Contacts of the helix formed by residues 43 - 55 (chain B) in PDB entry 2FBW
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 MET 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A ILE* 3.6 26.5 - - + +
347A PHE* 3.8 21.1 - - + -
42B PRO* 1.3 89.7 - - + +
44B VAL* 1.3 67.1 + - - +
45B LEU* 3.3 1.8 - - + +
46B ASP* 3.0 32.4 + - - +
47B ALA 3.3 4.3 + - - -
84B ALA 3.7 6.5 - - - +
85B CYS* 3.2 22.0 - - - +
86B THR* 3.6 21.3 - - - +
87B LYS 3.4 1.3 - - - -
88B LYS* 3.5 45.5 - - - +
89B ILE* 3.5 7.3 - - - +
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Residues in contact with VAL 44 (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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14B PHE* 4.7 11.7 - - + -
43B MET* 1.3 72.0 - - - +
45B LEU* 1.3 64.2 + - - +
47B ALA* 3.0 6.5 + - - +
48B LEU* 2.8 23.8 + - + +
77B ILE* 3.8 26.2 - - + -
84B ALA* 3.4 12.7 + - + +
87B LYS* 2.9 35.0 + - + +
88B LYS 4.3 4.3 - - - +
89B ILE* 3.7 18.1 - - + +
97B THR* 5.3 1.6 - - + -
99B ILE* 3.8 28.7 - - + -
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Residues in contact with LEU 45 (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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227A HIS* 4.9 7.2 - - + +
43B MET* 3.3 1.1 - - + -
44B VAL* 1.3 75.3 - - - +
46B ASP* 1.3 64.5 + - - +
48B LEU* 3.1 10.1 + - + +
49B ILE* 2.8 39.9 + - + +
61B PHE* 3.9 21.5 - - + -
63B ARG* 3.8 32.3 - - + -
64B SER 5.6 0.7 - - - +
66B ARG* 4.9 8.1 - - - +
73B CYS* 4.6 7.0 - - + -
84B ALA* 3.0 15.8 + - + -
85B CYS* 3.5 42.0 - - + +
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Residues in contact with ASP 46 (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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40B CYS* 3.8 3.3 - - - -
41B GLY* 3.1 25.2 - - - +
42B PRO* 3.1 16.3 - - - +
43B MET* 3.0 39.1 + - - +
45B LEU* 1.3 80.4 - - - +
47B ALA* 1.3 54.7 + - - +
49B ILE* 3.3 9.5 + - - +
50B LYS* 2.9 30.1 + - - +
66B ARG* 5.5 5.0 + - - -
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Residues in contact with ALA 47 (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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14B PHE* 3.8 38.1 - - + -
35B VAL* 4.6 5.8 - - + -
40B CYS* 3.5 12.7 - - - -
43B MET 3.3 2.4 + - - -
44B VAL* 3.0 8.8 + - + +
46B ASP* 1.3 78.9 - - - +
48B LEU* 1.3 60.2 + - + +
50B LYS* 3.3 3.0 + - - +
51B ILE* 2.9 37.0 + - + +
89B ILE* 3.9 12.1 - - + -
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Residues in contact with LEU 48 (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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14B PHE* 6.2 0.7 - - + -
16B ILE* 3.8 29.4 - - + -
44B VAL* 2.8 22.2 + - + +
45B LEU* 3.5 13.2 - - + +
47B ALA* 1.3 73.9 - - + +
49B ILE* 1.3 62.1 + - - +
51B ILE* 3.3 7.6 + - + +
52B LYS* 3.0 19.1 + - - +
59B LEU* 4.2 10.4 - - + +
61B PHE* 3.7 29.8 - - + -
75B MET* 3.8 36.6 - - + -
84B ALA* 4.2 14.1 - - + -
99B ILE* 4.0 12.3 - - + -
111B LEU* 4.5 8.5 - - + -
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Residues in contact with ILE 49 (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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227A HIS* 3.6 39.7 - - + +
45B LEU* 2.8 37.5 + - + +
46B ASP* 3.9 7.4 - - - +
48B LEU* 1.3 72.7 - - - +
50B LYS* 1.3 59.1 + - - +
52B LYS* 3.4 3.5 + - + +
53B ASN* 2.8 50.1 + - - +
61B PHE* 4.0 22.4 - - + -
63B ARG* 4.8 6.3 - - + +
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Residues in contact with LYS 50 (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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35B VAL* 4.0 23.1 - - + +
36B ASP* 4.1 11.2 - - - +
39B LYS* 3.1 42.4 + - - +
40B CYS* 3.8 14.1 - - + -
46B ASP 2.9 17.2 + - - +
47B ALA* 3.7 5.8 - - - +
48B LEU 3.3 0.2 - - - -
49B ILE* 1.3 78.2 - - - +
51B ILE* 1.3 57.3 + - - +
53B ASN* 3.3 4.4 + - - +
54B GLU* 2.8 76.7 + - + +
55B LEU* 6.4 1.1 - - + -
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Residues in contact with ILE 51 (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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14B PHE* 4.8 8.1 - - + -
16B ILE* 4.1 18.2 - - + -
33B TYR* 3.6 52.7 - - + -
35B VAL* 3.6 24.5 - - + -
47B ALA* 2.9 25.6 + - + +
48B LEU* 3.3 7.6 + - + +
50B LYS* 1.3 75.3 - - - +
52B LYS* 1.3 57.8 + - - +
55B LEU* 2.7 39.8 + - + -
56B ASP* 2.9 13.3 + - + +
59B LEU* 3.8 15.7 - - + -
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Residues in contact with LYS 52 (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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464A ARG* 3.5 6.4 + - - -
517A THR* 2.6 35.7 + - - -
518A ASP* 3.8 5.2 - - - +
521A GLU* 3.5 33.9 - - - +
48B LEU 3.0 17.0 + - - +
49B ILE* 3.8 3.6 - - - +
51B ILE* 1.3 78.4 - - - +
53B ASN* 1.3 66.7 + - - +
54B GLU 3.4 0.2 + - - -
56B ASP 3.4 9.9 - - - +
57B SER* 2.8 52.7 + - - -
58B THR 4.3 0.2 - - - -
59B LEU* 2.6 28.4 + - + +
60B THR* 4.3 1.8 + - - +
61B PHE* 4.3 20.6 - - + -
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Residues in contact with ASN 53 (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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464A ARG* 3.4 11.5 + - - -
466A SER* 2.7 32.5 + - - -
469A ARG* 2.9 32.2 + - - +
521A GLU* 4.5 6.8 - - - +
49B ILE* 2.8 42.7 + - - +
50B LYS* 3.9 4.6 - - - +
52B LYS* 1.3 79.3 - - - +
54B GLU* 1.3 68.5 + - + +
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Residues in contact with GLU 54 (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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464A ARG* 3.8 16.7 + - - +
50B LYS* 2.8 56.5 + - + +
53B ASN* 1.3 90.7 - - + +
55B LEU* 1.3 71.3 + - + +
56B ASP 4.0 0.2 - - - -
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Residues in contact with LEU 55 (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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464A ARG* 4.9 3.8 - - - -
33B TYR* 4.4 17.4 - - + -
34B GLU 3.5 26.5 - - - +
35B VAL* 4.7 1.8 - - + -
50B LYS* 6.4 1.1 - - + -
51B ILE* 2.7 43.4 + - + +
54B GLU* 1.3 86.4 - - + +
56B ASP* 1.3 60.9 + - - +
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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