Contacts of the helix formed by residues 8 - 18 (chain O) 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 GLN 8 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9O ILE* 1.3 92.6 + - + +
10O ALA* 3.1 7.5 + - + +
11O GLU* 3.2 9.9 + - - +
12O PHE* 3.2 22.0 + - - +
39O LEU* 5.5 4.4 - - - +
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Residues in contact with ILE 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O GLN* 1.3 99.6 - - + +
10O ALA* 1.3 60.3 + - + +
12O PHE* 4.2 10.1 - - + -
13O LYS* 2.8 32.5 + - - +
65O PHE* 4.0 10.9 - - + -
69O LEU* 4.0 26.2 - - + -
72O MET* 6.0 4.9 - - + -
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Residues in contact with ALA 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O GLN* 3.1 3.6 + - + +
9O ILE* 1.3 82.7 - - + +
11O GLU* 1.4 61.5 + - - +
13O LYS* 3.8 4.8 - - - +
14O GLU* 3.2 20.1 + - - +
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Residues in contact with GLU 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814M ARG* 2.8 42.6 + - - -
8O GLN 3.2 10.4 + - - +
10O ALA* 1.4 75.1 - - - +
12O PHE* 1.3 60.2 + - - +
14O GLU* 3.2 9.4 + - - +
15O ALA* 2.8 30.7 + - + +
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Residues in contact with PHE 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O GLN 3.2 16.8 + - - +
9O ILE* 4.0 9.4 - - + +
11O GLU* 1.3 75.9 - - - +
13O LYS* 1.3 55.7 + - - +
15O ALA* 3.3 10.7 + - + -
16O PHE* 2.8 31.9 + + - +
35O VAL* 3.8 30.5 - - + -
39O LEU* 3.6 49.9 - - + +
65O PHE* 3.5 29.6 - + - -
68O PHE* 3.3 41.1 - + - -
69O LEU* 5.5 4.5 - - + -
72O MET* 5.6 5.4 - - + -
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Residues in contact with LYS 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ILE 2.8 23.5 + - - +
10O ALA* 3.8 5.8 - - - +
11O GLU 3.3 0.2 - - - -
12O PHE* 1.3 72.3 - - - +
14O GLU* 1.3 57.5 + - - +
16O PHE* 3.3 8.2 + - + +
17O SER* 2.9 48.3 + - - +
65O PHE* 3.5 38.3 - - + -
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Residues in contact with GLU 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814M ARG* 2.6 37.9 + - - +
10O ALA 3.2 10.6 + - - +
11O GLU* 3.2 24.5 + - - +
13O LYS* 1.3 73.7 - - - +
15O ALA* 1.3 60.7 + - - +
17O SER* 3.0 13.8 + - - -
18O LEU* 3.0 21.8 + - - +
89P PHE* 3.2 26.0 - - + -
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Residues in contact with ALA 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814M ARG* 5.2 5.8 - - - +
11O GLU* 2.8 21.1 + - + +
12O PHE* 3.4 23.1 - - + +
14O GLU* 1.3 71.5 - - - +
16O PHE* 1.3 59.6 + - - +
18O LEU* 3.4 9.3 + - - +
19O PHE* 3.3 29.7 + - - -
35O VAL* 5.1 2.0 - - + -
38O SER* 4.3 21.8 - - - +
39O LEU* 5.7 0.7 - - - -
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Residues in contact with PHE 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O PHE* 2.8 30.9 + + + +
13O LYS* 3.4 14.6 - - + +
15O ALA* 1.3 71.6 - - - +
17O SER* 1.3 57.7 + - - +
18O LEU 3.2 0.4 - - - -
19O PHE* 2.9 6.4 + - - +
20O ASP* 2.8 31.4 + - + +
25O GLY* 3.4 23.6 - - - -
27O ILE* 3.6 33.2 - - + -
35O VAL* 4.5 9.3 - - + +
63O ILE* 3.4 18.6 - - + -
64O ASP 3.6 3.1 - - - -
65O PHE* 3.4 54.7 - + + -
68O PHE* 4.5 9.6 - + + -
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Residues in contact with SER 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817M ARG* 5.6 4.0 + - - -
13O LYS* 2.9 35.3 + - - +
14O GLU* 3.0 19.0 + - - -
16O PHE* 1.3 73.6 - - - +
18O LEU* 1.3 57.0 + - - +
20O ASP* 3.2 23.6 + - - +
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Residues in contact with LEU 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810M ALA* 4.5 15.3 - - + -
813M LEU* 4.2 34.6 - - + +
814M ARG* 3.6 39.7 - - + +
817M ARG* 4.7 17.7 - - + +
14O GLU* 3.0 16.2 + - - +
15O ALA* 3.6 7.9 - - - +
16O PHE 3.2 0.2 - - - -
17O SER* 1.3 76.2 - - - +
19O PHE* 1.3 77.8 + - + +
20O ASP 3.6 4.0 - - - +
21O LYS* 3.3 18.1 + - - +
38O SER* 5.6 0.4 - - - +
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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