Contacts of the strand formed by residues 153 - 164 (chain E) in PDB entry 3BXB
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 GLY 153 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE* 3.7 11.4 - - - -
149E PRO* 3.8 0.2 - - - +
150E ALA 3.3 25.1 + - - -
151E ASP* 3.2 6.3 + - - +
152E GLY* 1.3 79.2 + - - +
154E LEU* 1.3 61.9 + - - -
178E TYR 3.4 13.0 - - - -
179E ARG* 5.0 4.7 - - - -
180E SER 5.3 0.2 - - - -
189E MET* 3.4 15.1 - - - +
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Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E PHE* 3.5 42.3 - - + -
80E PHE* 4.2 10.3 - - + -
147E LEU* 4.4 6.1 - - + -
148E TYR 3.8 7.4 - - - +
149E PRO* 4.0 19.1 - - + -
150E ALA 5.0 1.8 - - - -
153E GLY* 1.3 72.5 - - - -
155E GLU* 1.3 64.8 + - - +
177E THR* 3.6 1.6 - - - +
178E TYR* 2.6 52.1 + - + +
189E MET* 3.8 13.2 - - + -
190E PRO* 3.7 23.3 - - + -
193E TYR* 4.0 23.8 - - + +
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Residues in contact with GLU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LEU* 3.2 8.1 - - - +
148E TYR* 3.0 70.1 + - + +
150E ALA* 4.1 22.9 - - + +
151E ASP* 4.6 8.7 - - - +
154E LEU* 1.3 79.2 - - - +
156E GLY* 1.3 58.7 + - - +
157E ARG* 3.4 13.3 + - - +
176E THR 3.3 11.9 - - - +
177E THR* 3.8 22.2 + - + +
178E TYR* 4.2 4.0 - - - -
125H ASN* 4.7 5.8 - - - +
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Residues in contact with GLY 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E GLU* 3.3 23.8 - - - -
146E MET 3.4 5.6 - - - -
147E LEU* 4.5 0.4 - - - -
155E GLU* 1.3 74.4 - - - +
157E ARG* 1.3 81.5 + - - -
174E LEU 3.6 1.9 - - - +
176E THR* 2.8 30.4 + - - -
178E TYR* 4.0 3.2 - - - -
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Residues in contact with ARG 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E THR 4.1 0.5 - - - +
145E GLU* 3.4 2.8 - - - +
146E MET* 3.0 41.1 + - + +
148E TYR* 3.0 37.3 + - + -
155E GLU* 3.4 15.6 + - - +
156E GLY* 1.3 90.3 + - - +
158E SER* 1.3 63.1 + - - +
173E ASN* 5.2 2.9 - - - +
174E LEU 3.4 3.4 - - - -
175E LYS* 3.6 33.1 - - - +
176E THR 3.8 10.5 + - - +
177E THR* 5.6 0.2 + - - -
97F GLU* 2.7 44.7 + - - -
159F ASP* 3.9 27.4 - - + +
171F ILE* 3.9 13.6 - - + +
125H ASN* 4.3 10.7 + - - +
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Residues in contact with SER 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E SER* 4.2 0.3 + - - -
144E THR 2.8 10.5 + - - -
145E GLU* 4.3 3.6 - - - -
157E ARG* 1.3 76.0 - - - +
159E ASP* 1.3 63.6 + - - +
160E MET* 4.2 1.2 - - - +
172E CYS 4.0 0.2 - - - +
173E ASN* 3.2 4.4 + - - +
174E LEU* 2.7 51.6 + - - +
197E ARG* 2.7 46.6 + - - -
159F ASP* 3.5 9.5 + - - -
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Residues in contact with ASP 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E SER* 3.7 19.1 - - - -
144E THR 4.5 4.1 + - - +
158E SER* 1.3 74.7 + - - +
160E MET* 1.3 61.2 + - - +
171E ILE* 4.6 3.2 - - + +
172E CYS 3.7 6.1 - - - +
173E ASN* 3.8 9.9 + - - +
146F MET* 4.0 14.7 - - + +
157F ARG* 3.7 34.2 - - + +
158F SER* 3.3 17.6 + - - -
159F ASP* 2.6 31.0 + - - +
173F ASN* 3.6 18.9 + - - -
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Residues in contact with MET 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E THR* 3.8 18.2 - - + -
63E NRQ 3.3 41.5 - - + +
140E TRP* 3.5 51.1 - - + -
141E GLU 4.7 2.5 - - - +
143E SER* 4.0 15.9 - - - +
158E SER* 4.4 3.4 - - - +
159E ASP* 1.3 79.8 - - - +
161E ALA* 1.3 60.6 + - - +
162E LEU 4.2 0.4 - - - -
170E LEU 3.8 0.5 - - - +
171E ILE* 3.4 7.1 - - - +
172E CYS* 3.1 40.2 + - - -
174E LEU* 3.7 22.2 - - + -
199E LEU* 5.6 0.7 - - + -
146F MET* 4.0 4.0 - - - -
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Residues in contact with ALA 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E TRP* 3.6 5.9 - - - -
141E GLU* 2.9 45.5 + - + +
142E ALA 5.6 0.2 + - - -
160E MET* 1.3 73.5 - - - +
162E LEU* 1.3 61.5 + - - +
169E HIS* 3.8 18.4 - - + -
170E LEU 3.5 3.6 - - - -
171E ILE* 3.7 19.3 - - + -
146F MET* 3.7 17.6 - - + +
148F TYR* 5.4 3.6 - - + -
192F VAL* 5.7 0.2 - - + -
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Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ASP* 3.6 28.7 - - + +
57E ILE* 4.9 1.3 - - + -
96E TYR* 4.4 8.3 - - + -
132E VAL* 4.2 16.8 - - + -
137E THR* 3.8 30.5 - - + +
139E GLY 3.6 8.5 - - - +
140E TRP* 3.5 45.9 - - + -
161E ALA* 1.3 72.6 - - - +
163E LYS* 1.3 65.1 + - - +
164E LEU* 3.8 1.8 - - + +
169E HIS* 3.3 4.5 - - - -
170E LEU* 2.7 50.4 + - + +
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Residues in contact with LYS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E THR* 3.4 6.4 - - - -
138E LEU* 2.7 54.8 + - + +
139E GLY 2.7 17.8 + - - +
140E TRP 3.9 20.2 + - - -
141E GLU* 3.3 38.7 + - + +
161E ALA 3.9 0.4 + - - -
162E LEU* 1.3 73.2 - - - +
164E LEU* 1.3 59.7 + - - +
168E GLY 4.0 4.0 - - - +
169E HIS* 3.7 9.6 - - + +
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Residues in contact with LEU 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PRO* 3.7 36.3 - - + -
136E LYS 3.6 5.2 - - - +
137E THR* 4.3 7.6 - - + -
138E LEU* 3.9 10.2 - - - +
162E LEU* 3.8 13.2 - - + +
163E LYS* 1.3 85.6 - - - +
165E VAL* 1.3 67.1 + - - +
166E GLY 3.3 0.2 + - - -
167E GLY* 3.1 26.7 + - - +
168E GLY* 3.1 14.5 + - - +
169E HIS 3.9 22.4 - - - +
170E LEU* 3.9 15.3 - - + +
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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