Contacts of the helix formed by residues 9 - 18 (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 THR 9 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLU* 1.3 77.6 - - - +
10D LEU* 1.3 65.3 + - - +
11D GLU* 3.9 14.0 + - - +
12D ALA* 3.3 23.5 + - - +
13D ARG* 3.1 22.4 + - - +
36D GLN* 5.7 0.2 - - - -
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Residues in contact with LEU 10 (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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9D THR* 1.3 72.4 - - - +
11D GLU* 1.3 64.4 + - - +
13D ARG* 3.0 7.2 + - - +
14D ILE* 2.9 29.8 + - - +
33D PHE* 3.7 23.3 - - + +
36D GLN* 3.6 31.8 - - + +
37D LEU* 3.6 25.1 - - - +
43D GLY* 3.6 28.5 - - - +
46D LEU* 3.9 21.5 - - + -
47D ALA* 4.0 9.0 - - + +
50D LEU* 4.1 9.6 - - + -
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Residues in contact with GLU 11 (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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58C PRO 5.8 0.9 - - - +
59C GLN* 3.7 37.7 - - + +
9D THR* 3.9 11.7 + - - +
10D LEU* 1.3 82.4 + - - +
12D ALA* 1.3 63.0 + - - +
14D ILE* 3.0 15.1 - - - +
15D ASN* 2.9 26.2 + - - +
46D LEU* 3.9 21.9 - - - +
50D LEU* 3.8 19.0 - - + +
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Residues in contact with ALA 12 (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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21C LEU* 5.7 10.5 - - + -
8D GLU* 3.7 19.7 - - + +
9D THR* 3.3 24.5 + - - +
11D GLU* 1.3 80.8 - - - +
13D ARG* 1.3 64.6 + - - +
15D ASN* 3.7 7.9 + - - +
16D ARG* 3.5 22.9 + - - +
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Residues in contact with ARG 13 (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* 3.6 38.9 + - + +
9D THR 3.1 17.4 + - - +
10D LEU* 3.0 9.7 + - - +
12D ALA* 1.3 74.1 - - - +
14D ILE* 1.3 60.2 + - - +
16D ARG* 3.1 15.6 + - - +
17D ALA* 2.8 30.4 + - - +
28D ALA 5.4 1.0 + - - -
29D SER* 4.2 9.7 + - - +
32D GLY* 3.2 41.8 + - - -
33D PHE* 3.9 16.4 - - + +
36D GLN* 3.4 34.3 + - - +
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Residues in contact with ILE 14 (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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59C GLN* 4.7 3.6 - - - +
10D LEU 2.9 18.7 + - - +
11D GLU* 3.0 20.0 - - - +
13D ARG* 1.3 73.1 - - - +
15D ASN* 1.3 74.0 + - - +
17D ALA* 4.2 2.2 - - - -
18D THR* 2.8 49.5 + - + +
33D PHE* 3.7 20.7 - - + -
50D LEU* 4.5 19.5 - - + +
51D LEU* 3.7 30.1 - - + -
54D LYS* 4.4 13.7 - - + -
69D VAL* 4.0 14.1 - - + -
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Residues in contact with ASN 15 (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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20C PRO* 3.9 20.0 - - + +
21C LEU* 6.1 3.0 - - + +
59C GLN* 2.9 41.0 + - - -
11D GLU* 2.9 19.4 + - - +
12D ALA* 4.1 7.2 - - - +
13D ARG 3.3 0.2 - - - -
14D ILE* 1.3 83.6 - - - +
16D ARG* 1.3 57.9 + - - +
18D THR* 3.8 3.5 + - - -
19D ASN* 2.9 35.0 + - - +
54D LYS* 3.2 19.8 + - - +
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Residues in contact with ARG 16 (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* 2.5 44.0 + - - -
12D ALA* 3.5 16.5 + - - +
13D ARG* 3.1 12.4 + - - +
15D ASN* 1.3 78.5 - - - +
17D ALA* 1.3 59.3 - - - +
19D ASN* 3.5 9.5 + - + +
22D ASN* 2.8 29.1 + - - +
26D ASP* 3.2 11.2 - - - +
29D SER* 2.7 51.8 + - - +
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Residues in contact with ALA 17 (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 2.8 16.6 + - - +
14D ILE* 3.8 8.7 - - + +
16D ARG* 1.3 77.5 - - - +
18D THR* 1.3 57.1 - - - +
19D ASN 3.5 0.2 - - - -
22D ASN* 3.8 0.3 + - - -
26D ASP* 4.6 2.9 - - - +
29D SER* 3.9 8.5 - - - +
30D ILE* 3.8 44.8 - - + +
33D PHE* 5.3 1.3 - - + -
65D GLN* 2.9 24.8 + - - +
69D VAL* 4.0 12.2 - - + +
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Residues in contact with THR 18 (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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14D ILE* 2.8 37.5 + - + +
15D ASN 3.8 1.3 + - - -
17D ALA* 1.3 80.4 - - - +
19D ASN* 1.3 66.6 + - - +
20D PRO* 3.1 8.1 - - - +
54D LYS* 3.3 26.0 - - + +
62D GLU* 3.5 25.5 + - - +
65D GLN* 3.5 14.0 - - - +
66D ALA* 3.5 35.4 - - + +
69D VAL* 4.3 3.4 - - + -
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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