Contacts of the helix formed by residues 54 - 66 (chain F) in PDB entry 2BS3
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 GLY 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F THR 3.7 3.3 - - - +
51F ILE 3.3 13.4 + - - -
52F LEU 3.3 1.2 - - - -
53F LEU* 1.3 80.7 - - - +
55F ASP* 1.3 68.9 + - - -
56F ASN* 3.2 4.0 - - - -
57F VAL* 3.0 19.0 + - - +
58F MET* 3.3 6.6 + - - +
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Residues in contact with ASP 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ILE* 3.9 7.1 - - - +
54F GLY* 1.3 73.1 - - - +
56F ASN* 1.3 62.7 + - - +
58F MET* 3.6 0.5 + - - +
59F LEU* 2.9 33.8 + - - +
156F PRO* 3.5 30.1 - - + +
157F VAL* 4.8 5.7 - - - +
234F LYS* 2.9 39.0 + - - +
252F ARG* 5.7 4.7 + - - +
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Residues in contact with ASN 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLY* 3.2 1.6 - - - -
55F ASP* 1.3 80.1 - - - +
57F VAL* 1.3 59.4 + - + +
59F LEU* 3.7 14.8 - - - +
60F TRP* 3.0 29.1 + - - +
252F ARG* 5.5 1.0 + - - -
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Residues in contact with VAL 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F THR* 4.0 10.1 - - + +
53F LEU* 3.0 60.1 - - + +
54F GLY* 3.0 7.1 + - - +
56F ASN* 1.3 76.6 - - + +
58F MET* 1.3 67.1 + - - +
60F TRP* 3.0 12.5 + - + +
61F VAL* 3.0 29.6 + - + +
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Residues in contact with MET 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F PHE 5.6 2.7 - - - +
48F VAL* 6.0 0.9 - - - -
50F THR* 2.9 29.6 - - - +
51F ILE* 4.0 16.8 - - + +
54F GLY 3.3 3.2 + - - +
55F ASP 4.0 1.3 - - - +
57F VAL* 1.3 80.5 - - - +
59F LEU* 1.3 54.4 + - - +
61F VAL* 3.6 2.5 - - - +
62F THR* 2.6 61.7 + - - +
154F ILE* 4.3 9.4 - - + -
155F GLY* 3.8 22.0 - - - +
156F PRO* 3.5 36.3 - - + -
159F SER* 4.5 2.0 - - - +
231F TYR* 3.5 26.7 - - - +
1256F HEM 5.3 3.4 - - + -
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ASP 2.9 21.3 + - - +
56F ASN* 3.7 15.9 - - - +
58F MET* 1.3 81.2 - - - +
60F TRP* 1.3 60.8 + - - +
62F THR* 3.4 8.7 + - + -
63F LYS* 3.1 44.1 + - + +
154F ILE 5.7 0.9 - - - +
155F GLY* 5.2 1.1 - - - -
156F PRO* 4.0 15.7 - - + -
249F ASP* 4.2 17.3 - - + +
252F ARG* 2.9 41.1 - - - +
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Residues in contact with TRP 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F ASN 3.0 20.1 + - - +
57F VAL* 3.0 8.9 + - + +
59F LEU* 1.3 74.5 - - - +
61F VAL* 1.3 80.9 + - + +
63F LYS* 3.4 13.5 + - + +
64F LYS* 3.1 71.0 + - + +
68F ASP* 6.0 1.8 - - - -
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Residues in contact with VAL 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F PHE* 3.3 43.5 - - + +
50F THR* 4.0 21.1 - - + +
57F VAL* 3.0 22.8 + - + +
58F MET* 3.6 7.0 - - - +
60F TRP* 1.3 90.9 - - + +
62F THR* 1.3 64.9 + - - +
64F LYS* 3.1 22.4 + - + +
65F PHE* 3.4 17.4 + - + -
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Residues in contact with THR 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F MET* 2.6 48.1 + - - +
59F LEU* 3.5 11.1 - - + -
61F VAL* 1.3 73.5 - - - +
63F LYS* 1.3 63.3 + - + +
64F LYS 3.4 0.5 + - - -
65F PHE* 3.4 14.6 + - - +
66F GLU* 3.3 30.4 + - + +
79F VAL* 6.1 2.0 - - + -
154F ILE* 3.9 36.5 - - + +
155F GLY* 5.4 1.1 - - - -
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Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F LEU* 3.1 35.5 + - + +
60F TRP* 3.7 12.1 - - + +
61F VAL 3.3 0.2 - - - -
62F THR* 1.3 75.6 - - + +
64F LYS* 1.3 62.4 + - - +
65F PHE 3.4 0.2 - - - -
66F GLU* 3.3 22.8 + - - +
68F ASP* 3.0 48.0 + - + +
73F GLY* 4.5 14.8 - - - +
74F GLY* 4.8 0.9 - - - -
253F THR* 3.8 28.6 + - - +
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Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F TRP* 3.1 69.9 + - + +
61F VAL* 3.1 13.4 + - + +
63F LYS* 1.3 73.4 - - - +
65F PHE* 1.3 61.8 + - + +
66F GLU 3.0 4.7 - - - -
67F LEU* 2.9 24.3 + - - +
68F ASP* 3.8 10.9 + - + -
69F PHE* 4.2 26.3 - - + -
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Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F PHE* 3.3 55.6 - + + -
61F VAL* 3.4 12.6 + - + -
62F THR* 3.8 10.3 - - - +
63F LYS 3.4 0.4 - - - -
64F LYS* 1.3 82.5 - - + +
66F GLU* 1.3 58.1 + - - +
67F LEU* 3.1 5.0 + - - +
78F VAL* 3.2 23.7 - - - +
79F VAL* 4.5 15.5 - - + +
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F THR* 3.3 26.7 - - + +
63F LYS* 3.3 17.3 + - - +
64F LYS 3.0 1.2 - - - -
65F PHE* 1.3 78.1 - - - +
67F LEU* 1.3 72.1 + - - +
68F ASP 3.5 1.1 - - - -
71F PHE* 4.4 0.7 - - - -
73F GLY 4.2 11.3 - - - +
74F GLY* 3.3 2.5 - - - +
75F LYS 2.9 39.9 + - - +
76F PRO* 3.0 38.0 - - - +
78F VAL* 3.9 4.6 - - - +
79F VAL* 4.0 16.4 - - + +
151F PRO 4.1 9.9 - - - +
152F GLN* 4.9 0.9 - - - -
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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