Contacts of the helix formed by residues 26 - 38 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 3.2 27.4 - - - +
17D ALA* 4.6 3.6 - - - -
22D ASN* 4.3 12.4 - - - +
24D GLU* 3.3 4.9 + - - +
25D LEU* 1.3 70.9 - - - +
27D TRP* 1.3 47.9 + - - +
28D ALA* 3.4 10.2 + - - +
29D SER* 2.3 42.6 + - - -
30D ILE* 2.8 38.4 + - - +
65D GLN* 4.4 3.6 - - - +
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Residues in contact with TRP 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 3.3 46.2 + - + +
26D ASP* 1.3 72.4 - - - +
28D ALA* 1.3 62.6 + - - +
30D ILE* 3.7 15.0 - - + +
31D ASN* 2.9 61.0 + - - +
68D THR* 4.3 10.3 - - + -
72D THR* 3.3 38.6 - - + -
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 5.4 0.5 + - - -
26D ASP* 3.0 9.4 + - - +
27D TRP* 1.3 81.3 - - - +
29D SER* 1.3 61.8 + - - +
31D ASN* 4.6 1.0 - - - +
32D GLY* 3.4 16.1 + - - -
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Residues in contact with SER 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 4.2 10.6 - - - +
16D ARG* 2.7 40.7 + - - +
17D ALA* 3.9 15.5 - - - +
26D ASP* 2.3 38.3 + - - -
28D ALA* 1.3 73.0 - - - +
30D ILE* 1.3 66.0 + - - +
32D GLY* 3.6 1.9 + - - -
33D PHE* 3.2 20.3 + - - +
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ALA* 3.8 26.9 - - + +
25D LEU* 4.5 13.0 - - + -
26D ASP 2.8 36.5 + - - +
27D TRP* 3.8 28.7 - - + +
29D SER* 1.3 70.1 - - - +
31D ASN* 1.3 68.5 + - - +
33D PHE* 3.0 20.0 + - - +
34D CYS* 3.3 8.7 + - - -
65D GLN* 5.3 1.1 - - + +
68D THR* 4.3 19.1 - - + -
69D VAL* 3.9 24.4 - - + +
72D THR* 4.2 17.3 - - + -
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Residues in contact with ASN 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D TRP* 2.9 55.6 + - - +
28D ALA* 4.7 1.3 - - - +
30D ILE* 1.3 75.7 - - - +
32D GLY* 1.3 57.5 + - - +
34D CYS* 3.5 7.6 + - - +
35D GLU* 3.0 32.2 + - - +
72D THR* 3.9 16.7 - - - +
76D SER* 4.7 6.1 + - - -
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Residues in contact with GLY 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 3.2 30.6 + - - -
28D ALA 3.4 16.2 + - - -
29D SER 3.6 1.5 + - - -
30D ILE 3.1 1.0 - - - -
31D ASN* 1.3 78.4 - - - +
33D PHE* 1.3 60.2 + - - +
35D GLU* 4.0 6.3 - - - +
36D GLN* 3.2 21.0 + - - +
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Residues in contact with PHE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.7 35.8 - - + +
13D ARG* 3.9 12.6 - - + +
14D ILE* 3.7 35.0 - - + +
17D ALA* 5.3 1.1 - - + -
29D SER 3.2 11.0 + - - +
30D ILE* 3.0 12.1 + - - +
32D GLY* 1.3 74.1 - - - +
34D CYS* 1.3 62.5 + - - +
36D GLN* 3.1 2.1 + - - +
37D LEU* 2.9 37.6 + - + +
47D ALA* 3.5 42.2 - - + -
50D LEU* 4.7 3.8 - - + -
51D LEU* 4.2 10.3 - - + -
69D VAL* 3.8 20.9 - - + -
73D CYS* 3.8 12.1 - - - -
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Residues in contact with CYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.3 13.6 + - - -
31D ASN* 3.9 7.0 - - - +
33D PHE* 1.3 78.3 - - - +
35D GLU* 1.3 58.9 - - - +
36D GLN 3.2 0.9 + - - -
37D LEU* 3.3 18.0 - - - +
38D ASN* 3.0 16.6 + - - -
69D VAL* 4.0 1.8 - - - -
72D THR* 3.9 15.0 - - + -
73D CYS* 2.0 63.7 - - + -
76D SER* 4.8 8.3 - - - +
77D CYS* 3.6 14.2 - - - -
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASN 3.0 19.8 + - - +
32D GLY* 4.0 6.1 - - - +
34D CYS* 1.3 76.2 - - - +
36D GLN* 1.3 58.0 + - - +
38D ASN* 2.8 30.9 + - - +
39D GLU* 4.2 10.3 - - - +
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Residues in contact with GLN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLU 4.2 11.4 + - - +
10D LEU* 3.6 19.5 - - + +
13D ARG* 3.4 27.8 + - - +
32D GLY 3.2 17.6 + - - +
33D PHE 3.1 2.2 + - - +
35D GLU* 1.3 78.3 - - - +
37D LEU* 1.3 54.7 + - - +
38D ASN 2.7 17.9 + - - -
39D GLU* 2.9 47.1 + - - +
40D ASP* 4.1 13.2 + - - +
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.6 16.0 - - + +
33D PHE* 2.9 19.9 + - + +
34D CYS* 3.3 31.6 - - - +
36D GLN* 1.3 75.0 - - - +
38D ASN* 1.3 64.5 + - + +
40D ASP 5.0 0.2 - - - -
43D GLY* 3.4 5.0 - - - -
44D PRO* 3.2 36.3 - - + +
47D ALA* 3.7 17.9 - - + -
73D CYS* 3.7 16.8 - - - -
77D CYS* 4.1 8.5 - - + -
80D ARG* 5.7 0.4 - - + -
81D PHE* 3.9 41.1 - - + +
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Residues in contact with ASN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D CYS 3.0 18.9 + - - +
35D GLU* 2.8 33.2 + - - +
36D GLN 2.7 5.7 + - - -
37D LEU* 1.3 83.8 - - + +
39D GLU* 1.3 89.0 + - - +
40D ASP 2.8 6.6 - - - +
44D PRO* 4.9 0.7 - - - -
77D CYS* 4.8 9.1 - - + -
80D ARG* 2.6 39.4 + - + +
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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