Contacts of the helix formed by residues 71 - 87 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 3.9 19.3 - - + -
69C LEU* 3.3 17.7 - - + +
70C VAL* 1.3 87.9 - - + +
72C SER* 1.3 65.0 - - - +
73C GLY* 4.4 2.7 - - - +
74C ILE* 3.0 35.8 + - + +
75C VAL* 3.3 10.0 + - - +
100C ARG* 4.4 0.7 - - - +
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Residues in contact with SER 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PRO* 1.3 72.7 - - - +
73C GLY* 1.3 58.0 + - - +
75C VAL* 3.2 7.6 + - - +
76C LEU* 2.9 30.3 + - - +
98C TYR* 5.7 0.2 + - - -
100C ARG* 3.4 24.0 - - - +
101C GLU* 4.8 4.4 - - - -
103C LYS 5.6 0.2 - - - -
104C GLN* 4.1 33.9 + - - +
107C GLU* 5.6 6.2 - - - +
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Residues in contact with GLY 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO* 3.2 3.3 - - - +
72C SER* 1.3 82.1 + - - +
74C ILE* 1.3 60.8 + - - +
76C LEU* 3.7 11.6 - - - +
77C GLU* 3.2 25.6 + - - +
107C GLU* 6.1 2.5 - - - -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ARG* 4.6 8.3 - - + -
59C LEU* 4.5 23.1 - - + -
60C ILE* 3.5 39.3 - - + -
63C ILE* 4.8 3.6 - - + -
70C VAL* 4.2 9.0 - - + -
71C PRO* 3.0 38.2 + - + +
73C GLY* 1.3 74.7 - - - +
75C VAL* 1.3 67.7 + - - +
77C GLU* 3.3 22.0 - - - +
78C LEU* 3.1 23.0 + - + +
151F LYS* 6.3 0.4 - - + -
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR* 3.6 37.2 - - + +
45C LEU* 4.8 3.9 - - + +
46C LEU* 4.9 5.2 - - + -
70C VAL* 3.8 24.9 - - + -
71C PRO 3.3 5.8 + - - +
72C SER* 3.2 6.9 + - - +
74C ILE* 1.3 76.0 - - - +
76C LEU* 1.3 56.7 + - - +
78C LEU* 3.2 12.1 + - + +
79C LEU* 2.9 28.5 + - + +
98C TYR* 4.2 9.9 - - + -
100C ARG* 4.1 18.2 - - - +
104C GLN* 4.0 17.3 - - - +
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C SER 2.9 17.3 + - - +
73C GLY* 3.7 9.4 - - - +
75C VAL* 1.3 73.8 - - - +
77C GLU* 1.3 55.6 + - - +
79C LEU* 3.6 5.4 - - + +
80C LYS* 2.8 38.2 + - + +
98C TYR* 3.7 20.8 + - - +
104C GLN 5.2 0.4 - - - +
107C GLU* 3.7 29.8 - - + +
108C PHE* 3.9 18.2 - - + +
111C ARG* 3.9 25.8 - - + -
112C ILE* 3.5 26.9 - - + -
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ARG* 3.0 42.1 + - - +
73C GLY 3.2 11.9 + - - +
74C ILE* 3.3 24.8 - - - +
76C LEU* 1.3 77.6 - - - +
78C LEU* 1.3 59.1 + - - +
80C LYS* 3.4 5.8 + - - +
81C GLU* 3.0 38.9 + - - +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 3.8 36.1 - - + +
46C LEU* 3.8 29.2 - - + -
49C GLU* 3.8 20.2 - - + +
56C ARG* 3.3 40.8 - - - +
60C ILE* 4.3 6.3 - - + -
74C ILE* 3.1 15.1 + - + +
75C VAL* 3.2 11.9 + - + +
77C GLU* 1.3 80.4 - - - +
79C LEU* 1.3 61.5 + - - +
81C GLU* 3.5 6.3 + - - +
82C ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.9 24.7 - - + -
41C SER 6.1 0.2 - - - -
45C LEU* 3.6 23.8 - - + +
75C VAL* 2.9 18.7 + - + +
76C LEU* 3.6 5.8 - - + +
78C LEU* 1.3 74.5 - - - +
80C LYS* 1.3 59.5 + - - +
82C ALA* 3.4 3.4 + - - +
83C MET* 3.0 37.3 + - - +
95C ILE* 4.2 15.3 - - + -
98C TYR* 3.5 45.8 - - + +
108C PHE* 3.7 23.1 - - + -
112C ILE* 4.6 1.6 - - + -
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Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.5 12.6 - - + -
76C LEU* 2.8 19.4 + - + +
77C GLU* 3.8 6.3 - - - +
79C LEU* 1.3 74.1 - - - +
81C GLU* 1.3 62.3 + - + +
83C MET* 3.2 5.7 + - - +
84C VAL* 2.8 41.1 + - + +
111C ARG* 4.8 8.1 - - + +
112C ILE* 3.8 23.7 - - + +
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU* 5.1 0.2 - - - +
56C ARG* 2.9 43.5 + - - -
77C GLU* 3.0 26.2 + - - +
78C LEU* 3.8 7.1 - - - +
80C LYS* 1.3 78.4 - - + +
82C ALA* 1.3 57.0 + - - +
84C VAL* 3.2 8.7 + - - +
85C ALA* 2.9 31.3 + - - +
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 4.0 21.2 - - + +
45C LEU* 3.6 31.2 - - + -
48C GLU* 5.3 2.7 - - - +
78C LEU 3.1 9.0 + - - +
79C LEU 3.7 4.5 - - - +
80C LYS 3.3 0.2 - - - -
81C GLU* 1.3 74.4 - - - +
83C MET* 1.3 60.5 + - - +
85C ALA* 3.5 5.9 + - - +
86C SER* 3.0 27.8 + - - -
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Residues in contact with MET 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.7 22.6 - - + +
13C ILE* 3.9 19.5 - - + -
40C LEU* 3.8 16.6 - - + -
79C LEU* 3.0 25.3 + - - +
80C LYS* 3.6 4.7 - - - +
82C ALA* 1.3 75.4 - - - +
84C VAL* 1.3 59.0 + - - +
86C SER 3.4 0.5 + - - -
87C LEU* 2.9 30.0 + - - +
93C PHE* 3.4 36.6 - - + -
95C ILE* 4.1 17.7 - - + -
108C PHE* 4.2 8.3 - - + -
112C ILE* 3.5 34.3 - - + -
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C MET 6.0 0.9 - - - +
8C LEU* 4.3 20.0 - - + -
80C LYS* 2.8 28.7 + - + +
81C GLU* 3.6 6.5 - - - +
83C MET* 1.3 77.4 - - - +
85C ALA* 1.3 63.2 + - - +
86C SER 3.2 1.0 + - - -
87C LEU* 3.3 25.9 + - + +
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLU 2.9 17.3 + - - +
82C ALA* 4.0 6.3 - - - +
83C MET 3.3 0.2 - - - -
84C VAL* 1.3 77.9 - - + +
86C SER* 1.3 59.4 + - - +
87C LEU 4.8 1.8 - - - +
89C ASP* 4.8 2.1 - - - +
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Residues in contact with SER 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR* 3.7 21.9 - - - +
82C ALA 3.0 17.9 + - - -
84C VAL 3.2 0.2 - - - -
85C ALA* 1.3 76.4 - - - +
87C LEU* 1.3 66.9 + - - +
89C ASP* 3.2 13.2 - - - +
90C THR* 3.1 27.5 + - - -
93C PHE* 3.1 21.8 - - - -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C MET 5.6 1.1 - - - +
7C ASP* 3.5 37.7 - - + +
8C LEU* 4.0 23.8 - - + +
11C CYS* 3.7 30.3 - - + -
83C MET 2.9 13.6 + - - +
84C VAL* 3.3 19.7 + - + +
85C ALA 4.8 1.4 - - - +
86C SER* 1.3 77.8 - - - +
88C GLY* 1.3 60.9 + - - +
89C ASP* 3.9 1.4 + - - +
90C THR* 4.1 8.1 - - + -
93C PHE* 4.3 7.2 - - + -
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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