Contacts of the helix formed by residues 20 - 33 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY 3.2 1.2 - - - -
19B SER* 1.3 79.4 - - - +
21B LYS* 1.3 65.6 + - - +
23B THR* 3.4 1.7 + - - -
24B GLN* 3.1 32.1 + - - +
118B VAL* 4.5 2.2 - - - -
632B AP5 3.1 41.6 + - - -
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.5 37.4 - - + +
14B VAL 3.8 1.1 - - - -
15B GLY 3.0 37.8 + - - +
16B GLY 3.1 6.3 + - - -
19B SER* 3.6 9.8 - - - +
20B GLY* 1.3 76.2 - - - +
22B GLY* 1.3 58.1 + - - +
24B GLN* 3.3 2.2 + - - +
25B CYS* 2.8 32.7 + - - +
93B ASP* 3.4 26.5 - - - +
94B GLY* 4.2 11.0 - - - +
118B VAL* 4.2 11.2 - - + +
632B AP5 2.7 54.2 + - - +
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 1.3 76.0 - - - +
23B THR* 1.3 61.9 + - - +
25B CYS* 3.2 4.4 + - - +
26B GLU* 3.0 32.2 + - - +
36B HIS* 4.4 6.7 - - - -
93B ASP* 3.7 13.4 + - - -
611B ZN 4.4 4.0 - - - -
632B AP5 3.0 19.0 + - - -
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Residues in contact with THR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY 3.7 5.2 - - - -
21B LYS 3.2 0.2 - - - -
22B GLY* 1.3 78.0 - - - +
24B GLN* 1.3 65.6 + - - +
26B GLU* 3.6 6.3 + - - +
27B LYS* 3.5 21.3 + - + +
179B VAL* 4.0 35.9 - - + -
632B AP5 2.8 48.9 + - + +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 6.3 1.1 - - + -
20B GLY* 3.1 19.6 + - - +
21B LYS* 3.8 3.4 - - - +
23B THR* 1.3 78.1 - - - +
25B CYS* 1.3 66.0 + - - +
27B LYS* 3.1 7.9 + - - +
28B ILE* 3.0 29.3 + - + +
116B LEU* 6.0 2.0 - - + -
118B VAL* 5.2 10.3 - - + -
179B VAL* 3.3 39.4 + - - +
182B VAL* 3.6 27.3 - - + +
183B PHE* 3.2 34.2 + - - +
186B VAL* 3.6 13.0 - - + +
632B AP5 5.4 2.8 + - - -
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Residues in contact with CYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 4.0 29.2 - - - -
21B LYS 2.8 25.4 + - - +
22B GLY 3.2 3.3 + - - +
24B GLN* 1.3 72.8 - - - +
26B GLU* 1.3 57.8 + - - +
28B ILE* 3.2 13.6 + - - +
29B VAL* 3.0 32.3 + - - +
36B HIS* 3.4 40.4 - - + +
91B LEU* 3.8 11.0 - - + +
93B ASP* 4.1 7.2 - - - -
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLY 3.0 14.9 + - - +
23B THR* 4.0 6.3 - - - +
24B GLN 3.3 0.2 - - - -
25B CYS* 1.3 75.5 - - - +
27B LYS* 1.3 58.1 + - + +
29B VAL* 3.3 14.8 + - - +
30B GLN* 3.0 47.9 + - - +
36B HIS* 3.0 8.4 + - - -
643B ZN 2.0 37.1 - - - -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B THR* 3.5 12.7 + - + +
24B GLN* 3.1 10.4 + - - +
26B GLU* 1.3 75.1 - - + +
28B ILE* 1.3 60.5 + - - +
30B GLN* 3.5 19.8 + - - +
31B LYS* 3.0 23.6 + - - +
179B VAL* 3.6 26.3 - - + +
180B ASP* 4.2 19.3 + - - -
183B PHE* 3.4 51.5 - - + -
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 6.2 0.2 - - + -
13B VAL* 5.7 0.2 - - + -
24B GLN* 3.0 22.8 + - + +
25B CYS* 3.2 16.6 + - - +
27B LYS* 1.3 74.1 - - - +
29B VAL* 1.3 55.9 + - - +
32B TYR* 2.7 47.3 + - + +
34B TYR* 4.6 6.3 - - + -
91B LEU* 3.7 36.1 - - + -
116B LEU* 4.3 13.7 - - + -
183B PHE* 3.8 7.9 - - + -
186B VAL* 3.8 31.4 - - + -
190B LEU* 3.8 21.8 - - + -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B CYS 3.0 20.9 + - - +
26B GLU* 3.3 17.7 + - - +
28B ILE* 1.3 74.3 - - - +
30B GLN* 1.3 62.0 - - + +
33B GLY* 2.9 28.5 + - - -
34B TYR 3.5 30.1 - - - +
36B HIS* 3.8 26.9 - - + +
91B LEU* 4.1 6.5 - - + -
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Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 3.0 34.5 + - - +
27B LYS* 3.7 24.3 + - - +
29B VAL* 1.3 82.2 - - + +
31B LYS* 1.3 60.3 + - - +
33B GLY 4.8 0.2 + - - -
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS 3.0 17.6 + - - +
30B GLN* 1.3 80.0 - - - +
32B TYR* 1.3 93.1 + - + +
33B GLY 3.7 0.2 - - - -
183B PHE* 4.0 11.3 - - + -
187B CYS* 3.0 35.3 - - - +
191B ASP* 4.6 7.2 + - - -
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 2.7 35.6 + - + +
31B LYS* 1.3 110.2 - - + +
33B GLY* 1.3 60.1 + - - +
34B TYR* 3.5 21.8 + - + -
88B LYS* 3.0 25.1 + - - -
183B PHE* 4.5 2.9 - + - -
187B CYS* 3.6 20.4 + - - -
190B LEU* 3.7 22.6 - - + +
191B ASP* 2.6 31.3 + - - -
194B LEU* 3.6 29.2 - - + -
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE 3.7 0.2 + - - -
29B VAL* 2.9 19.4 + - - -
30B GLN 4.8 0.4 + - - -
31B LYS 3.7 1.0 - - - -
32B TYR* 1.3 77.9 - - - +
34B TYR* 1.3 66.0 + - - +
35B THR* 5.1 0.2 + - - -
88B LYS* 3.6 28.8 + - - +
701B SO4 5.0 6.4 + - - -
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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