Contacts of the helix formed by residues 21 - 34 (chain C) in PDB entry 2ZZ0
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 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLY 3.2 6.7 + - - -
20C GLY* 1.3 78.7 - - - +
22C SER* 1.3 66.7 + - - +
23C GLY 3.4 2.0 - - - -
24C GLY* 3.6 1.1 - - - -
25C LEU* 2.8 30.0 + - - +
42C ASP* 4.1 0.2 + - - -
56C GLY 3.3 14.1 - - - -
57C GLY* 3.6 4.0 - - - -
160C ALA 4.8 0.2 + - - -
900C FAD 3.3 24.3 + - - -
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Residues in contact with SER 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY* 1.3 73.0 - - - +
23C GLY* 1.3 63.3 + - - +
25C LEU* 4.2 1.5 - - - +
26C ALA* 3.3 20.4 + - - +
56C GLY 3.7 6.2 + - - -
59C CYS* 4.0 10.7 - - - +
60C VAL* 5.7 1.2 - - - +
343C THR* 3.0 36.7 + - - +
346C ALA* 4.1 7.0 - - - -
347C ILE* 4.0 13.6 - - - +
900C FAD 3.2 23.7 + - - -
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C SER* 1.3 77.4 - - - +
24C GLY* 1.3 68.9 + - - +
26C ALA* 3.3 2.4 + - - +
27C ALA* 3.0 18.2 + - - +
332C ILE* 3.3 32.3 - - - +
346C ALA* 3.5 21.6 - - - +
900C FAD 3.1 9.3 + - - -
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Residues in contact with GLY 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 3.9 15.1 - - - +
19C GLY 3.2 25.4 - - - -
21C GLY 3.1 6.1 + - - -
23C GLY* 1.3 80.0 - - - +
25C LEU* 1.3 58.2 + - - +
27C ALA* 3.2 4.2 + - - +
28C ALA* 2.9 25.1 + - - +
158C LEU* 5.3 0.2 - - - -
160C ALA* 3.9 13.2 - - - +
332C ILE* 4.9 0.2 - - - -
900C FAD 4.0 0.8 + - - -
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLY* 3.5 31.9 - - - +
21C GLY 2.8 20.5 + - - +
22C SER* 4.4 1.6 - - - +
24C GLY* 1.3 68.0 - - - -
26C ALA* 1.3 59.2 + - - +
28C ALA* 3.6 2.8 - - - +
29C LYS* 3.0 48.7 + - + +
40C VAL* 4.0 10.1 - - + -
55C LEU* 4.3 6.3 - - + -
56C GLY* 4.2 9.4 - - - +
116C TYR* 3.5 41.5 - - + -
120C LEU* 4.0 31.2 - - + -
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C SER 3.3 19.0 + - - +
23C GLY 3.3 3.5 + - - +
24C GLY 3.2 0.8 - - - -
25C LEU* 1.3 75.7 - - - +
27C ALA* 1.3 66.2 + - - +
29C LYS* 3.9 8.3 - - - +
30C GLU* 3.0 24.3 + - - +
347C ILE* 3.4 42.4 - - + +
350C GLY* 4.6 2.9 - - - -
351C ARG* 4.5 8.5 - - + +
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 5.6 1.3 - - + -
17C ILE* 4.1 5.4 - - + -
23C GLY 3.0 13.0 + - - +
24C GLY 3.8 1.1 - - - +
26C ALA* 1.3 75.5 - - - +
28C ALA* 1.3 64.7 + - - +
30C GLU* 3.9 1.5 - - - +
31C ALA* 2.9 28.1 + - - +
158C LEU* 3.4 33.2 - - + -
350C GLY* 3.4 28.1 - - - +
353C LEU* 5.1 2.0 - - + -
354C ALA* 4.2 3.7 - - + +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 3.6 11.3 - - + +
24C GLY 2.9 11.1 + - - +
25C LEU* 3.6 12.6 - - - +
27C ALA* 1.3 77.7 - - - +
29C LYS* 1.3 61.3 + - - +
31C ALA* 3.5 2.1 + - - +
32C ALA* 3.2 22.2 + - - +
38C VAL* 4.5 5.6 - - - +
40C VAL* 3.3 32.8 - - + -
120C LEU* 4.2 12.3 - - + -
125C VAL* 4.1 9.2 - - + +
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Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.0 33.1 + - - +
26C ALA* 3.9 6.5 - - - +
28C ALA* 1.3 73.6 - - - +
30C GLU* 1.3 66.6 + - - +
32C ALA* 3.4 6.4 + - - +
33C GLN* 3.2 26.1 + - - +
116C TYR* 3.4 34.6 + - - -
119C ALA* 4.3 21.8 - - + +
120C LEU* 4.7 14.8 - - + -
123C LYS* 4.8 29.0 - - + +
125C VAL* 5.2 0.2 - - - -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA 3.0 16.4 + - - +
29C LYS* 1.3 76.4 - - - +
31C ALA* 1.3 62.9 + - - +
33C GLN* 3.2 19.9 + - - +
34C TYR* 3.0 42.3 + - + -
351C ARG* 3.5 46.6 + - + +
354C ALA* 3.8 13.0 - - + -
355C GLN* 3.3 22.7 + - + -
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 5.0 6.5 - - + -
27C ALA 2.9 18.6 + - - +
28C ALA* 3.9 3.4 - - - +
30C GLU* 1.3 78.9 - - - +
32C ALA* 1.3 62.9 + - - +
34C TYR* 3.1 16.9 + - - +
35C GLY 3.8 0.2 + - - -
36C LYS* 3.7 17.5 + - + +
38C VAL* 4.0 17.3 - - + -
354C ALA* 3.8 15.4 - - + +
358C TYR* 4.2 19.0 - - + -
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA 3.2 15.3 + - - +
29C LYS 3.9 4.5 - - - +
30C GLU 3.3 0.2 - - - -
31C ALA* 1.3 79.1 - - - +
33C GLN* 1.3 58.9 + - - +
35C GLY* 2.7 22.3 + - - -
36C LYS 3.9 15.2 + - - +
38C VAL* 4.4 3.0 - - + +
123C LYS* 3.5 31.9 - - + +
124C LYS 5.2 0.9 - - - +
125C VAL* 3.7 14.4 - - + -
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS 3.2 10.6 + - - +
30C GLU* 3.3 24.0 - - - +
31C ALA 3.1 1.0 - - - -
32C ALA* 1.3 80.1 - - - +
34C TYR* 1.3 65.8 + - + +
35C GLY 3.3 2.3 + - - -
123C LYS* 3.5 36.9 + - - +
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU* 3.0 49.6 + - + -
31C ALA* 3.1 10.0 + - - +
32C ALA 3.0 1.2 + - - -
33C GLN* 1.3 84.2 - - + +
35C GLY* 1.3 63.1 + - - +
36C LYS* 3.6 10.5 - - - +
354C ALA 4.9 0.7 - - - -
355C GLN* 3.4 27.7 - - + +
358C TYR* 3.6 36.1 - - + +
359C ALA* 3.5 20.5 - - + +
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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