Contacts of the helix formed by residues 6 - 19 (chain E) in PDB entry 1PWY
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 6 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E GLY 4.9 3.6 - - - +
5E TYR* 1.3 79.2 - - - +
7E TYR* 1.3 56.3 + - - +
8E GLU* 3.2 19.8 + - - +
9E ASP* 2.7 51.5 + - - +
10E TYR* 3.2 10.3 - - - -
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Residues in contact with TYR 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E THR* 1.3 72.6 - - - +
8E GLU* 1.3 61.9 + - + +
10E TYR* 3.0 12.0 + - - +
11E LYS* 2.8 63.1 + - + +
104E HIS* 6.1 0.2 - - - -
105E LEU* 3.4 23.1 - - + +
152E ASP* 3.5 13.8 + - - +
154E ARG* 3.5 63.0 + - + +
155E PHE* 3.4 36.1 - + - -
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Residues in contact with GLU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E THR* 3.2 20.5 + - - +
7E TYR* 1.3 82.0 + - + +
9E ASP* 1.3 57.9 + - - +
10E TYR 3.3 0.2 - - - -
11E LYS* 3.7 29.4 - - - +
12E ASN* 2.6 43.3 + - - +
154E ARG* 5.4 5.5 + - - -
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Residues in contact with ASP 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLY 4.2 1.7 - - - +
5E TYR* 3.0 33.9 - - + +
6E THR* 2.7 49.5 + - - +
8E GLU* 1.3 73.1 - - - +
10E TYR* 1.3 56.9 + - - +
12E ASN* 3.6 1.5 - - - +
13E THR* 2.9 26.7 + - - -
55E ASN* 3.2 29.1 + - - +
98E PHE* 4.6 1.8 - - - -
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Residues in contact with TYR 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E GLU* 3.1 34.6 + - - -
5E TYR* 3.8 19.6 - - + +
6E THR 3.2 27.6 - - - -
7E TYR* 3.0 7.1 + - - +
9E ASP* 1.3 74.3 - - - +
11E LYS* 1.3 69.6 + - - +
13E THR* 3.2 1.8 + - - -
14E ALA* 2.8 22.5 + - - +
94E TRP 4.6 2.4 + - - -
98E PHE* 3.3 41.3 - + - -
101E ARG* 3.5 38.6 + - + +
102E VAL* 4.4 6.5 - - + +
105E LEU* 3.2 19.0 - - + +
152E ASP* 5.2 1.1 - - - -
155E PHE* 3.7 25.4 - + + -
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Residues in contact with LYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 2.8 46.8 + - + +
8E GLU* 3.7 28.6 - - - +
10E TYR* 1.3 76.3 - - - +
12E ASN* 1.3 67.6 + - - +
14E ALA* 2.9 2.0 + - - +
15E GLU* 2.9 50.3 + - + +
105E LEU* 3.3 12.0 - - + +
154E ARG* 5.4 1.8 - - - +
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Residues in contact with ASN 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLU* 2.6 38.7 + - - +
9E ASP* 3.6 4.9 - - - +
11E LYS* 1.3 79.1 - - - +
13E THR* 1.3 61.9 + - - +
15E GLU* 3.9 11.2 - - - +
16E TRP* 3.0 25.3 + - - +
54E PRO* 5.0 4.0 - - + +
55E ASN* 4.4 6.7 - - - +
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Residues in contact with THR 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ASP 2.9 16.9 + - - -
10E TYR 3.9 2.0 - - - -
12E ASN* 1.3 70.4 - - - +
14E ALA* 1.3 67.0 + - - +
16E TRP* 3.4 2.6 + - - +
17E LEU* 2.9 23.8 + - + +
53E ILE* 3.7 24.5 - - + -
54E PRO* 3.7 7.8 - - - +
55E ASN* 2.9 40.4 + - - +
56E PHE* 4.3 0.9 - - + -
98E PHE* 3.8 12.6 - - + -
102E VAL* 3.8 25.6 - - + -
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Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E TYR 2.8 20.2 + - - +
11E LYS* 3.4 3.1 - - - +
13E THR* 1.3 71.2 - - - +
15E GLU* 1.3 53.5 + - + +
17E LEU* 2.9 7.3 + - - +
18E LEU* 2.8 33.9 + - + +
102E VAL* 3.9 7.6 - - + +
105E LEU* 3.4 34.1 - - + +
106E LEU* 3.3 25.4 - - + +
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Residues in contact with GLU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LYS* 2.9 45.3 + - + +
12E ASN* 3.9 11.5 - - - +
14E ALA* 1.3 78.8 - - + +
16E TRP* 1.3 51.7 + - - +
18E LEU* 3.1 15.8 + - + +
19E SER* 2.7 36.9 + - - -
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Residues in contact with TRP 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASN 3.0 19.0 + - - +
13E THR 3.6 3.4 - - - +
15E GLU* 1.3 72.4 - - - +
17E LEU* 1.3 88.2 + - + +
19E SER* 3.2 7.6 + - - -
20E HIS* 2.7 66.4 + + + +
48E PHE* 3.4 42.0 - + - -
52E GLU* 3.6 27.8 - - + -
53E ILE* 4.4 4.7 - - + -
54E PRO* 3.4 36.3 - - + +
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Residues in contact with LEU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E THR* 2.9 25.5 + - + +
14E ALA 3.1 9.4 - - - +
16E TRP* 1.3 102.1 - - + +
18E LEU* 1.3 61.4 + - - +
20E HIS* 3.0 3.8 + - - +
21E THR* 2.9 28.1 + - - +
48E PHE* 4.5 5.6 - - + -
53E ILE* 3.9 22.7 - - + -
56E PHE* 4.6 0.7 - - + -
68E LEU* 4.5 8.3 - - + -
70E PHE* 3.9 28.9 - - + -
102E VAL* 3.6 27.4 - - + -
106E LEU* 4.0 17.0 - - + -
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Residues in contact with LEU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ALA* 2.8 22.5 + - + +
15E GLU* 3.1 19.3 + - + +
17E LEU* 1.3 71.4 - - - +
19E SER* 1.3 53.5 + - - +
20E HIS 2.6 16.7 + - - -
21E THR* 2.8 23.2 + - + +
23E HIS 4.6 2.2 - - - +
24E ARG* 2.8 44.6 + - + +
25E PRO* 5.0 1.3 - - + -
105E LEU 4.5 11.7 - - - +
106E LEU* 3.9 36.3 - - + +
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLU 2.7 18.5 + - - -
16E TRP* 3.2 8.7 + - - -
18E LEU* 1.3 69.6 - - - +
20E HIS* 1.3 81.9 + - - +
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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