Contacts of the helix formed by residues 22 - 34 (chain C) in PDB entry 1PZY
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 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ASP* 3.9 11.0 - - - -
17C GLY* 4.4 0.4 - - - +
20C GLY 3.9 1.0 + - - -
21C ILE* 1.3 77.0 - - - +
23C LEU* 1.3 64.6 + - - +
24C LEU* 3.3 17.1 + - - +
25C GLU* 2.7 36.1 + - - +
26C TRP* 3.2 24.7 + - - -
115C LEU* 5.1 1.2 - - - +
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Residues in contact with LEU 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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9C SER* 3.3 36.8 + - - +
10C HIS* 6.3 0.2 - - + -
12C ILE* 3.4 47.3 - - + +
13C LYS* 4.2 16.4 - - + -
15C ILE* 4.6 6.1 - - + -
16C ASP* 3.8 29.3 + - + +
22C SER* 1.3 73.4 - - - +
24C LEU* 1.3 64.1 + - + +
26C TRP* 3.7 2.4 - - + +
27C ALA* 2.9 31.2 + - - +
118C TRP 5.3 0.2 - - - -
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Residues in contact with LEU 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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22C SER* 3.1 13.0 - - - +
23C LEU* 1.3 83.3 - - + +
25C GLU* 1.3 57.3 + - - +
28C CYS* 3.1 24.4 + - - +
115C LEU* 3.8 35.7 - - + +
116C GLU* 4.6 2.9 - - - +
118C TRP* 3.3 17.5 - - - +
119C ARG* 3.2 72.0 - - + +
120C CYS 4.8 0.9 - - - +
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Residues in contact with GLU 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 3.7 5.5 - - - +
21C ILE* 3.4 24.1 - - + +
22C SER* 2.7 36.7 + - - +
23C LEU 3.2 0.2 - - - -
24C LEU* 1.3 79.1 - - - +
26C TRP* 1.3 60.3 + - - +
28C CYS* 3.5 5.8 + - - +
29C VAL* 2.8 35.6 + - - +
107C TYR* 2.7 39.7 + - + -
111C CYS* 4.2 1.9 - - - +
115C LEU* 3.6 29.2 - - + +
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Residues in contact with TRP 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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12C ILE* 3.7 21.8 - - + -
15C ILE* 4.0 34.6 + - + +
21C ILE* 3.5 27.3 + - + +
22C SER 3.2 27.4 + - - +
23C LEU* 3.4 4.2 + - + +
24C LEU 3.3 0.2 - - - -
25C GLU* 1.3 73.2 - - - +
27C ALA* 1.3 59.3 + - - +
29C VAL* 4.0 14.6 - - + -
30C LEU* 2.6 55.8 + - + +
53C PHE* 3.7 25.6 - + - -
92C ALA* 4.9 0.7 - - + -
96C LEU* 3.8 30.5 - - + +
101C ILE* 4.2 6.7 - - + -
104C TRP* 3.6 46.4 - + - -
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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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5C LYS* 4.3 8.3 - - + +
8C VAL* 5.5 4.0 - - - -
9C SER* 5.3 9.9 - - - +
12C ILE* 5.2 1.5 - - - +
23C LEU 2.9 19.3 + - - +
24C LEU 3.6 4.9 - - - +
26C TRP* 1.3 77.6 - - - +
28C CYS* 1.3 63.8 + - - +
30C LEU* 4.9 1.6 - - - -
31C PHE* 3.1 12.3 + - - +
36C TYR* 2.9 34.3 + - + +
118C TRP* 3.6 24.9 - - + +
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Residues in contact with CYS 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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24C LEU 3.1 8.6 + - - +
25C GLU* 3.5 3.6 - - - +
27C ALA* 1.3 83.2 - - - +
29C VAL* 1.3 63.6 + - - +
31C PHE* 3.3 8.1 + - - +
32C HIS* 3.4 22.0 + - - -
110C MET 3.3 15.3 - - - -
111C CYS* 2.0 46.4 - - + -
115C LEU* 4.8 1.1 - - + -
118C TRP* 3.4 47.7 - - + +
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Residues in contact with VAL 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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21C ILE* 5.9 0.4 - - + -
25C GLU* 2.8 31.6 + - + +
26C TRP* 3.7 18.8 - - + +
28C CYS* 1.3 73.3 - - - +
30C LEU* 1.3 59.7 + - + +
32C HIS* 3.3 2.1 + - - +
33C THR* 2.7 43.9 + - - +
101C ILE* 4.9 4.0 - - + -
104C TRP* 3.7 31.4 - - + -
106C ALA* 4.5 3.7 - - + +
107C TYR* 3.7 36.1 - - + +
111C CYS* 3.7 11.4 - - - -
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Residues in contact with LEU 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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8C VAL* 3.7 23.8 - - + -
12C ILE* 4.0 18.4 - - + -
26C TRP* 2.6 39.3 + - + +
29C VAL* 1.3 71.4 - - + +
31C PHE* 1.3 61.2 + - - +
33C THR* 4.3 4.5 - - - -
34C SER* 2.9 29.6 + - - -
35C GLY 3.1 4.9 + - - -
36C TYR* 3.6 17.6 + - + -
52C LEU* 3.3 39.3 - - + +
53C PHE* 3.8 27.1 - - + -
104C TRP* 5.0 0.9 - - - +
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Residues in contact with PHE 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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27C ALA 3.1 7.0 + - - +
28C CYS 3.3 2.4 + - - +
30C LEU* 1.3 76.3 - - - +
32C HIS* 1.3 75.1 + + - +
35C GLY* 2.9 35.3 + - - +
36C TYR* 3.4 29.9 - + + -
118C TRP* 3.7 31.9 - + + -
280D PHE* 4.0 25.1 - + - -
285D PRO* 3.6 24.7 - - + -
286D TYR* 3.4 26.7 - + - -
406D NAG 3.8 18.8 + - - -
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Residues in contact with HIS 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 CYS* 3.4 25.4 + - - -
29C VAL 3.3 3.8 + - - +
30C LEU 3.2 0.2 - - - -
31C PHE* 1.3 84.4 - + - +
33C THR* 1.3 63.8 + - - +
35C GLY 4.7 0.2 - - - -
106C ALA* 3.8 19.3 - - + -
110C MET* 3.4 51.1 + - + +
111C CYS* 4.4 0.9 - - - -
118C TRP* 3.9 14.9 - + - -
286D TYR* 3.6 32.3 - + - -
288D GLN* 5.8 0.6 + - - -
359D ARG* 3.8 8.5 + - - -
360D PHE* 3.7 18.6 - - + -
406D NAG 2.8 29.4 + - - +
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Residues in contact with THR 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 VAL* 2.7 36.3 + - - +
30C LEU* 3.3 6.0 + - - -
32C HIS* 1.3 81.0 - - - +
34C SER* 1.3 57.1 + - - +
42C VAL* 5.9 1.0 - - - +
52C LEU 4.2 2.9 - - - +
53C PHE 3.9 13.0 - - - +
54C GLN* 3.4 40.1 - - + +
104C TRP* 3.8 13.7 - - + +
106C ALA* 4.2 9.1 - - - +
359D ARG* 4.6 7.9 + - - +
360D PHE* 5.2 2.9 - - - -
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Residues in contact with SER 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 LEU 2.9 7.1 + - - -
33C THR* 1.3 75.5 - - - +
35C GLY* 1.3 65.5 + - - +
36C TYR* 3.3 12.3 + - - -
37C ASP* 3.1 26.0 + - - +
40C ALA* 4.0 10.8 - - - +
51C GLY 3.7 14.8 - - - -
52C LEU* 2.7 34.5 + - - +
54C GLN* 4.3 2.0 - - - -
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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