Contacts of the helix formed by residues 65 - 76 (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 PHE 65 (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* 4.1 12.6 - - + -
12G PHE* 3.5 35.4 - + - -
13G LYS* 3.6 57.0 - - + -
16G PHE* 3.4 43.9 - + + -
64G ASP* 1.3 79.6 + - - +
66G PRO* 1.3 68.8 - - + +
68G PHE* 3.3 4.9 + - - +
69G LEU* 2.9 48.1 + - + +
64S ASP* 5.8 0.4 - - - -
66S PRO* 5.1 6.3 - - + -
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Residues in contact with PRO 66 (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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64G ASP* 3.2 21.8 - - - +
65G PHE* 1.3 95.1 - - + +
67G GLU* 1.4 55.5 + - - -
69G LEU* 3.6 8.4 - - + +
70G THR* 2.7 35.9 + - - -
66S PRO* 3.2 24.2 - - + +
67S GLU* 3.8 19.5 - - + -
70S THR* 3.0 32.1 - - + +
71S MET* 5.4 0.7 - - + -
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Residues in contact with GLU 67 (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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32G LEU* 5.1 1.2 - - - +
56G ASP* 4.6 16.8 - - - +
57G ALA* 3.3 24.1 - - - +
60G ASN* 5.6 2.5 - - - +
63G ILE* 3.2 36.8 - - + +
64G ASP* 3.3 16.6 + - + +
66G PRO* 1.4 71.9 - - - +
68G PHE* 1.3 80.4 + - - +
70G THR* 3.1 4.3 + - - -
71G MET* 2.8 63.8 + - + +
951M MET* 5.0 0.2 - - - +
70S THR* 3.2 22.0 + - + +
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Residues in contact with PHE 68 (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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12G PHE* 3.2 36.8 - + - -
16G PHE* 4.6 6.3 - + + -
32G LEU* 3.7 16.8 - - + -
35G VAL* 3.2 37.9 - - + -
36G MET* 3.4 44.9 - - + -
39G LEU* 5.0 8.1 - - + -
63G ILE* 4.4 6.3 - - + -
64G ASP 3.1 10.5 + - - +
65G PHE* 3.4 11.4 - - - +
67G GLU* 1.3 88.1 + - - +
69G LEU* 1.3 57.2 + - - +
71G MET* 3.3 5.5 + - + +
72G MET* 2.9 35.3 + - + +
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Residues in contact with LEU 69 (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* 4.4 23.3 - - + -
12G PHE* 5.7 6.1 - - + -
65G PHE* 2.9 40.1 + - + +
66G PRO* 3.3 8.9 + - + +
68G PHE* 1.3 77.4 - - - +
70G THR* 1.3 56.9 + - - +
72G MET* 3.3 27.1 + - + +
73G ALA* 3.0 26.3 + - + +
56S ASP* 3.3 39.7 - - - +
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Residues in contact with THR 70 (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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66G PRO 2.7 18.9 + - - -
67G GLU* 3.2 10.8 - - - -
69G LEU* 1.3 75.2 - - - +
71G MET* 1.3 61.2 + - + +
73G ALA* 3.5 7.0 + - + +
74G ARG* 3.1 55.3 + - + +
54S GLU* 3.1 38.5 + - + +
56S ASP* 5.8 5.8 - - - +
70S THR* 4.4 7.4 - - + +
71S MET* 5.0 1.9 - - - +
74S ARG* 5.3 3.6 - - - -
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Residues in contact with MET 71 (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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32G LEU* 5.4 2.0 - - + -
36G MET* 4.9 8.5 - - + -
54G GLU* 3.9 15.9 - - + +
56G ASP* 5.5 4.5 - - + +
57G ALA* 5.2 1.3 - - + -
67G GLU* 2.8 69.6 + - + +
68G PHE* 3.3 10.3 - - + +
70G THR* 1.3 73.7 - - + +
72G MET* 1.3 64.7 + - - +
74G ARG* 3.2 36.4 + - - +
75G LYS* 3.3 18.8 + - - +
951M MET* 3.4 48.5 - - + +
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Residues in contact with MET 72 (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* 6.4 1.1 - - + -
12G PHE* 6.0 3.6 - - + -
36G MET* 5.3 6.8 - - + +
39G LEU* 3.5 31.9 - - + -
41G GLN* 4.9 10.1 - - - +
51G MET* 6.2 0.2 - - - -
68G PHE* 2.9 23.1 + - + +
69G LEU* 3.5 34.1 - - + +
71G MET* 1.3 74.7 - - - +
73G ALA* 1.3 55.5 + - + +
75G LYS* 5.1 2.0 - - - -
76G MET* 2.8 49.0 + - + +
79G THR* 4.6 10.7 + - + -
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Residues in contact with ALA 73 (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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69G LEU* 3.0 14.5 + - + +
70G THR* 3.6 13.0 - - + +
71G MET 3.4 0.4 - - - -
72G MET* 1.3 78.5 - - + +
74G ARG* 1.3 64.1 + - + +
76G MET* 3.6 21.2 - - - +
55S VAL* 3.8 29.1 - - + +
56S ASP* 4.7 9.0 - - + +
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Residues in contact with ARG 74 (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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54G GLU* 2.8 28.6 + - - -
70G THR* 3.1 43.7 + - + +
71G MET* 3.2 36.4 - - - +
72G MET 3.4 0.4 - - - -
73G ALA* 1.3 79.0 - - + +
75G LYS* 1.3 63.3 + - - +
76G MET* 5.2 0.2 - - - +
77G LYS* 4.1 6.6 - - - +
951M MET* 3.7 13.6 - - - +
952M ASN* 3.4 28.4 - - + +
953M ASN* 4.0 33.9 + - + +
54S GLU* 5.0 2.4 + - - -
74S ARG* 6.2 0.6 - - - +
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Residues in contact with LYS 75 (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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47G GLU* 3.2 42.7 + - - +
50G ASP* 5.9 3.8 - - - +
51G MET* 3.8 26.2 - - + +
71G MET 3.3 10.9 + - - +
72G MET* 4.3 0.9 - - - +
74G ARG* 1.3 78.1 - - - +
76G MET* 1.4 51.9 + - - +
77G LYS* 2.9 6.7 + - - -
78G ASP* 2.7 66.8 + - - +
79G THR* 3.3 11.9 - - - +
951M MET* 3.8 8.5 - - - -
952M ASN* 3.4 42.5 - - + +
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Residues in contact with MET 76 (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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72G MET* 2.8 32.4 + - + +
73G ALA* 3.6 18.4 - - - +
75G LYS* 1.4 66.1 - - - +
77G LYS* 1.4 61.0 + - + +
79G THR* 2.9 9.7 + - - -
80G ASP* 2.8 58.4 + - - +
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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