Contacts of the helix formed by residues 8 - 20 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G ILE* 1.4 89.0 + - + +
10G ALA* 3.3 5.1 - - + +
11G GLU* 3.1 23.3 + - - +
12G PHE* 3.1 14.6 + - - +
39G LEU* 5.4 5.8 - - - +
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Residues in contact with ILE 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G GLN* 1.4 97.2 - - + +
10G ALA* 1.3 59.1 + - + +
12G PHE* 3.9 10.0 - - + +
13G LYS* 2.7 34.4 + - + +
65G PHE* 4.1 9.5 - - + -
69G LEU* 4.4 24.5 - - + -
72G MET* 6.4 1.3 - - + -
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Residues in contact with ALA 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G GLN* 3.1 2.7 + - + +
9G ILE* 1.3 80.0 - - + +
11G GLU* 1.4 61.5 + - - +
13G LYS* 3.2 6.2 + - - -
14G GLU* 3.1 36.6 + - + +
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Residues in contact with GLU 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A LYS* 3.8 17.2 + - - +
907A LYS* 2.6 42.2 + - - +
8G GLN 3.1 14.8 + - - +
10G ALA* 1.4 77.1 - - - +
12G PHE* 1.3 57.9 + - + +
14G GLU* 3.6 6.7 + - - +
15G ALA* 3.1 28.0 + - + +
38G SER 5.2 0.8 - - - +
39G LEU* 5.9 6.3 - - + +
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Residues in contact with PHE 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906A LEU* 4.1 10.5 - - + -
8G GLN 3.1 14.9 + - - +
9G ILE* 3.9 8.7 - - + +
11G GLU* 1.3 77.3 - - - +
13G LYS* 1.3 57.9 + - - +
15G ALA* 3.0 4.4 - - - +
16G PHE* 2.9 31.7 + + - +
35G VAL* 3.4 26.7 - - + -
39G LEU* 3.6 50.0 - - + -
65G PHE* 3.5 33.9 - + - -
68G PHE* 3.2 40.6 - + - -
69G LEU* 5.6 8.1 - - + -
72G MET* 6.0 3.4 - - + -
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Residues in contact with LYS 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ILE 2.7 23.3 + - - +
10G ALA* 3.2 6.0 + - - +
12G PHE* 1.3 69.0 - - - +
14G GLU* 1.4 69.2 + - - +
16G PHE* 3.1 3.8 + - + +
17G SER* 2.8 30.1 + - - -
65G PHE* 3.6 40.9 - - + -
64S ASP* 4.0 20.4 + - - -
66S PRO* 5.0 7.6 - - - +
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Residues in contact with GLU 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA* 3.1 24.1 + - + +
11G GLU* 3.8 6.1 - - - +
13G LYS* 1.4 85.5 - - - +
15G ALA* 1.3 62.1 + - - +
17G SER* 3.4 8.2 + - - -
18G LEU* 3.0 39.6 + - + +
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Residues in contact with ALA 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906A LEU* 3.1 52.8 - - + +
907A LYS* 5.5 4.7 - - - +
909A LEU 3.6 3.8 - - - +
11G GLU* 3.1 18.4 + - + +
12G PHE* 3.0 20.4 - - - +
14G GLU* 1.3 73.1 - - - +
16G PHE* 1.3 58.5 + - - +
18G LEU* 3.2 3.7 + - - -
19G PHE 3.1 16.3 + - - -
38G SER 5.3 0.2 - - - +
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Residues in contact with PHE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906A LEU* 3.6 7.8 - - - +
12G PHE* 2.9 31.7 + + + +
13G LYS* 3.1 5.6 + - + +
15G ALA* 1.3 71.1 - - - +
17G SER* 1.3 58.8 + - - +
19G PHE* 3.0 17.6 + - - +
20G ASP* 3.0 15.9 + - + +
25G GLY* 3.4 23.3 - - - -
27G ILE* 3.6 41.7 - - + -
35G VAL* 4.6 4.0 - - + -
63G ILE* 3.4 18.8 - - + -
64G ASP 4.0 3.6 - - - -
65G PHE* 3.4 54.5 - + + -
68G PHE* 4.6 8.3 - + + -
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Residues in contact with SER 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 2.8 14.5 + - - -
14G GLU* 3.4 17.5 - - - -
16G PHE* 1.3 77.1 - - - +
18G LEU* 1.3 69.4 + - - +
20G ASP* 3.2 25.1 - - - +
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906A LEU 5.4 1.1 - - - +
907A LYS* 5.8 1.3 - - - -
908A LYS 4.6 9.0 - - - +
909A LEU* 2.9 41.4 - - + +
14G GLU* 3.0 34.8 + - + +
15G ALA* 3.2 3.3 + - - +
17G SER* 1.3 88.3 - - - +
19G PHE* 1.4 49.7 + - - +
20G ASP 3.1 1.2 - - - +
21G LYS* 2.6 28.1 + - - -
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Residues in contact with PHE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905A GLU* 5.1 10.1 - - + -
906A LEU* 3.8 33.9 - - + -
909A LEU* 3.1 11.1 + - + -
15G ALA 3.1 5.5 + - - -
16G PHE* 3.0 10.3 + - - +
18G LEU* 1.4 72.0 - - - +
20G ASP* 1.3 59.4 + - - +
21G LYS* 2.6 31.1 + - + +
27G ILE* 3.9 23.3 - - + +
28G THR 5.8 0.7 - - - -
31G GLU* 3.4 34.1 - - + -
34G THR* 3.1 37.9 - - - -
35G VAL* 3.8 14.8 - - + -
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Residues in contact with ASP 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G PHE* 3.0 19.0 + - + +
17G SER* 3.2 19.3 - - - +
18G LEU* 3.1 6.1 - - - +
19G PHE* 1.3 71.7 - - - +
21G LYS* 1.3 73.4 + - - +
22G ASP* 3.6 3.8 + - - +
23G GLY* 2.7 33.1 + - - -
24G ASP 3.2 8.1 + - - -
25G GLY* 2.8 30.8 + - - -
26G THR 3.8 12.9 - - - +
27G ILE* 3.5 14.6 - - + +
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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