Contacts of the helix formed by residues 22 - 35 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP* 3.8 9.9 - - - -
17A GLY* 4.3 1.3 - - - +
20A GLY 4.1 1.2 + - - -
21A ILE* 1.3 77.1 - - - +
23A LEU* 1.3 64.6 + - - +
24A LEU* 3.5 12.6 + - - +
25A GLU* 2.8 36.8 + - - +
26A TRP* 3.1 22.9 + - - -
115A LEU* 5.1 1.2 - - - +
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Residues in contact with LEU 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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9A SER* 3.5 29.6 + - - +
12A ILE* 3.7 44.9 - - + +
13A LYS* 4.4 12.6 - - + -
15A ILE* 4.4 2.9 - - + -
16A ASP* 3.7 38.1 + - + +
22A SER* 1.3 72.6 - - - +
24A LEU* 1.3 70.9 + - + +
26A TRP* 3.7 2.4 - - + +
27A ALA* 2.8 26.2 + - - +
118A TRP 5.7 0.2 - - - -
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Residues in contact with LEU 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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22A SER* 3.2 10.7 - - - +
23A LEU* 1.3 82.7 - - + +
25A GLU* 1.3 63.5 + - - +
27A ALA* 3.3 1.1 + - - -
28A CYS* 3.1 19.2 + - - +
115A LEU* 3.6 39.7 - - + +
116A GLU* 4.0 8.3 - - - +
118A TRP* 3.4 14.9 - - - +
119A ARG* 3.2 72.5 - - + +
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Residues in contact with GLU 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 GLY 3.6 6.1 - - - +
21A ILE* 3.2 18.6 - - + -
22A SER* 2.8 41.2 + - - +
23A LEU 3.3 0.2 - - - -
24A LEU* 1.3 79.3 - - - +
26A TRP* 1.3 57.3 + - - +
28A CYS* 3.2 4.4 + - - +
29A VAL* 2.8 33.7 + - - +
107A TYR* 2.8 39.8 + - + -
111A CYS* 4.2 2.2 - - - +
115A LEU* 3.7 35.4 - - + +
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Residues in contact with TRP 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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12A ILE* 3.6 20.9 - - + -
15A ILE* 3.6 43.5 + - + +
21A ILE* 3.3 37.9 + - + +
22A SER 3.1 14.5 + - - +
23A LEU* 3.2 6.3 + - + +
25A GLU* 1.3 75.4 - - - +
27A ALA* 1.3 57.8 + - - +
29A VAL* 3.0 17.9 + - + -
30A LEU* 2.6 51.7 + - + +
53A PHE* 3.6 30.1 - + - -
96A LEU* 3.7 17.3 - - + +
101A ILE* 3.8 10.5 - - + -
104A TRP* 3.5 44.4 - + - -
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Residues in contact with ALA 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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5A LYS* 4.3 3.4 - - + +
8A VAL* 5.4 4.3 - - + -
9A SER* 4.1 15.3 - - - +
12A ILE* 5.0 1.7 - - - +
23A LEU 2.8 17.4 + - - +
24A LEU 3.6 5.4 - - - +
26A TRP* 1.3 75.1 - - - +
28A CYS* 1.3 61.9 + - - +
30A LEU* 4.9 2.5 - - - -
31A PHE* 3.1 13.9 + - - +
36A TYR* 2.7 34.2 + - + +
118A TRP* 3.7 24.7 - - + +
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Residues in contact with CYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU 3.1 11.3 + - - +
25A GLU* 3.3 7.6 - - - +
26A TRP 3.1 0.4 - - - -
27A ALA* 1.3 75.1 - - - +
29A VAL* 1.3 65.0 + - - +
31A PHE* 3.3 2.8 + - - +
32A HIS* 3.3 30.6 + - - -
110A MET 3.3 14.6 - - - -
111A CYS* 2.0 46.9 - - + -
115A LEU* 4.6 0.4 - - + -
118A TRP* 3.5 44.1 - - + +
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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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21A ILE* 5.8 0.2 - - + -
25A GLU* 2.8 26.7 + - + +
26A TRP* 3.5 20.6 - - + +
28A CYS* 1.3 73.9 - - - +
30A LEU* 1.3 56.3 + - - +
32A HIS* 3.4 1.9 + - - +
33A THR* 2.7 46.4 + - - +
101A ILE* 5.0 4.7 - - + -
104A TRP* 3.7 30.5 - - + -
106A ALA* 4.5 4.6 - - + +
107A TYR* 3.8 35.7 - - + +
111A CYS* 4.0 10.5 - - - -
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Residues in contact with LEU 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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8A VAL* 3.6 26.5 - - + -
12A ILE* 4.0 17.0 - - + -
26A TRP* 2.6 31.3 + - + +
29A VAL* 1.3 73.0 - - + +
31A PHE* 1.3 66.5 + - - +
33A THR* 4.2 3.4 - - - -
34A SER* 3.0 24.3 + - - -
35A GLY 3.3 3.1 + - - -
36A TYR* 3.7 18.3 + - + -
52A LEU* 3.4 37.7 - - + +
53A PHE* 3.8 34.3 - - + -
104A TRP* 5.0 0.4 - - - +
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA 3.1 19.0 + - - +
28A CYS 3.7 3.4 - - - +
29A VAL 3.3 0.4 - - - -
30A LEU* 1.3 75.7 - - - +
32A HIS* 1.3 72.8 + + - +
35A GLY* 2.6 42.6 + - - +
36A TYR* 3.3 31.9 - + + +
118A TRP* 3.8 18.6 - + + -
280B PHE* 3.9 26.2 - + - -
285B PRO* 4.0 20.0 - - + -
286B TYR* 3.6 26.2 - + - -
405B NAG 3.8 20.8 + - - -
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Residues in contact with HIS 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 CYS* 3.3 29.7 + - - +
30A LEU 3.3 0.2 - - - -
31A PHE* 1.3 85.4 - + - +
33A THR* 1.3 62.9 + - - +
35A GLY 4.7 0.5 + - - -
106A ALA* 3.7 19.1 - - + -
110A MET* 3.5 38.7 + - + +
111A CYS* 4.4 1.1 - - - -
118A TRP* 4.0 15.3 - + - -
286B TYR* 3.6 45.1 - + - -
288B GLN* 6.3 0.2 - - - -
359B ARG* 4.0 8.7 + - - -
360B PHE* 3.9 16.6 - - + -
405B NAG 2.8 30.7 + - - +
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Residues in contact with THR 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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29A VAL* 2.7 38.0 + - - +
30A LEU* 3.9 7.2 - - - -
32A HIS* 1.3 79.6 - - - +
34A SER* 1.3 59.5 + - - +
42A VAL* 5.7 1.9 - - - +
52A LEU 4.2 3.1 - - - +
53A PHE 4.0 12.1 - - - +
54A GLN* 3.3 39.4 - - + +
104A TRP* 3.8 11.7 - - + +
106A ALA* 4.3 8.9 + - - +
359B ARG* 4.7 6.8 + - - +
360B PHE* 5.2 4.3 - - - -
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Residues in contact with SER 34 (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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30A LEU 3.0 5.4 + - - -
33A THR* 1.3 77.1 - - - +
35A GLY* 1.3 65.8 + - - +
36A TYR 3.5 9.0 + - - -
37A ASP* 3.0 22.4 + - - +
40A ALA* 3.9 16.3 - - - +
51A GLY 3.6 16.2 - - - -
52A LEU* 2.8 34.0 + - - +
54A GLN* 4.0 2.9 - - - -
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Residues in contact with GLY 35 (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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2A GLU* 5.1 8.8 - - - +
3A LEU 4.8 0.9 - - - +
31A PHE* 2.6 40.8 + - - -
32A HIS 4.7 0.2 + - - -
33A THR 3.9 0.2 - - - -
34A SER* 1.3 73.8 - - - +
36A TYR* 1.3 72.2 + - - +
37A ASP* 3.2 2.9 + - - +
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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