Contacts of the helix formed by residues 71 - 87 (chain B) in PDB entry 2BWJ
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 PRO 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.7 20.6 - - + -
69B LEU* 3.4 17.7 - - + +
70B VAL* 1.3 90.0 - - + +
72B SER* 1.3 66.0 + - - +
73B GLY* 3.1 5.6 - - - +
74B ILE* 3.1 32.4 + - + +
75B VAL* 3.4 9.9 + - - +
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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
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69B LEU* 5.8 0.4 - - - +
70B VAL 3.4 2.0 + - - -
71B PRO* 1.3 72.8 - - - +
73B GLY* 1.3 56.4 + - - +
75B VAL* 3.3 4.6 + - - +
76B LEU* 2.9 30.1 + - - +
98B TYR* 5.7 0.2 + - - -
100B ARG* 3.4 20.4 + - - +
101B GLU* 3.5 11.6 + - - -
104B GLN* 3.6 26.8 + - - +
107B GLU* 3.4 19.5 - - - +
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Residues in contact with GLY 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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71B PRO* 3.1 4.7 - - - +
72B SER* 1.3 76.3 - - - +
74B ILE* 1.3 60.8 + - - +
76B LEU* 3.8 7.7 - - - +
77B GLU* 3.1 29.2 + - - +
107B GLU* 4.1 12.6 + - - -
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Residues in contact with ILE 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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151A LYS* 6.2 0.7 - - + -
56B ARG* 4.4 14.6 - - + -
59B LEU* 3.9 31.0 - - + -
60B ILE* 3.6 33.7 - - + -
63B ILE* 4.6 4.0 - - + -
70B VAL* 4.2 8.5 - - + -
71B PRO* 3.1 38.4 + - + +
73B GLY* 1.3 72.6 - - - +
75B VAL* 1.3 69.2 + - - +
77B GLU* 3.1 15.9 + - - +
78B LEU* 3.0 24.8 + - + +
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Residues in contact with VAL 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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66A ARG 4.8 3.8 - - - +
42B THR* 3.5 33.0 - - + -
45B LEU* 5.1 0.8 - - + +
46B LEU* 5.0 13.0 - - + -
70B VAL* 4.0 14.8 - - + -
71B PRO 3.4 11.8 + - - +
72B SER 3.3 7.1 + - - +
74B ILE* 1.3 77.1 - - - +
76B LEU* 1.3 57.5 + - - +
78B LEU* 3.1 13.2 + - + +
79B LEU* 3.0 26.6 + - + +
98B TYR* 4.3 6.3 - - + -
100B ARG* 3.7 21.1 - - - +
104B GLN* 3.8 17.0 - - - +
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Residues in contact with LEU 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 2.9 16.8 + - - +
73B GLY* 3.8 6.7 - - - +
75B VAL* 1.3 75.3 - - - +
77B GLU* 1.3 55.3 + - - +
79B LEU* 3.3 6.5 + - + +
80B LYS* 2.8 37.5 + - + +
98B TYR* 4.0 8.7 + - - +
104B GLN* 5.4 0.4 - - + +
107B GLU* 3.9 29.2 - - + +
108B PHE* 3.8 30.5 - - + +
111B ARG* 3.9 26.2 - - + -
112B ILE* 3.7 26.2 - - + -
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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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56B ARG* 3.2 38.1 + - - +
73B GLY 3.1 13.0 + - - +
74B ILE* 3.3 21.1 - - - +
76B LEU* 1.3 74.3 - - - +
78B LEU* 1.3 63.4 + - - +
80B LYS* 3.5 5.9 + - - +
81B GLU* 3.0 36.6 + - + +
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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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45B LEU* 3.9 41.2 - - + +
46B LEU* 3.9 26.2 - - + +
49B GLU* 3.7 25.4 - - + +
56B ARG* 3.4 35.9 - - - +
60B ILE* 4.4 4.7 - - + -
74B ILE* 3.0 16.6 + - + +
75B VAL* 3.1 11.2 + - + +
77B GLU* 1.3 76.8 - - - +
79B LEU* 1.3 59.9 + - - +
81B GLU* 3.6 6.4 + - - +
82B ALA* 3.2 22.9 + - - +
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Residues in contact with LEU 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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40B LEU* 4.2 17.9 - - + -
41B SER 5.9 0.2 - - - -
42B THR* 4.8 2.5 - - + -
45B LEU* 3.7 23.3 - - + -
75B VAL* 3.0 19.8 + - + +
76B LEU* 3.5 10.3 - - - +
78B LEU* 1.3 74.3 - - - +
80B LYS* 1.3 60.5 + - - +
82B ALA* 3.1 2.9 + - - +
83B MET* 2.8 39.1 + - - +
95B ILE* 4.2 28.0 - - + -
98B TYR* 3.6 46.2 - - + +
108B PHE* 4.2 7.4 - - + -
112B ILE* 4.4 7.9 - - + -
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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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4B PHE* 5.0 1.8 - - - +
5B MET* 4.7 13.7 - - - +
8B LEU* 3.2 28.9 - - + +
76B LEU* 2.8 23.2 + - + +
77B GLU* 3.9 6.7 - - - +
79B LEU* 1.3 73.1 - - - +
81B GLU* 1.3 54.8 + - + +
83B MET* 3.2 4.6 + - - +
84B VAL* 2.7 49.8 + - + +
111B ARG* 4.5 13.8 + - + +
112B ILE* 4.0 22.6 - - + +
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Residues in contact with GLU 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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56B ARG* 3.0 39.9 + - - -
77B GLU* 3.0 27.4 + - + +
78B LEU* 3.8 8.5 - - - +
80B LYS* 1.3 78.2 - - + +
82B ALA* 1.3 56.0 + - - +
84B VAL* 3.9 6.1 - - - +
85B ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 82 (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 LEU* 4.1 20.9 - - + -
45B LEU* 3.6 22.7 - - + -
48B GLU* 5.7 0.9 - - - +
78B LEU 3.2 17.4 + - - +
79B LEU 3.1 5.2 + - - +
81B GLU* 1.3 77.1 - - - +
83B MET* 1.3 62.1 + - - +
85B ALA* 3.4 6.5 + - - +
86B SER* 3.0 29.7 + - - -
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Residues in contact with MET 83 (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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8B LEU* 3.6 24.9 - - + +
13B ILE* 4.1 17.5 - - + -
40B LEU* 3.7 18.8 - - + -
79B LEU* 2.8 22.3 + - - +
80B LYS* 3.6 3.1 - - - +
82B ALA* 1.3 74.7 - - - +
84B VAL* 1.3 64.4 + - - +
86B SER 3.1 1.4 + - - -
87B LEU* 3.1 22.5 + - - +
93B PHE* 3.4 45.0 - - + -
95B ILE* 4.4 8.3 - - + -
108B PHE* 4.1 14.4 - - + -
112B ILE* 3.8 32.8 - - + -
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Residues in contact with VAL 84 (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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4B PHE* 4.2 17.9 - - + -
8B LEU* 3.7 24.9 - - + -
80B LYS* 2.7 34.5 + - + +
81B GLU* 4.0 5.8 - - - +
83B MET* 1.3 74.9 - - - +
85B ALA* 1.3 61.9 + - - +
86B SER 3.2 0.9 + - - -
87B LEU* 3.5 19.3 + - + +
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Residues in contact with ALA 85 (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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81B GLU 2.9 19.2 + - - +
82B ALA* 3.6 8.1 - - - +
83B MET 3.3 0.2 - - - -
84B VAL* 1.3 77.8 - - - +
86B SER* 1.3 59.9 + - - +
87B LEU 4.6 1.6 - - - +
89B ASP* 4.4 5.4 - - - +
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Residues in contact with SER 86 (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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38B THR* 3.8 24.1 - - - +
40B LEU* 5.4 0.7 - - - +
82B ALA 3.0 18.4 + - - -
83B MET 3.1 0.4 + - - -
85B ALA* 1.3 78.5 - - - +
87B LEU* 1.3 61.3 + - - +
89B ASP* 3.1 19.5 - - - +
90B THR* 2.3 22.1 + - - -
93B PHE* 3.8 20.9 - - - -
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Residues in contact with LEU 87 (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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4B PHE* 4.3 13.5 - - + -
7B ASP* 4.1 24.9 - - + +
8B LEU* 3.9 33.2 - - + -
11B CYS* 4.5 14.4 - - + -
83B MET 3.1 16.8 + - - +
84B VAL* 3.5 15.9 + - + +
85B ALA 4.6 2.1 - - - +
86B SER* 1.3 81.3 - - - +
88B GLY* 1.3 61.5 + - - +
89B ASP* 3.0 8.5 + - - +
90B THR* 3.2 8.3 - - - +
93B PHE* 4.4 17.5 - - + -
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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