - - +
70A SER* 3.6 21.1 - - - +
71A PHE* 3.7 37.5 - - + +
74A ALA* 4.4 2.2 - - + -
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Residues in contact with ILE 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 MET* 2.8 30.9 + - + +
27A ASP* 3.7 11.0 - - - +
29A MET* 1.3 72.6 - - - +
31A SER* 1.3 59.4 + - - +
33A GLY* 3.0 19.4 + - - -
35A LEU* 3.6 31.6 - - + +
36A THR 4.5 4.0 - - - +
37A ILE* 4.3 20.4 - - + -
40A GLU* 3.2 39.3 - - + +
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Residues in contact with SER 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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27A ASP 3.1 13.7 + - - -
28A HIS* 3.2 10.9 + - - -
30A ILE* 1.3 77.8 - - - +
32A ASP* 1.3 65.1 + - - +
33A GLY* 3.1 1.3 + - - -
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Residues in contact with ASP 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 HIS* 2.9 20.1 + - - +
29A MET 3.8 1.8 - - - +
30A ILE 3.2 0.4 - - - -
31A SER* 1.3 80.7 + - - +
33A GLY* 1.3 61.2 + - - +
34A PHE* 3.3 28.2 - - + -
70A SER* 2.8 37.7 + - - +
73A ASN* 5.2 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