Contacts of the helix formed by residues 113 - 134 (chain D) in PDB entry 4BPW
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 SER 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B GLU* 3.9 9.9 - - - -
112D GLN* 1.3 79.1 - - - +
114D GLU* 1.3 59.3 + - - +
115D GLU* 3.2 6.3 - - - -
116D LEU* 3.0 28.4 + - - +
117D ARG* 2.8 35.4 + - - +
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLN 4.8 0.3 - - - +
113B SER* 3.8 12.2 - - - -
114B GLU* 3.2 56.3 + - + +
115B GLU 5.3 0.7 + - - -
235B ARG* 3.8 9.6 + - - +
113D SER* 1.3 72.4 - - - +
115D GLU* 1.3 62.6 + - - +
117D ARG* 3.3 25.8 + - - +
118D ARG* 3.1 24.3 + - - +
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 5.1 1.6 + - - +
113D SER* 3.2 7.0 - - - -
114D GLU* 1.3 78.1 - - - +
116D LEU* 1.3 67.5 + - + +
118D ARG* 3.4 34.1 + - - +
119D TRP* 3.2 29.7 + - + +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ALA 4.1 9.4 - - - +
110D TYR* 3.4 39.0 - - + +
112D GLN* 4.0 19.1 - - + +
113D SER* 3.0 33.4 + - - +
115D GLU* 1.3 83.1 - - + +
117D ARG* 1.3 64.1 + - - +
119D TRP* 3.4 6.6 + - + +
120D PHE* 3.0 25.6 + - - +
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 5.4 1.0 + - - -
235B ARG* 4.1 24.3 - - - +
110D TYR 3.3 16.6 - - - +
111D CYS* 3.1 25.9 + - - +
112D GLN 4.2 8.3 + - - -
113D SER 2.8 19.4 + - - +
114D GLU* 3.3 44.1 - - - +
116D LEU* 1.3 77.9 - - - +
118D ARG* 1.3 56.4 + - - +
120D PHE* 3.3 2.0 + - - +
121D ILE* 2.8 41.9 + - + +
227D SER* 5.3 3.6 - - - +
230D LEU* 4.0 33.8 + - + -
231D ALA* 4.9 6.5 - - - +
234D ALA* 4.3 11.3 - - - +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D GLU 3.1 15.1 + - - +
115D GLU* 3.4 37.5 + - - +
117D ARG* 1.3 79.6 - - - +
119D TRP* 1.3 74.2 + - - +
121D ILE* 3.8 8.7 - - - +
122D GLN* 3.0 50.4 + - + +
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Residues in contact with TRP 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL 4.8 0.7 - - - -
53D LEU* 3.9 31.0 - - + -
54D LYS* 3.7 35.7 - - + -
57D GLU* 3.1 40.1 + - - -
110D TYR* 3.6 39.7 - + + -
115D GLU* 3.2 27.2 + - - +
116D LEU* 3.6 8.1 - - + +
118D ARG* 1.3 90.8 - - - +
120D PHE* 1.3 69.1 + - - +
121D ILE 3.3 0.2 + - - -
122D GLN* 4.8 1.8 - - - -
123D GLN* 2.5 47.2 + - + +
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Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 5.1 0.4 - - - -
53D LEU* 3.5 23.1 - - + -
103D HIS* 3.6 32.5 - + - -
106D LEU* 3.6 27.8 - - + -
107D ARG* 4.3 15.3 - - + -
110D TYR* 3.4 37.9 - + + +
116D LEU 3.0 9.6 + - - +
117D ARG 3.8 2.7 - - - +
119D TRP* 1.3 83.0 - - - +
121D ILE* 1.3 63.9 + - - +
123D GLN* 3.7 1.7 + - - +
124D GLU* 3.1 48.4 + - - +
226D LEU* 4.5 7.4 - - + -
230D LEU* 4.2 23.6 - - + -
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG* 2.8 29.8 + - + +
118D ARG* 3.8 7.6 - - - +
120D PHE* 1.3 77.0 - - - +
122D GLN* 1.3 52.9 + - - +
124D GLU* 3.2 2.8 + - - +
125D MET* 2.7 57.4 + - + +
223D ARG* 4.0 17.9 - - + +
226D LEU* 3.9 25.2 - - + +
227D SER* 3.8 33.2 - - - +
230D LEU* 3.9 12.6 - - + -
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Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLU* 5.7 1.6 - - - +
65D LYS* 5.5 1.4 - - - +
118D ARG* 3.0 42.9 + - + +
119D TRP* 3.8 3.8 - - - +
121D ILE* 1.3 79.3 - - - +
123D GLN* 1.3 76.0 + - - +
125D MET* 3.2 10.7 + - + +
126D ASP* 2.9 49.0 + - - +
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Residues in contact with GLN 123 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.0 49.2 - - + +
56D VAL* 3.8 16.5 - - + +
57D GLU* 3.3 35.3 + - + +
119D TRP* 2.5 60.8 + - + +
120D PHE 4.2 2.7 - - - +
122D GLN* 1.3 100.6 + - - +
124D GLU* 1.3 58.4 + - - +
126D ASP* 3.6 2.1 + - - +
127D LEU* 3.0 26.9 + - - +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 4.5 5.3 - - + -
49D ARG* 2.4 37.5 + - - -
53D LEU* 3.5 16.2 - - - +
103D HIS* 2.9 30.1 + - + -
120D PHE* 3.1 42.9 + - + +
121D ILE 3.7 2.7 - - - +
123D GLN* 1.3 74.7 - - - +
125D MET* 1.3 58.6 + - - +
127D LEU* 3.4 8.8 + - + +
128D LEU* 2.9 28.6 + - - +
222D PHE* 4.2 13.9 - - + -
226D LEU* 4.4 9.6 - - + -
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Residues in contact with MET 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ILE* 2.7 34.9 + - + +
122D GLN* 3.4 10.1 - - + +
124D GLU* 1.3 71.1 - - - +
126D ASP* 1.3 60.3 + - - +
128D LEU* 2.9 4.2 + - - +
129D ARG* 2.7 37.1 + - - +
219D LEU* 3.8 44.6 - - + +
220D ASN* 6.0 0.2 - - - -
222D PHE* 4.4 13.2 - - + -
223D ARG* 3.7 41.7 - - + +
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Residues in contact with ASP 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 3.5 28.4 - - + +
60D GLY* 5.3 1.2 - - - -
65D LYS* 2.6 41.9 + - + +
70D TYR* 3.6 13.1 + - - +
74D LEU* 4.9 0.4 - - - +
122D GLN* 2.9 35.0 + - - +
123D GLN* 5.0 2.3 - - - +
125D MET* 1.3 78.9 - - - +
127D LEU* 1.3 58.0 + - - +
129D ARG* 3.3 13.8 + - - +
130D PHE* 3.0 27.0 + - - +
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 4.9 2.7 - - + +
49D ARG* 3.6 28.9 - - - +
52D LEU* 4.3 7.9 - - + -
53D LEU* 4.3 13.9 - - + -
56D VAL* 4.4 17.0 - - + +
74D LEU* 4.9 3.4 - - + -
78D LEU* 4.0 24.7 - - + -
123D GLN 3.0 19.0 + - - +
124D GLU* 3.4 13.2 - - + +
125D MET 3.0 0.2 - - - -
126D ASP* 1.3 74.3 - - - +
128D LEU* 1.3 63.7 + - - +
130D PHE* 3.2 6.2 + - - +
131D ARG* 3.0 60.1 + - + +
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 4.3 24.2 - - + +
124D GLU 2.9 18.0 + - - +
125D MET* 2.9 4.9 + - - +
127D LEU* 1.3 73.6 - - - +
129D ARG* 1.3 66.8 + - - +
131D ARG* 3.3 13.0 + - + +
132D PHE* 3.1 26.2 + - + +
143D PHE* 5.1 22.9 - - + -
218D ILE* 5.1 7.0 - - + +
219D LEU* 4.9 9.4 - - + -
222D PHE* 3.6 41.3 - - + -
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Residues in contact with ARG 129 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D LYS* 3.4 45.0 - - - +
125D MET* 2.7 13.8 + - - +
126D ASP* 3.3 17.4 + - - +
128D LEU* 1.3 78.2 - - - +
130D PHE* 1.3 52.7 + - - +
132D PHE* 3.6 4.7 + - - +
133D SER* 2.6 39.5 + - - +
215D VAL* 5.2 14.1 - - + +
219D LEU* 4.1 33.0 - - + +
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D TYR* 4.6 10.5 - + + -
71D GLN* 3.3 45.8 - - + -
74D LEU* 3.7 21.1 - - + -
75D GLU* 3.7 25.8 - - + -
78D LEU* 3.5 29.2 - - + -
126D ASP 3.0 14.0 + - - +
127D LEU 3.2 7.6 + - - +
129D ARG* 1.3 75.0 - - - +
131D ARG* 1.3 69.3 + - + +
133D SER* 2.8 24.7 + - - -
134D ILE* 3.2 46.5 + - + +
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 4.2 4.0 + - - -
52D LEU* 4.1 5.3 - - - +
78D LEU* 3.6 27.1 - - + +
83D PHE* 4.1 12.4 - - - +
84D SER* 5.2 3.2 - - - +
99D ASP* 2.7 47.4 + - - +
127D LEU* 3.0 45.2 + - + +
128D LEU* 3.3 15.2 + - + +
130D PHE* 1.3 89.5 - - + +
132D PHE* 1.3 57.7 + - - +
134D ILE* 3.6 17.9 - - - +
135D LEU* 3.7 10.9 - - - +
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 3.1 18.2 + - + +
129D ARG* 4.0 4.3 - - - +
131D ARG* 1.3 73.9 - - - +
133D SER* 1.3 67.0 + - - +
134D ILE 3.2 2.2 - - - -
135D LEU* 3.1 25.0 + - + +
140D ILE* 3.5 48.0 - - + +
143D PHE* 3.3 47.6 - + + -
144D LEU* 6.0 2.2 - - + -
211D LEU* 5.0 5.8 - - + -
214D ILE* 5.6 3.1 - - + -
215D VAL* 3.7 42.4 - - + -
218D ILE* 6.3 0.7 - - + -
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Residues in contact with SER 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLN* 3.9 22.7 + - - -
129D ARG* 2.6 26.0 + - - +
130D PHE* 2.8 14.0 + - - -
132D PHE* 1.3 81.6 - - - +
134D ILE* 1.3 59.9 + - - +
135D LEU 3.3 3.2 + - - +
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Residues in contact with ILE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLN* 4.1 17.3 - - + +
75D GLU* 3.9 17.9 - - + +
130D PHE* 3.2 52.5 + - + +
131D ARG* 3.6 13.0 - - + +
133D SER* 1.3 78.5 - - - +
135D LEU* 1.3 60.1 + - - +
136D PRO* 3.9 4.3 - - - +
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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