Contacts of the helix formed by residues 71 - 87 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F ILE* 3.9 17.9 - - + -
69F LEU* 3.5 15.0 - - + +
70F VAL* 1.3 92.3 - - + +
72F SER* 1.3 66.7 + - - +
73F GLY* 4.4 2.7 - - - +
74F ILE* 3.0 38.5 + - + +
75F VAL* 3.4 7.8 + - - +
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Residues in contact with SER 72 (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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69F LEU* 5.7 1.2 - - - +
70F VAL 3.4 3.8 + - - -
71F PRO* 1.3 72.0 - - - +
73F GLY* 1.3 58.0 + - - +
75F VAL* 3.3 10.6 + - - +
76F LEU* 2.9 29.4 + - - +
98F TYR* 5.2 2.6 + - - -
101F GLU* 5.2 5.2 - - - -
104F GLN* 4.8 19.3 - - - -
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Residues in contact with GLY 73 (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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71F PRO* 3.1 3.7 - - - +
72F SER* 1.3 78.8 + - - +
74F ILE* 1.3 63.0 + - - +
76F LEU* 3.3 8.8 + - - +
77F GLU* 2.9 30.1 + - - +
107F GLU* 6.3 2.5 - - - -
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Residues in contact with ILE 74 (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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151C LYS* 6.4 1.3 - - + +
46F LEU* 5.6 0.2 - - + -
56F ARG* 4.7 14.3 + - - +
59F LEU* 5.1 15.3 - - + -
60F ILE* 3.6 37.0 - - + -
63F ILE* 6.2 0.7 - - + -
70F VAL* 4.1 9.2 - - + -
71F PRO* 3.0 39.6 + - + +
73F GLY* 1.3 77.7 - - - +
75F VAL* 1.3 65.9 + - + +
77F GLU* 3.2 8.6 + - - +
78F LEU* 3.1 25.7 + - + +
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Residues in contact with VAL 75 (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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66C ARG 3.9 20.6 - - - +
42F THR* 3.5 33.0 - - + -
45F LEU* 4.9 3.0 - - + +
46F LEU* 4.6 15.7 - - + -
70F VAL* 4.3 17.5 - - + +
71F PRO 3.4 9.2 + - - +
72F SER* 3.3 12.2 + - - +
74F ILE* 1.3 77.5 - - - +
76F LEU* 1.3 63.1 + - - +
78F LEU* 3.3 10.4 + - + +
79F LEU* 3.1 22.0 + - + +
98F TYR* 4.4 13.9 - - + +
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Residues in contact with LEU 76 (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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72F SER 2.9 18.1 + - - +
73F GLY* 3.7 7.6 - - - +
75F VAL* 1.3 76.0 - - - +
77F GLU* 1.3 65.2 + - - +
79F LEU* 3.4 5.9 + - + -
80F LYS* 3.0 22.4 + - + +
98F TYR* 3.9 21.1 - - - +
107F GLU* 3.7 32.8 - - + +
108F PHE* 3.9 13.9 - - + +
111F ARG* 3.7 32.5 - - + -
112F ILE* 3.4 31.2 - - + -
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Residues in contact with GLU 77 (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 ARG* 4.2 15.0 - - - +
73F GLY 2.9 15.1 + - - +
74F ILE* 3.2 10.3 + - - +
76F LEU* 1.3 75.4 - - - +
78F LEU* 1.3 63.3 + - - +
80F LYS* 3.2 28.3 + - - +
81F GLU* 2.9 49.7 + - - +
111F ARG* 5.8 4.2 - - - -
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Residues in contact with LEU 78 (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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45F LEU* 3.9 32.7 - - + +
46F LEU* 3.9 28.7 - - + +
49F GLU* 3.9 22.0 - - + +
56F ARG* 3.4 39.0 - - - +
60F ILE* 4.3 6.7 - - + -
74F ILE* 3.1 16.8 + - + +
75F VAL* 3.3 10.0 + - + +
77F GLU* 1.3 75.8 - - - +
79F LEU* 1.3 57.4 + - - +
81F GLU* 3.3 7.2 + - - +
82F ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 79 (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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40F LEU* 3.8 27.6 - - + -
41F SER 5.8 0.7 - - - -
42F THR* 5.6 3.8 - - + +
45F LEU* 3.6 24.5 - - + +
75F VAL* 3.1 12.5 + - + +
76F LEU* 3.5 12.1 - - + +
78F LEU* 1.3 75.3 - - - +
80F LYS* 1.3 65.1 + - - +
82F ALA* 3.4 3.1 + - - +
83F MET* 3.0 33.3 + - - +
95F ILE* 4.7 10.1 - - + -
98F TYR* 3.7 34.3 - - + -
108F PHE* 3.6 33.0 - - + -
112F ILE* 4.3 1.1 - - + -
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Residues in contact with LYS 80 (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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5F MET* 5.8 9.5 - - - +
76F LEU* 3.0 13.6 + - + +
77F GLU* 3.2 29.9 + - - +
79F LEU* 1.3 75.7 - - - +
81F GLU* 1.3 52.7 + - + +
83F MET* 3.2 5.2 + - - +
84F VAL* 2.7 56.2 + - + +
111F ARG* 3.9 25.9 + - + +
112F ILE* 4.0 21.2 - - + +
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Residues in contact with GLU 81 (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 ARG* 2.9 42.9 + - - -
77F GLU* 2.9 36.3 + - - +
78F LEU* 3.7 10.3 - - - +
80F LYS* 1.3 76.5 - - + +
82F ALA* 1.3 57.3 + - - +
84F VAL* 3.8 7.0 - - + +
85F ALA* 2.9 32.1 + - - +
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Residues in contact with ALA 82 (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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38F THR* 5.4 0.2 - - - +
40F LEU* 3.9 20.3 - - + +
45F LEU* 3.4 33.2 - - + -
48F GLU* 5.6 2.2 - - - +
78F LEU 2.9 8.3 + - - +
79F LEU 3.7 4.9 - - - +
81F GLU* 1.3 76.1 - - - +
83F MET* 1.3 57.7 + - - +
85F ALA* 3.5 5.3 + - - +
86F SER* 3.2 28.9 + - - -
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Residues in contact with MET 83 (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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8F LEU* 5.3 10.5 - - + -
13F ILE* 4.0 16.4 - - + -
40F LEU* 3.5 18.2 - - + -
79F LEU* 3.0 27.7 + - - +
80F LYS* 3.5 4.3 - - + +
82F ALA* 1.3 75.7 - - - +
84F VAL* 1.3 65.2 + - + +
86F SER 3.2 0.7 + - - -
87F LEU* 3.0 24.4 + - - +
93F PHE* 3.5 49.9 - - + -
95F ILE* 4.3 8.7 - - + -
108F PHE* 4.3 3.1 - - + -
112F ILE* 3.7 40.8 - - + -
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Residues in contact with VAL 84 (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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8F LEU* 6.3 2.9 - - + -
80F LYS* 2.7 45.5 + - + +
81F GLU* 3.9 6.5 - - - +
83F MET* 1.3 72.3 - - + +
85F ALA* 1.3 64.9 + - - +
86F SER 3.3 0.5 + - - -
87F LEU* 3.4 26.4 + - + +
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Residues in contact with ALA 85 (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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81F GLU 2.9 19.1 + - - +
82F ALA* 3.8 7.0 - - - +
84F VAL* 1.3 78.7 - - - +
86F SER* 1.3 58.6 + - - +
87F LEU 3.4 4.4 + - - +
89F ASP* 4.4 6.2 - - - +
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Residues in contact with SER 86 (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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38F THR* 3.2 28.0 + - - +
82F ALA 3.2 17.9 + - - -
83F MET 3.2 0.6 + - - -
84F VAL 3.2 0.4 - - - -
85F ALA* 1.3 76.2 - - - +
87F LEU* 1.3 65.5 + - - +
89F ASP* 3.1 25.8 + - - +
90F THR* 3.2 15.6 + - - -
93F PHE* 4.0 16.8 - - - -
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Residues in contact with LEU 87 (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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7F ASP* 3.5 35.2 - - + +
8F LEU* 3.8 18.8 - - + +
11F CYS* 4.0 27.4 - - + -
83F MET 3.0 15.1 + - - +
84F VAL* 3.6 19.7 - - + +
85F ALA 3.4 6.3 - - - +
86F SER* 1.3 82.0 - - - +
88F GLY* 1.3 61.4 + - - +
89F ASP* 3.3 5.2 + - - +
90F THR* 4.1 11.9 - - + -
93F PHE* 4.3 5.2 - - + -
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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