Contacts of the helix formed by residues 65 - 75 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLU* 3.4 30.1 - - + -
12B PHE 3.7 17.9 - - - -
13B LYS* 3.3 48.7 - - + -
16B PHE* 3.4 44.9 - + + -
64B ASP* 1.3 79.7 + - - +
66B PRO* 1.3 67.2 - - + +
68B PHE* 3.2 16.0 + + - +
69B LEU* 2.8 51.1 + - + +
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Residues in contact with PRO 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASP* 3.4 22.7 - - + +
65B PHE* 1.3 98.2 - - + +
67B GLU* 1.3 59.4 + - - +
69B LEU* 3.5 14.2 + - + +
70B THR* 3.1 28.8 + - + +
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 5.2 3.3 - - - +
55B VAL* 4.0 13.7 - - + +
57B ALA* 4.5 5.3 - - + +
60B ASN* 5.3 9.2 - - - +
63B ILE* 3.2 33.6 - - + +
64B ASP* 3.2 21.4 + - + +
66B PRO* 1.3 75.9 - - - +
68B PHE* 1.3 77.3 + - - +
70B THR* 2.7 26.6 + - - +
71B MET* 3.1 37.7 + - + +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PHE* 3.6 24.9 - + + -
32B LEU* 3.7 16.8 - - + -
35B VAL* 3.5 42.2 - - + -
36B MET* 4.1 23.3 - - + -
39B LEU* 4.1 21.5 - - + -
41B GLN* 5.8 0.2 - - - -
63B ILE* 4.5 7.6 - - + -
64B ASP 3.2 9.5 + - - +
65B PHE* 3.5 23.1 - + - +
67B GLU* 1.3 84.4 + - - +
69B LEU* 1.4 60.7 + - - +
71B MET* 3.5 4.6 + - + +
72B MET* 3.0 45.7 + - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU* 3.3 47.1 - - + +
65B PHE* 2.8 46.1 + - + +
66B PRO* 3.5 17.3 - - + +
68B PHE* 1.4 75.0 - - - +
70B THR* 1.3 63.6 + - + +
72B MET* 3.5 10.4 + - + +
73B ALA* 3.1 24.8 + - - +
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PRO* 3.1 13.2 + - + +
67B GLU* 2.7 22.9 + - - +
69B LEU* 1.3 77.8 - - + +
71B MET* 1.3 71.3 + - - +
73B ALA* 3.4 6.4 + - - +
74B ARG* 3.0 30.8 + - - +
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 5.7 7.2 - - + -
36B MET* 5.3 3.8 - - + -
51B MET* 3.4 38.7 - - + +
52B ILE* 6.0 0.2 - - - -
55B VAL* 3.7 37.7 - - + -
67B GLU* 3.1 41.2 + - + +
68B PHE* 3.8 8.5 - - + +
69B LEU 3.4 0.2 - - - -
70B THR* 1.3 94.4 + - - +
72B MET* 1.3 64.9 + - - +
74B ARG* 3.4 29.4 + - - +
75B LYS* 3.1 20.1 + - - +
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Residues in contact with MET 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA 4.1 11.9 - - - +
11B GLU* 3.4 48.2 - - + -
36B MET* 5.6 2.0 - - + -
39B LEU* 4.0 7.0 - - + -
41B GLN* 5.0 14.3 + - - +
51B MET* 4.2 8.2 - - + +
68B PHE* 3.0 53.1 + - + +
69B LEU* 3.6 17.0 - - + +
71B MET* 1.3 75.5 - - - +
73B ALA* 1.3 60.9 + - + +
75B LYS* 3.5 1.0 - - - +
76B MET* 2.9 33.5 + - - +
79B THR* 4.4 3.6 + - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU 3.1 17.1 + - - +
70B THR* 3.7 6.5 - - - +
71B MET 3.4 0.2 - - - -
72B MET* 1.3 77.6 - - + +
74B ARG* 1.3 63.3 + - - +
76B MET* 3.4 37.3 - - + +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B MET 5.3 0.2 - - - -
54B GLU* 2.7 77.1 + - - +
55B VAL* 3.3 24.5 - - - +
70B THR 3.0 16.4 + - - +
71B MET* 3.6 27.4 - - - +
73B ALA* 1.3 76.1 - - - +
75B LYS* 1.3 69.9 + - + +
76B MET* 3.5 1.6 + - - +
77B LYS* 6.2 0.2 - - - +
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU* 5.1 4.2 - - - +
50B ASP* 5.2 6.9 - - - +
51B MET* 3.7 42.0 - - + +
54B GLU* 3.1 27.7 + - - +
71B MET 3.1 16.9 + - - +
72B MET 3.5 2.5 - - - +
74B ARG* 1.3 92.8 - - + +
76B MET* 1.4 63.4 + - - +
77B LYS* 3.2 4.6 + - - -
78B ASP* 2.7 34.8 + - - +
79B THR* 3.1 22.9 + - + -
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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