Contacts of the helix formed by residues 65 - 75 (chain S) 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 65 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9S ILE* 4.1 13.9 - - + -
12S PHE* 3.5 33.0 - + - -
13S LYS* 3.6 41.1 - - + -
16S PHE* 3.4 44.4 - + + -
64S ASP* 1.3 77.0 + - - +
66S PRO* 1.4 76.2 - - + +
68S PHE* 3.5 3.9 + - - +
69S LEU* 3.0 41.9 + - + +
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Residues in contact with PRO 66 (chain S).
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* 5.0 11.2 - - - +
64G ASP* 3.9 13.0 - - - +
65G PHE* 5.1 5.4 - - + -
66G PRO* 3.2 29.8 - - + +
64S ASP* 3.4 22.0 - - - +
65S PHE* 1.4 100.1 - - + +
67S GLU* 1.4 62.1 + - - +
69S LEU* 3.0 8.6 + - + +
70S THR 3.0 19.6 + - - -
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Residues in contact with GLU 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G PRO* 3.8 14.3 - - + +
32S LEU* 5.9 0.3 - - - +
56S ASP* 6.3 2.5 - - + -
57S ALA* 3.3 25.9 - - + +
60S ASN* 5.7 6.1 - - - +
63S ILE* 3.2 41.0 - - + +
64S ASP* 3.2 22.0 + - + +
66S PRO* 1.4 78.1 - - - +
68S PHE* 1.3 75.8 + - - +
70S THR* 3.2 2.3 + - - -
71S MET* 3.0 53.6 + - + +
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Residues in contact with PHE 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S PHE* 3.2 41.1 - + - -
16S PHE* 4.6 8.1 - + + -
32S LEU* 3.7 22.9 - - + -
35S VAL* 3.4 29.6 - - + -
36S MET* 3.6 40.8 - - + -
39S LEU* 5.0 3.6 - - + -
63S ILE* 4.4 4.9 - - + -
64S ASP 3.2 9.5 + - - +
65S PHE* 3.7 10.5 - - - +
67S GLU* 1.3 87.3 + - - +
69S LEU* 1.3 58.5 + - - +
71S MET* 3.1 6.1 + - + +
72S MET* 3.0 43.0 + - + +
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Residues in contact with LEU 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G THR* 5.8 4.5 - - + -
64G ASP* 3.8 20.9 - - + +
9S ILE* 4.5 22.2 - - + -
12S PHE* 5.8 5.2 - - + -
65S PHE* 3.0 33.6 + - + +
66S PRO* 3.0 12.7 + - + +
68S PHE* 1.3 78.0 - - - +
70S THR* 1.3 58.1 + - - +
72S MET* 3.4 25.0 - - + +
73S ALA* 3.0 27.5 + - + +
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Residues in contact with THR 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G ASP* 5.3 3.1 - - - +
64G ASP* 4.0 6.9 + - - +
66G PRO* 3.0 32.0 - - - +
67G GLU* 3.2 30.9 + - + +
70G THR* 4.4 5.4 - - - +
66S PRO 3.0 5.3 + - - -
67S GLU 3.4 8.1 - - - -
69S LEU* 1.3 75.8 - - - +
71S MET* 1.3 77.4 + - + +
73S ALA* 3.1 8.4 + - + +
74S ARG* 3.0 31.3 + - + +
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Residues in contact with MET 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G PRO* 5.4 1.1 - - + -
70G THR* 5.0 2.5 - - - +
32S LEU* 5.1 10.1 - - + -
36S MET* 5.1 4.7 - - + -
51S MET* 3.5 29.9 - - + +
54S GLU* 3.1 20.2 - - - +
57S ALA* 4.4 7.9 - - + -
67S GLU* 3.0 66.6 + - + +
68S PHE* 3.1 8.9 + - + +
70S THR* 1.3 87.4 - - + +
72S MET* 1.3 61.6 + - - +
74S ARG* 3.2 31.5 - - - +
75S LYS* 3.3 17.3 + - - +
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Residues in contact with MET 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S ILE* 6.4 2.2 - - + -
12S PHE* 5.6 4.7 - - + -
36S MET* 5.9 1.3 - - - +
39S LEU* 3.5 31.9 - - + -
41S GLN* 5.1 9.2 - - - +
51S MET* 5.2 2.2 - - - -
68S PHE* 3.0 26.7 + - + +
69S LEU* 3.4 31.6 - - + +
71S MET* 1.3 74.3 - - - +
73S ALA* 1.4 61.0 + - + +
75S LYS 3.6 1.0 - - - -
76S MET* 3.0 39.5 + - + +
79S THR* 4.9 11.1 + - + -
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Residues in contact with ALA 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G ASP* 3.7 20.2 - - - +
60G ASN* 5.6 5.6 - - - +
69S LEU* 3.0 18.2 + - + +
70S THR* 3.1 11.6 + - + +
72S MET* 1.4 76.0 - - + +
74S ARG* 1.3 62.9 + - - +
76S MET* 3.2 24.1 + - - +
77S LYS* 6.0 0.2 - - - +
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Residues in contact with ARG 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G VAL 5.7 0.5 - - - +
56G ASP* 3.3 30.0 + - + +
70G THR* 5.3 3.1 - - - -
74G ARG* 6.2 0.7 - - - +
51S MET* 2.7 36.5 + - - +
54S GLU* 2.7 46.3 + - - +
70S THR* 3.0 24.1 + - + +
71S MET* 3.2 35.2 - - - +
73S ALA* 1.3 75.0 - - - +
75S LYS* 1.3 79.9 + - - +
76S MET 3.6 0.4 - - - -
77S LYS* 5.7 5.8 - - - +
78S ASP* 5.3 0.7 - - - +
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Residues in contact with LYS 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47S GLU* 4.6 18.1 + - - +
50S ASP* 5.1 8.5 + - - +
51S MET* 3.8 35.3 - - + +
71S MET 3.3 13.7 + - - +
72S MET 3.6 1.6 - - - -
73S ALA 3.3 0.2 - - - -
74S ARG* 1.3 103.7 - - - +
76S MET* 1.4 61.0 + - - +
77S LYS* 3.3 3.4 + - - -
78S ASP* 2.6 46.0 + - - +
79S THR* 2.7 34.5 + - - +
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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