Contacts of the helix formed by residues 113 - 134 (chain B) in PDB entry 4BPU
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B CYS 3.2 1.0 + - - -
112B GLN* 1.3 80.5 - - - +
114B GLU* 1.3 59.5 + - - +
115B GLU* 3.8 7.3 + - - +
116B LEU* 3.1 34.5 + - - +
117B ARG* 2.9 37.4 + - - +
114D GLU* 3.7 13.9 - - - -
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Residues in contact with GLU 114 (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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113B SER* 1.3 72.0 - - - +
115B GLU* 1.3 57.4 + - - +
117B ARG* 3.4 28.1 + - - +
118B ARG* 2.9 31.2 + - - +
235B ARG* 4.7 2.5 + - - +
112D GLN 4.8 0.7 - - - +
113D SER* 3.6 14.6 - - - -
114D GLU* 3.1 56.4 + - + +
115D GLU* 5.1 1.4 + - - +
117D ARG* 5.1 1.0 + - - -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 3.2 7.3 - - - +
114B GLU* 1.3 79.2 - - - +
116B LEU* 1.3 65.3 - - + +
118B ARG* 2.8 41.0 + - - +
119B TRP* 2.9 36.8 + - + +
114D GLU* 5.2 0.8 + - - -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ALA 4.1 11.2 - - - +
110B TYR* 3.4 39.0 - - + +
112B GLN* 4.1 28.5 - - + +
113B SER* 3.1 21.8 + - - +
115B GLU* 1.3 82.6 - - + +
117B ARG* 1.3 61.0 + - - +
119B TRP* 3.4 6.5 + - + +
120B PHE* 2.9 32.2 + - - +
253B LEU* 4.8 17.0 - - + +
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Residues in contact with ARG 117 (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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110B TYR 3.4 14.6 - - - +
111B CYS* 3.2 20.8 + - - -
113B SER 2.9 19.9 + - - +
114B GLU* 3.4 36.3 - - - +
116B LEU* 1.3 77.0 - - - +
118B ARG* 1.3 57.8 + - - +
120B PHE* 3.3 2.0 + - - +
121B ILE* 2.8 43.4 + - + +
227B SER* 5.0 2.7 - - - +
230B LEU* 4.2 18.2 - - + -
231B ALA* 4.1 28.2 - - - +
234B ALA* 4.0 8.5 - - - +
235B ARG* 3.0 48.3 - - - +
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Residues in contact with ARG 118 (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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114B GLU 2.9 18.1 + - - +
115B GLU* 2.8 41.9 + - - +
117B ARG* 1.3 77.0 - - - +
119B TRP* 1.3 74.1 + - - +
121B ILE* 3.3 10.1 + - - +
122B GLN* 2.9 44.6 + - + +
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Residues in contact with TRP 119 (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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50B VAL 5.1 0.2 - - - -
53B LEU* 3.8 40.6 - - + -
54B LYS* 4.1 18.8 - - + -
57B GLU* 3.1 43.5 + - + -
110B TYR* 3.8 35.9 - + + -
115B GLU* 2.9 30.2 + - - +
116B LEU* 3.7 8.1 - - + +
118B ARG* 1.3 85.0 - - - +
120B PHE* 1.3 66.4 - - - +
122B GLN* 3.2 4.9 + - - -
123B GLN* 2.4 55.1 + - + +
253B LEU 5.4 2.2 - - - -
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Residues in contact with PHE 120 (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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49B ARG* 5.2 0.2 - - - -
53B LEU* 3.7 16.2 - - + -
103B HIS* 3.8 36.3 - + - -
106B LEU* 3.6 23.3 - - + -
107B ARG* 4.0 20.4 - - + -
110B TYR* 3.6 27.1 - + + -
116B LEU 2.9 18.7 + - - +
117B ARG* 3.7 3.4 - - - +
119B TRP* 1.3 82.5 - - - +
121B ILE* 1.3 64.6 + - - +
123B GLN* 3.6 0.7 + - - +
124B GLU* 2.9 52.1 + - - +
226B LEU* 4.6 7.2 - - + -
230B LEU* 3.7 23.3 - - + -
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Residues in contact with ILE 121 (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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117B ARG* 2.8 32.5 + - + +
118B ARG* 3.5 8.1 - - - +
120B PHE* 1.3 76.8 - - - +
122B GLN* 1.3 57.8 - - - +
124B GLU* 3.6 0.7 - - - +
125B MET* 2.7 41.2 + - + +
223B ARG* 3.3 40.2 - - + +
226B LEU* 3.9 24.7 - - + -
227B SER* 3.5 33.7 - - - +
230B LEU* 4.5 6.3 - - + -
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Residues in contact with GLN 122 (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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57B GLU* 5.9 0.8 - - - +
118B ARG* 2.9 36.6 + - + +
119B TRP* 3.6 6.2 - - - +
121B ILE* 1.3 77.6 - - - +
123B GLN* 1.3 82.9 + - - +
125B MET* 3.5 0.9 - - - +
126B ASP* 2.9 43.3 + - - +
223B ARG* 4.1 18.2 - - - +
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Residues in contact with GLN 123 (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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53B LEU* 3.3 46.6 - - + +
56B VAL* 3.9 12.7 - - + +
57B GLU* 3.7 22.7 + - - +
119B TRP* 2.4 78.8 + - + +
120B PHE 4.1 2.2 - - - +
122B GLN* 1.3 98.6 + - - +
124B GLU* 1.3 58.3 + - - +
125B MET 3.2 0.2 + - - -
126B ASP* 3.3 5.4 + - - +
127B LEU* 3.0 28.4 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 4.9 8.6 - - + -
49B ARG* 2.4 42.9 + - - +
53B LEU* 3.2 18.7 - - - +
103B HIS* 2.7 35.0 + - + +
120B PHE* 2.9 41.9 + - + +
121B ILE* 3.9 3.4 - - - +
123B GLN* 1.3 77.7 - - - +
125B MET* 1.3 62.9 + - - +
127B LEU* 3.8 8.9 - - + +
128B LEU* 3.4 18.7 + - - +
222B PHE* 5.0 4.6 - - + -
226B LEU* 4.7 6.7 - - + -
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Residues in contact with MET 125 (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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121B ILE* 2.7 26.4 + - + +
122B GLN 3.5 3.6 - - - +
124B GLU* 1.3 75.9 - - - +
126B ASP* 1.3 69.4 + - - +
127B LEU 3.1 1.1 - - - -
128B LEU* 2.9 15.8 + - - +
129B ARG* 2.9 10.4 + - - +
219B LEU* 3.0 51.6 - - + +
220B ASN* 6.0 0.2 - - - -
222B PHE* 3.4 26.9 - - + -
223B ARG* 3.4 51.4 - - + +
226B LEU* 4.4 5.6 - - + -
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Residues in contact with ASP 126 (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 VAL* 4.0 18.6 - - + +
60B GLY* 6.1 1.0 - - - -
70B TYR* 4.5 14.9 + - - +
122B GLN* 2.9 35.7 + - - +
123B GLN* 3.7 6.5 - - - +
125B MET* 1.3 78.6 - - - +
127B LEU* 1.3 61.9 + - - +
129B ARG* 3.2 14.7 + - - +
130B PHE* 2.9 21.3 + - - +
223B ARG* 5.5 2.3 + - - -
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Residues in contact with LEU 127 (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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29B TYR* 5.0 2.5 - - + +
49B ARG* 3.6 21.3 - - - +
52B LEU* 3.9 15.0 - - + -
53B LEU* 4.6 6.3 - - + -
56B VAL* 4.5 20.4 - - + +
74B LEU* 4.7 5.4 - - + -
78B LEU* 4.0 32.8 - - + -
123B GLN 3.0 17.0 + - - +
124B GLU* 3.8 9.6 - - + +
125B MET 3.1 0.2 - - - -
126B ASP* 1.3 78.0 - - - +
128B LEU* 1.3 56.4 + - - +
130B PHE* 3.1 9.8 + - + +
131B ARG* 2.9 61.8 + - + +
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Residues in contact with LEU 128 (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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29B TYR* 4.4 22.9 - - + +
124B GLU 3.4 11.8 + - - +
125B MET* 2.9 10.4 + - - +
127B LEU* 1.3 78.9 - - - +
129B ARG* 1.3 62.8 + - - +
131B ARG* 3.3 13.9 + - + +
132B PHE* 3.1 45.8 + - + +
218B ILE 5.2 0.7 - - - +
219B LEU* 3.7 24.0 - - + -
222B PHE* 3.9 38.6 - - + -
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Residues in contact with ARG 129 (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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65B LYS* 3.6 35.9 - - + +
125B MET 2.9 11.6 + - - +
126B ASP* 3.3 16.2 - - - +
128B LEU* 1.3 76.7 - - - +
130B PHE* 1.3 57.0 + - - +
132B PHE* 3.1 8.4 + - - +
133B SER* 2.8 34.3 + - - +
212B LYS 5.5 4.8 + - - -
213B ASP* 5.7 2.2 + - - -
215B VAL* 5.0 9.9 - - + +
216B ALA* 6.0 5.5 - - - +
219B LEU* 3.9 31.9 - - + +
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Residues in contact with PHE 130 (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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70B TYR* 4.5 5.2 - + + -
71B GLN* 3.1 51.1 - - - +
74B LEU* 3.5 29.4 - - + -
75B GLU* 4.2 26.7 - - + -
78B LEU* 3.6 28.0 - - + -
126B ASP 2.9 12.7 + - - +
127B LEU* 3.1 9.6 + - + +
129B ARG* 1.3 77.2 - - - +
131B ARG* 1.3 66.6 + - + +
133B SER* 2.7 28.0 + - - -
134B ILE* 3.2 42.8 + - + +
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Residues in contact with ARG 131 (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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29B TYR* 3.7 10.3 + - - -
52B LEU* 5.0 0.2 - - - +
78B LEU* 4.0 18.9 - - - +
83B PHE* 4.9 3.5 - - - +
99B ASP* 2.4 46.1 + - - +
127B LEU* 2.9 42.9 + - + +
128B LEU* 3.3 14.1 + - + +
130B PHE* 1.3 87.7 - - + +
132B PHE* 1.3 66.7 + - + +
134B ILE* 3.5 19.2 - - + +
135B LEU* 3.7 16.5 - - - +
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Residues in contact with PHE 132 (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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128B LEU* 3.1 35.9 + - + +
129B ARG* 3.1 8.8 + - - +
130B PHE 3.0 0.6 - - - -
131B ARG* 1.3 80.4 - - + +
133B SER* 1.3 65.0 + - - +
134B ILE 3.1 2.8 + - - -
135B LEU* 3.4 39.4 + - + +
140B ILE* 4.3 17.7 - - + +
143B PHE* 4.1 23.8 - + - -
215B VAL* 3.7 34.6 - - + +
218B ILE* 3.4 28.9 - - + -
219B LEU* 5.9 1.1 - - + -
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Residues in contact with SER 133 (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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65B LYS* 4.9 11.6 + - - +
71B GLN* 4.0 22.9 + - - +
129B ARG* 2.8 24.7 + - - +
130B PHE* 2.7 21.9 + - - -
132B PHE* 1.3 72.5 - - - +
134B ILE* 1.3 58.5 + - - +
135B LEU 3.5 1.6 - - - +
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN* 3.7 20.4 - - + +
75B GLU* 4.3 13.9 - - - +
130B PHE* 3.6 38.8 - - + +
131B ARG* 3.5 17.7 - - + +
132B PHE 3.1 0.2 - - - -
133B SER* 1.3 81.9 - - - +
135B LEU* 1.3 59.9 + - + +
136B PRO* 4.1 4.0 - - - +
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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