Contacts of the helix formed by residues 9 - 18 (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 THR 9 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLU* 1.3 105.3 + - - +
10C LEU* 1.3 68.2 + - - +
11C GLU* 4.0 12.1 + - - +
12C ALA* 3.1 13.5 + - - +
13C ARG* 2.8 27.8 + - - +
36C GLN* 4.8 3.8 - - - +
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Residues in contact with LEU 10 (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 THR* 1.3 71.9 - - - +
11C GLU* 1.3 56.6 + - - +
13C ARG* 2.9 5.9 + - - +
14C ILE* 2.7 34.0 + - - +
33C PHE* 3.7 40.7 - - + +
36C GLN* 3.9 21.4 - - + +
37C LEU* 4.0 13.5 - - + -
43C GLY* 3.5 33.7 - - - +
46C LEU* 3.3 32.3 - - + -
47C ALA* 4.2 5.4 - - + +
50C LEU* 4.2 6.7 - - + -
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Residues in contact with GLU 11 (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 THR* 4.0 11.6 + - - +
10C LEU* 1.3 77.9 + - - +
12C ALA* 1.3 60.9 + - - +
14C ILE* 3.1 9.9 - - - +
15C ASN* 2.7 35.7 + - - +
46C LEU* 3.2 36.7 - - - +
50C LEU* 3.7 12.5 - - + +
59D GLN* 3.7 33.4 - - + +
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Residues in contact with ALA 12 (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* 4.1 17.5 - - + +
9C THR* 3.1 27.6 + - - +
11C GLU* 1.3 81.1 - - - +
13C ARG* 1.3 63.2 + - - +
15C ASN* 3.4 7.6 + - - +
16C ARG* 3.1 28.9 + - - +
21D LEU* 6.2 4.5 - - + -
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Residues in contact with ARG 13 (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* 4.3 22.4 + - - +
9C THR 2.8 19.4 + - - +
10C LEU* 3.5 6.1 - - - +
12C ALA* 1.3 70.5 - - - +
14C ILE* 1.3 61.3 + - - +
16C ARG* 3.1 26.9 + - - +
17C ALA* 2.7 31.9 + - - +
28C ALA 5.2 0.2 + - - -
29C SER* 4.2 6.9 + - - +
32C GLY* 3.6 29.5 + - - -
33C PHE* 3.9 20.6 - - + +
36C GLN* 3.5 44.4 + - - +
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Residues in contact with ILE 14 (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 2.7 16.8 + - - +
11C GLU* 3.1 20.4 - - - +
13C ARG* 1.3 72.6 - - - +
15C ASN* 1.3 72.0 + - - +
17C ALA* 3.0 2.8 + - + +
18C THR* 2.7 56.4 + - + -
33C PHE* 3.8 26.4 - - + -
50C LEU* 4.1 19.3 - - + -
51C LEU* 3.9 20.6 - - + -
54C LYS* 4.1 19.1 - - + -
69C VAL* 4.0 14.1 - - + -
59D GLN* 4.5 0.7 - - - +
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Residues in contact with ASN 15 (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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11C GLU* 2.7 27.6 + - - +
12C ALA* 3.8 7.2 - - - +
14C ILE* 1.3 81.9 - - - +
16C ARG* 1.3 57.7 + - - +
18C THR* 3.8 1.0 - - - -
19C ASN* 3.2 32.0 + - - +
54C LYS* 2.9 30.3 + - - +
20D PRO* 4.3 18.9 - - + +
21D LEU* 6.5 1.1 - - + -
59D GLN* 2.9 33.7 + - - -
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Residues in contact with ARG 16 (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 3.9 22.0 - - - +
12C ALA* 3.1 21.8 + - - +
13C ARG* 3.1 27.4 + - - +
14C ILE 3.0 0.4 - - - -
15C ASN* 1.3 78.7 - - - +
17C ALA* 1.3 62.8 + - - +
18C THR 3.4 0.3 + - - -
19C ASN* 3.5 11.8 + - + +
22C ASN* 3.1 20.7 + - - +
26C ASP* 4.2 10.0 - - - +
29C SER* 3.2 31.5 + - - +
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Residues in contact with ALA 17 (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 2.7 19.2 + - - +
14C ILE* 3.8 8.3 - - + +
16C ARG* 1.3 75.6 - - - +
18C THR* 1.3 59.0 + - - +
19C ASN 3.5 0.4 - - - -
22C ASN* 4.1 1.6 + - - +
26C ASP* 5.0 3.6 + - - +
29C SER* 3.7 21.0 - - - +
30C ILE* 3.8 31.6 - - + +
33C PHE* 5.1 1.6 - - + -
65C GLN* 3.4 23.0 - - - +
69C VAL* 4.0 12.0 - - + +
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Residues in contact with THR 18 (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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14C ILE* 2.7 40.8 + - + -
15C ASN* 3.8 2.1 - - - -
17C ALA* 1.3 77.7 - - - +
19C ASN* 1.3 63.8 + - - +
20C PRO* 3.0 11.1 - - - +
54C LYS* 3.5 27.9 + - + +
62C GLU* 3.7 23.7 + - - +
65C GLN* 3.6 14.2 + - - +
66C ALA* 3.5 35.0 - - + +
69C VAL* 4.4 1.8 - - + -
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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