Contacts of the helix formed by residues 105 - 126 (chain C) in PDB entry 1BRR
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 GLN 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.6 39.8 + - + +
103C ALA 3.7 2.2 + - - +
104C ASP* 1.3 71.1 - - - +
106C GLY* 1.3 62.1 + - - +
108C ILE* 3.9 16.7 - - + +
109C LEU* 3.3 23.0 + - - +
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Residues in contact with GLY 106 (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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37B PRO 5.0 1.6 + - - -
40B LYS* 4.1 7.2 - - - -
41B LYS* 4.1 30.0 - - - +
44B ALA* 3.4 9.2 - - - +
104C ASP* 2.9 4.0 + - - +
105C GLN* 1.3 80.8 - - - +
107C THR* 1.3 56.5 + - - +
109C LEU* 3.5 1.2 + - - +
110C ALA 3.0 20.8 + - - -
1001C ARC 3.1 17.1 + - - -
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Residues in contact with THR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 3.5 30.1 - - + +
103C ALA* 3.7 19.4 - - - +
104C ASP* 2.9 12.0 + - + +
106C GLY* 1.3 72.9 - - - +
108C ILE* 1.3 61.9 + - - +
109C LEU 3.3 0.2 - - - -
110C ALA* 3.6 1.8 - - - +
111C LEU* 2.9 34.4 + - - +
151C VAL* 5.7 4.5 - - - -
156C PHE* 3.9 16.1 - - + -
1001C ARC 3.6 24.5 - - + -
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.7 28.0 - - + -
98C ALA* 3.9 25.4 - - + -
99C LEU* 4.9 12.6 - - + -
103C ALA* 3.9 18.4 - - + +
104C ASP 3.1 15.7 + - - +
105C GLN* 3.9 18.6 - - + +
106C GLY 3.3 0.2 - - - -
107C THR* 1.3 77.0 + - - +
109C LEU* 1.3 58.8 + - - +
111C LEU* 3.2 8.0 + - - +
112C VAL* 2.8 40.9 + - + +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 6.2 0.9 - - + -
44B ALA* 4.7 2.5 - - + -
45B ILE* 3.5 44.0 - - + +
48B LEU* 3.6 14.5 - - + +
92B LEU* 4.6 14.8 - - + -
95B LEU* 4.6 10.8 - - + -
1001B ARC 5.4 13.2 - - + -
105C GLN 3.3 14.5 + - - +
106C GLY* 3.8 4.0 - - - +
108C ILE* 1.3 77.0 - - - +
110C ALA* 1.3 57.9 + - - +
111C LEU 3.0 4.0 - - - -
112C VAL* 4.5 8.5 - - + +
113C GLY 3.0 27.0 + - - +
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Residues in contact with ALA 110 (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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44B ALA* 4.0 8.7 - - + +
48B LEU* 4.6 7.2 - - - -
106C GLY 3.0 18.6 + - - +
107C THR* 3.6 4.3 - - - +
109C LEU* 1.3 75.5 - - - +
111C LEU* 1.3 56.3 + - - +
114C ALA* 3.4 13.1 + - - +
147C TYR* 3.3 37.1 - - - +
1001C ARC 3.6 35.5 - - + +
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 4.2 26.6 - - + +
98C ALA* 5.2 3.8 - - + -
107C THR 2.9 17.7 + - - +
108C ILE* 3.3 7.6 - - - +
110C ALA* 1.3 81.8 - - - +
112C VAL* 1.3 68.1 + - + +
114C ALA* 3.2 4.0 + - - +
115C ASP* 3.0 22.3 + - - +
147C TYR* 4.5 1.3 - - + +
148C ILE* 4.1 29.3 - - + +
151C VAL* 3.2 33.4 - - + -
152C LEU* 4.7 3.1 - - + -
156C PHE* 3.5 35.9 - - + -
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Residues in contact with VAL 112 (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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1001B ARC 5.2 16.2 - - + -
91C PRO* 4.1 28.2 - - + +
94C LEU* 5.2 4.0 - - + -
95C LEU* 4.7 10.8 - - + -
108C ILE* 2.8 37.7 + - + +
109C LEU* 4.1 9.2 - - + +
111C LEU* 1.3 71.7 - - + +
113C GLY* 1.3 56.5 + - - +
115C ASP* 2.7 30.0 + - - +
116C GLY* 2.8 10.4 + - - -
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Residues in contact with GLY 113 (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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48B LEU* 3.6 23.8 - - - -
1001B ARC 3.3 27.4 - - - +
109C LEU* 3.0 16.4 + - - +
112C VAL* 1.3 77.6 - - - +
114C ALA* 1.3 59.6 + - - +
116C GLY 3.0 9.0 + - - -
117C ILE* 3.1 14.2 + - - +
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Residues in contact with ALA 114 (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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48B LEU* 3.8 3.9 - - - +
110C ALA 3.4 21.9 + - - +
111C LEU 3.2 5.1 + - - +
112C VAL 3.2 1.0 - - - -
113C GLY* 1.3 74.8 - - - +
115C ASP* 1.3 57.9 + - - +
117C ILE* 3.3 8.6 + - - +
118C MET* 2.9 26.5 + - - +
144C ALA* 3.8 10.7 - - + +
147C TYR* 3.8 14.6 - - + -
148C ILE* 3.7 18.8 - - + -
1001C ARC 4.0 14.6 - - + -
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Residues in contact with ASP 115 (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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86C TRP 4.3 0.2 - - - +
87C LEU 4.5 2.1 - - - +
90C THR* 2.5 32.4 + - - -
91C PRO* 3.0 21.5 - - + +
94C LEU* 3.9 8.1 - - + +
111C LEU 3.0 11.4 + - - +
112C VAL* 2.7 14.7 + - - +
114C ALA* 1.3 74.0 - - - +
116C GLY* 1.3 65.0 + - - +
118C MET* 3.0 28.3 + - - +
119C ILE* 2.9 25.5 + - - +
148C ILE* 3.5 11.5 - - + +
182C TRP* 3.8 9.9 - - - -
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Residues in contact with GLY 116 (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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1001B ARC 3.7 27.7 - - - +
87C LEU* 4.7 14.6 - - - +
112C VAL 2.8 12.7 + - - -
113C GLY 3.0 4.7 + - - -
115C ASP* 1.3 76.6 - - - +
117C ILE* 1.3 56.8 + - - +
119C ILE* 4.2 0.3 - - - +
120C GLY* 2.9 30.5 + - - -
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.0 17.3 - - + -
51B ALA* 4.0 28.9 - - + +
52B ILE* 4.3 13.0 - - + +
55B THR* 3.5 22.4 - - + +
1001B ARC 4.1 17.9 - - + -
113C GLY 3.1 9.9 + - - +
114C ALA* 3.7 10.3 - - - +
115C ASP 3.2 0.2 - - - -
116C GLY* 1.3 74.4 - - - +
118C MET* 1.3 55.5 + - - +
121C THR* 2.8 46.9 + - - +
140C ILE* 5.0 8.3 - - + -
141C SER* 6.2 0.2 - - - -
144C ALA* 4.7 10.3 - - + -
1001C ARC 5.3 11.7 - - + -
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Residues in contact with MET 118 (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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90C THR* 4.4 4.3 - - + -
114C ALA 2.9 14.8 + - - +
115C ASP* 3.0 39.0 + - - +
117C ILE* 1.3 76.8 - - - +
119C ILE* 1.3 74.3 + - + +
122C GLY 3.3 5.5 + - - -
141C SER* 2.6 39.3 + - - +
144C ALA* 4.0 13.6 - - + +
145C MET* 3.5 36.3 - - - -
148C ILE* 4.4 4.3 - - + -
182C TRP* 4.0 7.9 - - + -
999C RET 3.7 39.7 - - + +
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Residues in contact with ILE 119 (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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83C TYR* 3.4 36.9 - - + +
86C TRP* 3.3 42.2 - - + +
87C LEU* 3.6 20.6 - - + +
90C THR* 3.8 9.0 - - - +
115C ASP* 2.9 15.1 + - - +
116C GLY 4.2 1.3 - - - +
118C MET* 1.3 86.2 - - + +
120C GLY* 1.3 61.3 - - - +
122C GLY* 2.6 25.5 + - - -
123C LEU* 2.7 13.2 + - + -
999C RET 3.7 24.9 - - + -
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Residues in contact with GLY 120 (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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1001B ARC 3.9 24.8 - - - +
87C LEU* 4.6 5.7 - - - +
116C GLY 2.9 17.6 + - - -
119C ILE* 1.3 80.6 - - - +
121C THR* 1.3 60.8 + - - -
123C LEU* 3.2 11.9 + - - +
124C VAL* 3.1 25.9 + - - +
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Residues in contact with THR 121 (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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55B THR* 3.8 22.7 + - - +
1001B ARC 4.5 1.3 - - - +
117C ILE* 2.8 32.2 + - - +
120C GLY* 1.3 69.1 - - - +
122C GLY* 1.3 67.0 + - - +
124C VAL* 3.1 10.8 + - - +
125C GLY 3.0 18.5 + - - -
137C TRP* 3.1 48.8 - - + +
140C ILE* 4.1 8.7 - - + +
141C SER* 3.7 15.5 - - - +
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Residues in contact with GLY 122 (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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83C TYR* 3.6 9.3 + - - -
118C MET 3.3 10.4 + - - -
119C ILE 2.6 14.3 + - - -
121C THR* 1.3 73.0 - - - +
123C LEU* 1.3 61.9 + - - -
125C GLY* 3.0 4.1 + - - -
126C ALA* 2.8 22.3 + - - +
137C TRP* 5.5 1.3 - - - -
138C TRP* 6.3 0.9 - - - -
141C SER* 4.3 3.4 - - - -
189C TRP* 4.5 4.9 + - - -
999C RET 4.0 22.2 - - - -
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Residues in contact with LEU 123 (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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1001B ARC 3.9 25.1 - - + -
1002B ARC 5.9 0.4 - - + -
1005B GOL 4.7 0.4 - - + -
80C TRP* 4.3 6.1 - - + -
83C TYR* 3.5 43.5 - - + -
119C ILE* 2.7 13.7 + - + +
120C GLY* 3.2 13.4 + - - +
122C GLY* 1.3 71.0 - - - +
124C VAL* 1.3 62.4 + - - +
126C ALA* 3.0 6.3 + - + +
127C LEU* 3.0 50.5 + - + +
1002C ARC 3.3 41.3 - - + -
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Residues in contact with VAL 124 (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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55B THR* 5.6 0.7 - - + -
56B MET* 5.0 6.3 - - + -
59B SER* 5.2 0.7 - - - -
64B TYR* 3.9 35.2 - - + +
1001B ARC 3.3 35.2 - - + -
120C GLY 3.1 9.2 + - - +
121C THR* 3.1 10.7 + - - +
123C LEU* 1.3 74.1 - - - +
125C GLY* 1.3 52.5 + - - +
127C LEU 3.3 2.8 + - - -
128C THR* 2.6 35.6 + - - +
137C TRP* 3.3 41.7 - - + +
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Residues in contact with GLY 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR 3.0 10.7 + - - -
122C GLY 3.6 2.7 - - - -
124C VAL* 1.3 74.9 - - - +
126C ALA* 1.3 59.6 + - - +
128C THR* 3.4 2.3 + - - -
134C ARG* 2.8 41.5 + - - +
137C TRP* 3.6 29.8 - - - -
189C TRP* 4.1 7.6 - - - -
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Residues in contact with ALA 126 (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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69C VAL* 4.2 1.2 - - - +
78C ILE* 3.9 23.6 - - + +
83C TYR* 3.5 31.6 - - + +
122C GLY 2.8 12.0 + - - +
123C LEU* 3.2 10.8 - - + +
125C GLY* 1.3 78.9 - - - +
127C LEU* 1.3 57.9 + - + +
134C ARG* 2.6 30.6 + - - +
189C TRP* 4.1 4.0 - - - -
194C GLU* 3.9 6.5 - - - +
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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
------------------------------------------------------------
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