Contacts of the helix formed by residues 20 - 33 (chain A) in PDB entry 1Z83
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 GLY 20 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY 3.1 5.1 - - - -
19A SER* 1.3 79.3 - - - +
21A LYS* 1.3 65.7 + - - +
23A THR* 3.4 3.1 + - - -
24A GLN* 3.0 29.1 + - - +
118A VAL* 4.5 5.2 - - - -
631A AP5 3.2 38.4 + - - -
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Residues in contact with LYS 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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13A VAL* 3.7 37.6 - - + +
14A VAL 3.9 0.7 - - - -
15A GLY 3.1 35.6 + - - +
16A GLY 3.2 6.7 + - - -
19A SER* 3.7 9.8 - - - +
20A GLY* 1.3 76.1 - - - +
22A GLY* 1.3 57.3 + - - +
24A GLN* 3.8 3.5 - - - +
25A CYS* 2.9 33.6 + - - -
93A ASP* 3.5 25.4 - - - +
94A GLY* 4.2 11.2 - - - +
118A VAL* 4.5 8.9 - - + +
631A AP5 2.7 56.8 + - - +
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 1.3 74.1 - - - +
23A THR* 1.3 66.0 + - - +
25A CYS* 3.2 4.9 + - - +
26A GLU* 3.0 32.2 + - - +
36A HIS* 4.5 6.1 - - - -
93A ASP* 3.7 12.4 + - - -
601A ZN 4.5 3.4 - - - -
631A AP5 3.1 17.3 + - - -
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Residues in contact with THR 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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20A GLY 3.5 5.6 - - - -
22A GLY* 1.3 75.6 - - - +
24A GLN* 1.3 65.7 + - - +
26A GLU* 3.5 5.6 + - - +
27A LYS* 3.3 23.4 + - + +
179A VAL* 4.0 37.2 - - + -
631A AP5 2.8 52.7 + - + +
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Residues in contact with GLN 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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13A VAL* 6.2 1.6 - - + -
20A GLY* 3.0 21.8 + - - +
21A LYS* 3.9 3.6 - - - +
23A THR* 1.3 76.3 - - - +
25A CYS* 1.3 65.8 + - - +
27A LYS* 3.0 15.2 + - - +
28A ILE* 3.1 21.8 + - + +
116A LEU* 5.8 2.0 - - + -
118A VAL* 5.3 11.4 - - + -
179A VAL* 3.2 40.6 + - - +
182A VAL* 3.7 28.2 - - + +
183A PHE* 3.2 36.5 - - - +
186A VAL* 3.8 12.5 - - + +
631A AP5 5.5 3.0 + - - -
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Residues in contact with CYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 32.1 - - - -
21A LYS 2.9 28.3 + - - +
22A GLY 3.2 3.8 + - - +
24A GLN* 1.3 73.6 - - - +
26A GLU* 1.3 56.7 + - - +
28A ILE* 3.2 11.0 + - - +
29A VAL* 2.9 34.3 + - - +
36A HIS* 3.4 41.3 - - + +
91A LEU* 3.8 10.3 - - + +
93A ASP* 4.1 7.2 - - - -
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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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22A GLY* 3.0 20.8 + - - +
23A THR* 4.0 5.4 - - - +
24A GLN 3.2 0.2 - - - -
25A CYS* 1.3 75.3 - - - +
27A LYS* 1.3 62.9 + - + +
29A VAL* 3.5 14.5 + - - +
30A GLN* 3.1 41.3 + - - +
36A HIS* 3.1 8.2 + - - -
641A ZN 2.0 36.6 - - - -
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Residues in contact with LYS 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 THR* 3.3 17.3 - - + +
24A GLN* 3.0 11.6 + - - +
26A GLU* 1.3 76.7 - - + +
28A ILE* 1.3 59.4 + - - +
30A GLN* 3.3 22.0 + - - +
31A LYS* 3.0 23.2 + - - +
179A VAL* 3.8 25.8 - - + +
180A ASP* 3.7 18.5 + - - -
183A PHE* 3.4 50.1 - - + -
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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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11A ILE* 5.9 0.2 - - + -
24A GLN* 3.1 17.8 + - + +
25A CYS* 3.2 14.8 + - - +
27A LYS* 1.3 72.1 - - - +
29A VAL* 1.3 59.5 + - - +
32A TYR* 2.7 53.6 + - + +
33A GLY 3.7 0.3 + - - -
34A TYR* 4.7 6.1 - - + -
91A LEU* 3.7 33.7 - - + -
116A LEU* 4.0 16.6 - - + -
183A PHE* 3.9 10.1 - - + -
186A VAL* 3.7 32.1 - - + -
190A LEU* 4.1 12.6 - - + -
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Residues in contact with VAL 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 CYS 2.9 26.7 + - - +
26A GLU* 3.7 17.0 - - - +
28A ILE* 1.3 77.0 - - - +
30A GLN* 1.3 60.3 + - + +
33A GLY* 2.9 27.3 + - - -
34A TYR 3.7 26.7 - - - +
36A HIS* 3.6 28.9 - - + +
91A LEU* 3.8 7.0 - - + -
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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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26A GLU* 3.1 33.6 + - - +
27A LYS* 3.6 24.8 + - - +
28A ILE 3.2 0.2 - - - -
29A VAL* 1.3 81.5 - - + +
31A LYS* 1.3 60.5 + - + +
33A GLY 4.9 0.3 + - - -
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Residues in contact with LYS 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 LYS 3.0 15.8 + - - +
30A GLN* 1.3 80.0 - - - +
32A TYR* 1.3 91.4 + - + +
33A GLY 3.8 0.2 - - - -
183A PHE* 4.0 10.7 - - + -
187A CYS* 3.0 35.1 - - - +
191A ASP* 4.6 8.0 + - - -
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Residues in contact with TYR 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* 2.7 35.8 + - + +
31A LYS* 1.3 103.3 - - + +
33A GLY* 1.3 59.4 + - - +
34A TYR* 3.3 24.4 + - + -
88A LYS* 3.9 18.0 + - - -
183A PHE* 4.6 3.1 - + - -
187A CYS* 3.6 26.7 + - - -
190A LEU* 3.9 26.8 - - + +
191A ASP* 2.5 33.3 + - - -
194A LEU* 3.9 24.5 - - + -
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Residues in contact with GLY 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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28A ILE 3.7 0.2 + - - -
29A VAL* 2.9 18.2 + - - -
30A GLN 4.7 0.6 + - - -
31A LYS 3.8 1.2 - - - -
32A TYR* 1.3 76.4 - - - +
34A TYR* 1.3 67.2 + - - +
35A THR* 5.0 0.5 + - - -
88A LYS* 3.7 27.7 + - - +
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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