Contacts of the strand formed by residues 169 - 180 (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 HIS 169 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E GLU* 2.7 44.8 + - + +
161E ALA* 3.8 11.4 - - + -
162E LEU 3.3 13.0 - - - +
163E LYS* 3.7 9.9 - - + +
164E LEU* 3.9 9.8 - - - +
168E GLY* 1.3 84.5 - - - -
170E LEU* 1.3 61.0 + - - +
171E ILE* 4.1 13.4 + - + +
148F TYR* 4.2 32.3 - + + +
149F PRO* 4.9 8.9 + - + -
192F VAL* 3.6 17.7 - - + +
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Residues in contact with LEU 170 (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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96E TYR* 4.0 23.7 - - + -
97E GLU* 4.7 3.8 - - + +
98E ASP* 3.8 47.8 - - + +
131E PRO* 3.8 18.6 - - + -
132E VAL* 4.5 12.1 - - + -
140E TRP* 4.9 0.7 - - - -
160E MET 3.8 0.5 - - - +
161E ALA* 3.5 1.4 - - - -
162E LEU* 2.7 47.1 + - + +
164E LEU* 3.9 18.5 - - + +
169E HIS* 1.3 74.3 - - - +
171E ILE* 1.3 72.7 + - - +
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Residues in contact with ILE 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E TYR* 3.8 1.1 - - - -
97E GLU* 2.9 55.2 + - - +
159E ASP* 4.6 4.5 - - + +
160E MET 3.4 8.5 - - - +
161E ALA* 3.7 27.8 - - + -
169E HIS* 4.3 5.6 - - + +
170E LEU* 1.3 82.0 - - - +
172E CYS* 1.3 73.3 + - - +
146F MET* 4.2 3.4 - - + -
148F TYR* 3.2 49.8 - - + +
157F ARG* 3.8 18.4 - - + +
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Residues in contact with CYS 172 (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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94E THR* 3.6 24.0 - - + -
95E THR 3.0 15.7 - - - +
96E TYR* 3.7 19.3 - - + -
97E GLU* 5.1 1.3 - - - -
140E TRP* 3.9 22.4 - - - -
158E SER 4.0 0.2 - - - +
159E ASP* 3.7 3.3 - - - -
160E MET* 3.1 45.2 + - - +
170E LEU 4.1 0.2 + - - -
171E ILE* 1.3 79.8 - - - +
173E ASN* 1.3 57.8 + - - +
174E LEU* 3.6 13.0 - - - +
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Residues in contact with ASN 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL 3.6 1.9 - - - +
94E THR* 3.3 4.0 - - - -
95E THR* 2.8 42.1 + - - +
97E GLU* 5.8 0.8 - - - +
157E ARG* 5.2 2.7 - - - +
158E SER 3.2 17.4 + - - +
159E ASP* 3.8 12.6 + - - +
172E CYS* 1.3 73.5 - - - +
174E LEU* 1.3 65.7 + - - +
175E LYS* 3.5 33.8 + - - +
97F GLU* 5.4 0.3 - - - +
159F ASP* 3.3 23.6 + - - -
173F ASN* 4.4 15.0 - - - +
175F LYS* 5.9 2.9 - - - +
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Residues in contact with LEU 174 (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* 4.6 5.8 - - + +
63E NRQ 4.5 11.2 - - + -
92E ARG* 3.6 31.6 - - - +
93E VAL 3.6 2.9 - - - -
94E THR* 3.6 16.8 - - + +
156E GLY 3.6 0.9 - - - +
157E ARG* 3.4 8.7 - - - -
158E SER* 2.7 42.3 + - - +
160E MET* 3.7 33.2 - - + -
172E CYS* 3.6 29.8 - - - +
173E ASN* 1.3 75.9 + - - +
175E LYS* 1.3 64.6 + - - +
176E THR* 4.1 3.8 + - - +
197E ARG* 4.6 6.7 - - - +
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Residues in contact with LYS 175 (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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91E GLU 3.9 1.0 - - - +
92E ARG* 3.3 2.5 - - - -
93E VAL* 2.9 56.8 + - + +
95E THR* 5.6 5.0 + - - -
156E GLY 3.6 4.3 - - - -
157E ARG* 3.6 22.0 - - - +
173E ASN* 3.5 22.8 + - - +
174E LEU* 1.3 74.6 - - - +
176E THR* 1.3 62.3 + - - +
97F GLU* 3.4 35.7 + - - +
99H GLY* 5.3 1.8 - - - -
101H VAL* 6.0 2.9 - - - -
124H VAL* 5.7 0.2 - - - +
125H ASN* 4.0 23.1 - - - +
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Residues in contact with THR 176 (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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90E TRP* 4.2 9.0 - - + -
91E GLU 3.5 12.6 - - - +
92E ARG* 3.2 39.8 + - + +
145E GLU* 4.3 3.1 + - - -
155E GLU* 3.3 8.1 - - - +
156E GLY* 2.8 37.1 + - - +
157E ARG* 3.8 2.1 + - - +
174E LEU* 4.6 3.8 - - - +
175E LYS* 1.3 75.0 + - - +
177E THR* 1.3 64.2 + - - +
178E TYR* 3.8 37.4 + - + +
125H ASN* 6.0 0.2 - - - -
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Residues in contact with THR 177 (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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90E TRP* 3.4 3.8 - - - -
91E GLU* 2.9 35.1 + - - +
150E ALA 6.1 0.9 - - - +
154E LEU 3.6 8.1 - - - +
155E GLU* 3.8 19.1 + - + +
176E THR* 1.3 74.2 + - - +
178E TYR* 1.3 65.4 + - - +
179E ARG* 3.7 45.7 + - + +
125H ASN* 4.1 22.0 + - - +
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Residues in contact with TYR 178 (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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67E LYS* 2.8 41.2 + - + -
79E PHE* 4.0 6.4 - - + -
80E PHE* 3.5 25.4 - + + -
88E PHE* 5.6 0.4 - + + -
89E THR 3.6 4.5 - - - +
90E TRP* 3.6 19.5 - + + -
92E ARG* 4.3 6.0 + - - -
145E GLU* 2.4 33.3 + - - -
147E LEU* 3.6 13.7 - - + -
153E GLY* 3.4 6.6 - - - -
154E LEU* 2.6 57.8 + - + +
155E GLU 4.3 0.9 - - - -
156E GLY 4.0 10.5 - - - -
176E THR* 3.8 24.3 + - + +
177E THR* 1.3 74.6 - - - +
179E ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 179 (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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79E PHE* 4.2 1.3 - - - -
88E PHE* 3.2 5.8 - - - +
89E THR* 2.8 50.9 + - - +
90E TRP 5.6 0.2 - - - -
91E GLU* 2.8 44.0 + - - +
153E GLY* 5.0 4.0 - - - -
177E THR* 3.7 31.1 + - + +
178E TYR* 1.3 78.8 - - - +
180E SER* 1.3 65.1 + - - +
181E LYS* 5.0 0.7 - - - +
20H ASN* 3.7 31.3 + - - +
21H ASN* 3.8 25.7 - - - +
125H ASN* 5.2 3.0 - - - +
126H PHE 5.3 0.2 + - - -
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Residues in contact with SER 180 (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 23.2 - - - -
83E SER* 3.0 25.7 + - - -
88E PHE* 4.1 3.1 - - - -
152E GLY 5.4 1.7 + - - -
153E GLY* 5.3 0.6 - - - -
179E ARG* 1.3 77.0 - - - +
181E LYS* 1.3 60.8 + - - +
182E LYS* 2.8 31.9 + - - +
187E LEU* 3.5 13.9 - - - +
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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
------------------------------------------------------------
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