Contacts of the helix formed by residues 12 - 20 (chain P) in PDB entry 2DFS
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 PHE 12 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10P ALA* 3.4 20.1 + - + -
11P GLU* 1.3 82.2 - - - +
13P LYS* 1.3 64.5 + - - +
14P GLU* 3.3 4.7 - - + +
15P ALA* 3.3 23.2 + - + +
16P PHE 3.2 16.5 + - - -
39P LEU* 3.6 34.4 - - + +
65P PHE* 3.5 10.2 - - - -
68P PHE* 5.5 0.2 - - - -
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Residues in contact with LYS 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P GLU* 3.4 4.6 + - - +
12P PHE* 1.3 71.0 - - - +
14P GLU* 1.3 60.4 + - + +
16P PHE* 3.2 5.4 + - + +
17P SER* 2.9 29.2 + - - -
65P PHE* 3.3 44.0 - - + -
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Residues in contact with GLU 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE* 3.3 5.3 - - + -
13P LYS* 1.3 80.0 - - + +
15P ALA* 1.3 60.3 + - - +
17P SER* 3.3 11.1 + - - -
18P LEU* 3.2 28.1 + - + +
113Q GLY 5.4 3.1 - - - +
115Q LYS* 6.4 1.8 - - - -
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Residues in contact with ALA 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE* 3.3 27.1 + - + +
14P GLU* 1.3 76.1 - - - +
16P PHE* 1.4 61.8 + - - +
18P LEU* 3.1 24.6 + - + +
19P PHE* 3.3 18.8 + - - -
35P VAL* 5.0 3.1 - - + -
38P SER* 4.9 15.0 - - - +
39P LEU* 4.1 17.9 - - + -
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Residues in contact with PHE 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE 3.2 5.9 + - - -
13P LYS* 3.4 10.8 - - + +
15P ALA* 1.4 74.0 - - - +
17P SER* 1.3 51.7 + - - +
19P PHE* 2.9 8.2 + - - +
20P ASP* 2.8 39.8 + - + +
25P GLY* 3.5 25.8 - - - -
27P ILE* 3.6 39.3 - - + -
35P VAL* 4.5 4.8 - - + +
39P LEU* 5.7 0.2 - - - +
63P ILE* 3.6 19.3 - - + -
64P ASP 4.2 2.2 - - - -
65P PHE* 3.5 58.6 - + + -
68P PHE* 3.6 25.1 - + + -
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Residues in contact with SER 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P LYS* 2.9 14.5 + - - -
14P GLU* 3.5 14.4 - - - -
16P PHE* 1.3 73.1 - - - +
18P LEU* 1.3 58.8 + - - +
20P ASP* 2.9 21.6 - - - +
111Q ASN* 4.2 7.8 + - - +
112Q LEU* 4.0 10.0 - - - +
115Q LYS* 3.0 28.4 + - - -
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Residues in contact with LEU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835M TYR* 4.2 20.8 - - + +
839M ARG* 4.5 27.6 - - + -
14P GLU* 3.2 16.1 + - + +
15P ALA* 3.1 17.0 + - + +
17P SER* 1.3 75.8 - - - +
19P PHE* 1.3 64.6 + - + +
20P ASP 3.6 3.1 - - - -
21P LYS* 3.3 19.9 + - - +
38P SER* 6.1 0.9 - - - +
111Q ASN 4.7 1.6 - - - +
112Q LEU* 3.4 32.1 - - + +
113Q GLY 4.3 17.3 - - - +
115Q LYS* 6.0 2.0 - - - +
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Residues in contact with PHE 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835M TYR* 3.3 42.2 - + - -
15P ALA 3.3 13.8 + - - +
16P PHE 2.9 8.4 + - - +
18P LEU* 1.3 78.1 - - + +
20P ASP* 1.3 60.1 + - - +
21P LYS* 2.7 24.9 + - - +
27P ILE* 3.8 21.5 - - + +
31P GLU* 3.1 47.7 - - + +
34P THR* 3.7 28.0 - - - -
35P VAL* 3.7 22.9 - - + -
38P SER* 3.6 22.7 - - - -
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Residues in contact with ASP 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P PHE* 2.8 25.4 + - + +
17P SER* 2.9 29.3 - - - +
18P LEU* 3.6 3.1 - - - -
19P PHE* 1.3 71.3 - - - +
21P LYS* 1.3 59.4 + - - +
22P ASP* 3.6 4.6 + - - +
23P GLY* 2.7 34.3 + - - -
24P ASP* 3.3 4.3 + - - +
25P GLY* 2.9 31.9 + - - -
26P THR 4.0 9.5 - - - +
27P ILE* 3.4 16.5 - - + +
111Q ASN* 4.5 2.9 + - - -
112Q LEU* 5.0 0.5 - - - +
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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