Contacts of the helix formed by residues 67 - 81 (chain B) in PDB entry 4BPU
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 THR 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B TYR* 3.9 4.2 - - - +
64B VAL* 3.1 39.0 + - + +
65B LYS 3.5 2.0 + - - +
66B GLY* 1.3 80.4 - - - +
68B GLU* 1.3 64.2 + - - +
69B GLN* 3.7 12.3 + - - +
70B TYR* 3.0 16.6 + - - +
71B GLN* 2.9 21.0 + - - +
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Residues in contact with GLU 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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66B GLY 3.7 1.9 + - - -
67B THR* 1.3 71.2 - - - +
69B GLN* 1.3 57.0 + - + +
71B GLN* 3.2 5.5 + - - +
72B SER* 2.5 45.3 + - - -
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Residues in contact with GLN 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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63B TYR* 3.2 48.1 + - + +
67B THR* 3.9 7.3 + - - +
68B GLU* 1.3 81.2 - - + +
70B TYR* 1.3 57.6 + - - +
72B SER* 4.4 3.8 - - - -
73B LYS* 2.8 38.1 + - - +
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Residues in contact with TYR 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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56B VAL* 5.0 6.2 - - + +
59B LEU* 3.9 36.7 - - + +
60B GLY* 5.1 2.7 - - - -
63B TYR* 3.5 10.4 - - + -
64B VAL* 3.2 32.1 - - - +
65B LYS* 3.9 23.4 - - + +
67B THR* 3.0 13.8 + - - +
69B GLN* 1.3 74.8 - - - +
71B GLN* 1.3 84.2 + - - +
74B LEU* 2.8 62.2 + - + +
126B ASP* 4.5 24.1 + - - +
130B PHE* 4.5 6.1 - + + -
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Residues in contact with GLN 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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65B LYS* 4.4 4.0 - - - +
66B GLY* 3.5 28.1 - - - +
67B THR 2.9 18.3 + - - +
68B GLU* 3.4 4.7 - - - +
70B TYR* 1.3 95.5 - - - +
72B SER* 1.3 56.3 + - - +
75B GLU* 3.1 24.3 - - - +
130B PHE* 3.1 31.7 - - + +
133B SER* 4.0 18.4 + - - +
134B ILE* 3.7 14.7 - - + +
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 2.5 27.3 + - - -
69B GLN* 4.0 3.4 - - - -
71B GLN* 1.3 75.1 - - - +
73B LYS* 1.3 56.2 + - - +
74B LEU 3.3 0.2 - - - -
75B GLU* 3.3 4.0 + - - +
76B SER* 2.7 37.7 + - - -
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.1 19.1 - - + -
63B TYR* 4.1 20.2 - - + +
69B GLN* 2.8 25.5 + - - +
72B SER* 1.3 76.7 - - - +
74B LEU* 1.3 52.3 + - - +
76B SER* 3.4 14.3 + - - -
77B GLU* 2.6 45.9 + - - +
80B LYS* 5.7 4.6 - - - +
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Residues in contact with LEU 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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52B LEU* 4.6 8.3 - - + -
55B SER* 5.6 0.7 - - - -
56B VAL* 4.0 29.8 - - + +
59B LEU* 3.5 21.2 - - + +
70B TYR* 2.8 43.9 + - + +
73B LYS* 1.3 74.7 - - - +
75B GLU* 1.3 58.8 + - - +
77B GLU* 4.3 4.7 - - + -
78B LEU* 2.8 49.2 + - + +
126B ASP 5.6 0.4 - - - +
127B LEU* 4.7 4.9 - - + -
130B PHE* 3.5 37.9 - - + -
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Residues in contact with GLU 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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71B GLN 3.1 23.9 + - - +
72B SER* 3.3 4.8 + - - +
74B LEU* 1.3 78.5 - - - +
76B SER* 1.3 52.6 + - - +
78B LEU* 3.4 9.4 + - - +
79B ARG* 2.8 37.0 + - + +
83B PHE 5.6 1.0 - - - +
130B PHE* 4.2 14.4 - - + -
134B ILE* 4.3 18.8 - - - +
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Residues in contact with SER 76 (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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72B SER* 2.7 23.4 + - - -
73B LYS* 3.4 20.2 + - - +
75B GLU* 1.3 72.8 - - - +
77B GLU* 1.3 53.9 + - - +
79B ARG* 3.1 11.1 + - - +
80B LYS* 2.5 42.1 + - - +
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Residues in contact with GLU 77 (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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52B LEU* 5.1 2.7 - - + -
55B SER* 3.5 34.8 + - - +
59B LEU* 5.6 1.6 - - + -
73B LYS* 2.6 28.9 + - - +
74B LEU* 3.8 10.1 - - + +
76B SER* 1.3 70.8 - - - +
78B LEU* 1.3 60.5 + - - +
80B LYS* 3.1 42.7 + - - +
81B LEU* 2.8 52.7 + - + +
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Residues in contact with LEU 78 (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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52B LEU* 4.0 29.4 - - + -
74B LEU* 2.8 25.5 + - + +
75B GLU* 3.7 11.4 - - - +
77B GLU* 1.3 76.3 - - - +
79B ARG* 1.3 59.2 + - - +
81B LEU* 4.7 1.6 - - - -
82B LYS 3.3 1.6 + - - -
83B PHE* 2.8 65.8 + - + +
127B LEU* 4.0 12.1 - - + -
130B PHE* 3.6 35.2 - - + -
131B ARG* 4.0 19.3 - - + +
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Residues in contact with ARG 79 (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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75B GLU* 2.8 23.6 + - + +
76B SER* 3.1 11.2 + - - +
78B LEU* 1.3 79.1 - - - +
80B LYS* 1.3 62.2 + - - +
82B LYS* 3.2 15.7 + - - +
83B PHE 4.6 2.5 - - - -
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Residues in contact with LYS 80 (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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73B LYS* 5.7 5.0 - - - +
76B SER* 2.5 26.5 + - - +
77B GLU* 3.1 41.7 + - - +
79B ARG* 1.3 74.9 - - - +
81B LEU* 1.3 63.7 + - + +
82B LYS* 3.2 16.0 + - - +
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Residues in contact with LEU 81 (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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48B ASP* 4.0 25.5 - - + +
51B LYS* 4.2 19.7 - - + -
52B LEU* 3.4 41.7 - - + +
55B SER* 4.7 0.2 - - - +
77B GLU* 2.8 41.2 + - + +
78B LEU 4.5 0.4 - - - +
80B LYS* 1.3 82.7 - - + +
82B LYS* 1.3 63.3 + - - +
83B PHE* 3.2 19.8 + - + -
98B ARG* 2.5 30.0 + - - -
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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