Contacts of the helix formed by residues 26 - 38 (chain C) in PDB entry 1PY1
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 ASP 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ARG* 4.2 15.0 - - - +
17C ALA* 5.0 3.3 + - - -
22C ASN* 4.1 22.6 + - - +
24C GLU 3.5 2.2 + - - +
25C LEU* 1.3 74.6 - - - +
27C TRP* 1.3 60.0 + - - +
28C ALA* 3.0 13.2 + - - +
29C SER* 2.9 38.8 + - - +
30C ILE* 3.1 19.3 + - - +
65C GLN* 4.9 2.6 + - - -
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Residues in contact with TRP 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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25C LEU* 3.6 37.4 + - + +
26C ASP* 1.3 72.9 - - - +
28C ALA* 1.3 57.6 + - - +
30C ILE* 3.8 25.6 - - + -
31C ASN* 2.8 50.3 + - - +
68C THR* 3.7 15.0 - - + -
72C THR* 3.3 30.7 - - + -
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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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13C ARG* 5.2 0.5 + - - -
26C ASP* 3.0 10.9 + - - +
27C TRP* 1.3 78.2 - - - +
29C SER* 1.3 58.4 + - - +
31C ASN* 4.0 2.3 - - - +
32C GLY* 2.9 27.0 + - - -
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 4.2 7.6 + - - +
16C ARG* 3.2 36.1 + - - +
17C ALA* 3.7 25.7 - - - +
26C ASP* 2.9 30.3 + - - -
28C ALA* 1.3 75.8 - - - +
30C ILE* 1.3 61.1 + - - +
32C GLY* 3.3 1.7 + - - +
33C PHE* 2.8 31.7 + - - +
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Residues in contact with ILE 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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17C ALA* 3.9 16.6 - - + +
25C LEU* 4.2 24.2 - - + -
26C ASP 3.1 23.1 + - - +
27C TRP* 3.8 41.7 - - + +
29C SER* 1.3 76.1 - - - +
31C ASN* 1.3 63.7 + - - +
33C PHE* 3.3 4.4 + - - +
34C CYS* 3.2 23.4 + - - -
65C GLN 5.1 0.4 - - - +
68C THR* 4.3 6.1 - - + -
69C VAL* 3.5 32.8 - - + -
72C THR* 3.9 20.6 - - + +
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Residues in contact with ASN 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 TRP* 2.8 38.4 + - - +
28C ALA* 4.1 2.9 - - - +
30C ILE* 1.3 71.6 - - - +
32C GLY* 1.3 66.1 + - - +
34C CYS* 3.2 7.1 + - - +
35C GLU* 3.1 23.7 + - - +
72C THR* 3.7 24.4 - - - +
76C SER* 5.4 2.6 + - - -
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Residues in contact with GLY 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 3.6 24.5 + - - -
28C ALA 2.9 18.7 + - - -
29C SER 3.6 0.2 - - - -
31C ASN* 1.3 77.3 - - - +
33C PHE* 1.3 56.9 + - - +
35C GLU* 3.4 8.4 + - - +
36C GLN* 2.9 30.1 + - - +
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Residues in contact with PHE 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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10C LEU* 3.7 30.8 - - + +
13C ARG* 3.9 17.2 - - + +
14C ILE* 3.8 44.0 - - + -
17C ALA* 5.1 2.0 - - + -
29C SER 2.8 17.7 + - - +
30C ILE* 3.5 6.3 - - - +
32C GLY* 1.3 74.3 - - - +
34C CYS* 1.3 67.1 + - - +
36C GLN* 3.3 2.1 + - - +
37C LEU* 3.2 31.8 + - + +
47C ALA* 3.8 24.7 - - + -
50C LEU* 5.0 3.4 - - + -
51C LEU* 4.3 13.2 - - + -
69C VAL* 3.6 29.6 - - + -
73C CYS* 3.7 12.6 - - - -
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Residues in contact with CYS 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 ILE* 3.2 16.1 + - - -
31C ASN* 3.2 9.7 + - - +
33C PHE* 1.3 79.3 - - - +
35C GLU* 1.3 62.0 + - - +
37C LEU* 3.3 14.1 - - - +
38C ASN* 3.3 20.1 + - - -
69C VAL 4.0 1.6 - - - -
72C THR* 3.9 13.2 - - - -
73C CYS* 2.0 67.5 - - + -
76C SER* 4.2 12.1 - - - +
77C CYS* 4.3 0.3 - - - -
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Residues in contact with GLU 35 (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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31C ASN 3.1 15.8 + - - +
32C GLY* 3.8 7.6 - - - +
34C CYS* 1.3 78.6 - - - +
36C GLN* 1.3 64.9 + - - +
37C LEU 3.3 0.9 + - - -
38C ASN* 3.4 16.8 + - + +
39C GLU* 3.8 25.8 + - + +
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Residues in contact with GLN 36 (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 GLU 4.2 12.2 + - - +
9C THR* 5.5 1.4 - - - +
10C LEU* 3.9 21.4 - - + +
13C ARG* 3.5 35.8 + - - +
32C GLY 2.9 18.6 + - - +
33C PHE 3.3 4.5 + - - +
35C GLU* 1.3 79.3 + - - +
37C LEU* 1.3 59.4 + - - +
39C GLU* 3.6 31.3 + - - +
40C ASP* 4.5 7.4 + - - +
43C GLY* 5.7 0.2 - - - -
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Residues in contact with LEU 37 (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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10C LEU* 4.0 22.4 - - + -
33C PHE* 3.2 36.0 + - + +
34C CYS* 3.3 17.3 - - - +
36C GLN* 1.3 73.6 - - - +
38C ASN* 1.3 77.9 + - - +
39C GLU 3.0 10.0 + - - -
40C ASP 3.2 17.5 - - - +
43C GLY* 4.0 5.9 - - - -
44C PRO* 3.6 20.3 - - + +
47C ALA* 4.0 14.1 - - + -
73C CYS* 4.0 9.2 - - + -
77C CYS* 4.2 1.6 - - - -
81C PHE* 4.1 29.4 - - + -
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Residues in contact with ASN 38 (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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34C CYS 3.3 12.3 + - - -
35C GLU* 3.4 11.6 + - + +
37C LEU* 1.3 85.0 - - - +
39C GLU* 1.3 65.0 + - + +
40C ASP 4.6 0.2 - - - -
44C PRO* 5.5 1.1 - - - -
76C SER 3.3 9.1 + - - -
77C CYS* 2.9 43.9 - - - +
78C GLY 4.8 1.4 + - - -
80C ARG* 4.4 21.6 - - - +
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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