Contacts of the strand formed by residues 169 - 180 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A TYR* 4.3 23.6 - + + +
149A PRO* 4.9 9.6 + - + -
192A VAL* 3.6 17.0 - - + +
141B GLU* 2.6 44.1 + - + -
161B ALA* 3.9 11.0 - - + -
162B LEU 3.1 11.9 - - - +
163B LYS* 4.0 11.1 - - + +
164B LEU* 4.1 9.3 - - - +
168B GLY* 1.3 86.5 - - - -
170B LEU* 1.3 59.7 + - - +
171B ILE* 3.9 23.9 + - + +
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Residues in contact with LEU 170 (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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96B TYR* 3.7 29.3 - - + -
97B GLU* 4.5 4.3 - - + +
98B ASP* 3.6 45.5 - - + +
131B PRO* 4.2 19.3 - - + -
132B VAL* 4.3 14.1 - - + -
140B TRP* 4.8 0.7 - - - -
160B MET 4.0 0.2 - - - +
161B ALA* 3.6 0.3 - - - -
162B LEU* 2.7 47.3 + - + +
164B LEU* 3.9 20.3 - - + +
169B HIS* 1.3 72.6 - - - +
171B ILE* 1.3 66.1 + - - +
172B CYS 4.2 0.2 + - - -
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Residues in contact with ILE 171 (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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146A MET* 4.3 3.1 - - + -
148A TYR* 3.1 51.8 - - + +
157A ARG* 3.7 18.2 - - + -
96B TYR* 3.9 0.9 - - - -
97B GLU* 3.1 54.8 + - - +
159B ASP* 5.0 2.0 - - + +
160B MET 3.5 8.1 - - - +
161B ALA* 3.7 27.8 - - + -
169B HIS* 3.9 7.8 + - + +
170B LEU* 1.3 82.3 - - - +
172B CYS* 1.3 74.0 + - - +
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Residues in contact with CYS 172 (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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94B THR* 3.7 20.2 - - + -
95B THR 3.2 17.5 - - - +
96B TYR* 3.7 20.2 - - + -
97B GLU* 5.0 1.8 - - - -
140B TRP* 3.7 35.2 - - - -
159B ASP* 3.4 4.2 - - - +
160B MET* 2.9 41.5 + - - -
171B ILE* 1.3 81.6 - - - +
173B ASN* 1.3 59.4 + - - +
174B LEU* 4.1 3.8 - - - -
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Residues in contact with ASN 173 (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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159A ASP* 3.1 21.8 + - - +
173A ASN* 3.8 10.0 + - - +
93B VAL 3.6 1.6 - - - +
94B THR* 3.2 5.0 - - - -
95B THR* 2.9 40.6 + - - +
97B GLU* 6.0 0.2 - - - +
157B ARG* 4.8 2.3 - - - -
158B SER 2.8 15.9 + - - -
159B ASP* 2.6 26.4 + - - +
172B CYS* 1.3 76.0 - - - +
174B LEU* 1.3 71.5 + - - +
175B LYS* 3.5 26.5 + - - +
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Residues in contact with LEU 174 (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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60B THR* 4.5 6.5 - - - +
63B NRQ 4.3 14.4 - - + -
92B ARG* 3.7 31.0 - - - +
93B VAL 3.5 3.8 - - - -
94B THR* 3.7 15.5 - - + +
156B GLY 4.5 0.2 - - - -
157B ARG* 3.5 6.2 - - - -
158B SER* 2.9 45.1 + - - +
160B MET* 3.9 45.3 - - + -
172B CYS* 4.1 11.7 - - - -
173B ASN* 1.3 83.1 - - - +
175B LYS* 1.3 65.9 + - - +
176B THR* 4.1 3.1 - - - +
197B ARG* 5.0 1.1 - - - +
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Residues in contact with LYS 175 (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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97A GLU* 3.5 24.3 + - - +
173A ASN* 5.8 5.5 - - - +
91B GLU 3.9 0.5 - - - +
92B ARG* 3.3 2.6 - - - -
93B VAL* 2.9 52.4 + - + +
95B THR* 5.8 2.9 - - - -
156B GLY 3.6 0.2 - - - -
157B ARG* 3.4 36.1 - - - +
173B ASN* 3.5 18.6 + - - +
174B LEU* 1.3 77.8 - - - +
176B THR* 1.3 60.9 + - - +
99D GLY 5.8 0.4 - - - -
101D VAL* 6.5 0.4 - - - -
125D ASN* 4.1 25.1 - - - +
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Residues in contact with THR 176 (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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90B TRP* 4.0 4.7 - - + -
91B GLU 3.1 20.6 - - - +
92B ARG* 2.9 34.4 + - + +
145B GLU* 4.4 3.8 + - - -
155B GLU* 3.3 6.6 - - - +
156B GLY 2.9 33.6 + - - +
157B ARG* 3.9 2.8 + - - -
174B LEU* 4.6 3.8 - - - +
175B LYS* 1.3 76.3 + - - +
177B THR* 1.3 68.7 + - - +
178B TYR* 3.5 41.0 + - + +
125D ASN* 5.6 0.2 - - - -
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Residues in contact with THR 177 (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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89B THR 4.2 0.2 - - - +
90B TRP* 3.2 6.2 - - - +
91B GLU* 2.8 51.0 + - - +
154B LEU 3.8 7.4 - - - +
155B GLU* 4.3 19.0 + - + +
176B THR* 1.3 75.6 + - - +
178B TYR* 1.3 64.6 + - - +
179B ARG* 3.7 38.6 + - + +
125D ASN* 4.1 19.6 + - - +
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Residues in contact with TYR 178 (chain B).
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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67B LYS* 3.0 37.4 + - + -
79B PHE* 3.7 11.9 - - + -
80B PHE* 3.5 28.5 - + + -
88B PHE* 5.2 0.4 - + + -
89B THR 3.6 4.9 - - - +
90B TRP* 3.4 22.0 - + + -
92B ARG* 3.6 12.3 + - - -
145B GLU* 2.6 28.5 + - - -
147B LEU* 4.0 12.3 - - + -
153B GLY* 3.7 3.3 - - - -
154B LEU* 2.8 52.0 + - + +
156B GLY 4.3 7.2 - - - -
176B THR* 3.5 25.2 - - + +
177B THR* 1.3 74.4 - - - +
179B ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 179 (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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79B PHE* 4.2 1.8 - - - -
88B PHE* 3.4 2.7 - - - -
89B THR* 3.0 47.8 + - - +
91B GLU* 2.5 42.4 + - - -
151B ASP* 5.3 6.1 + - - -
153B GLY* 5.2 2.7 - - - -
177B THR* 3.7 21.8 - - + +
178B TYR* 1.3 76.0 - - - +
180B SER* 1.3 66.1 + - - +
181B LYS* 4.9 0.9 - - - +
20D ASN* 3.6 29.1 + - - +
21D ASN* 4.2 6.7 - - - +
125D ASN* 5.5 0.6 - - - +
126D PHE 5.2 0.2 + - - -
128D SER* 5.5 8.1 - - - -
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Residues in contact with SER 180 (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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79B PHE* 3.5 17.4 - - - -
83B SER* 2.7 27.9 + - - -
87B GLY 4.0 2.5 - - - -
88B PHE* 4.1 3.1 - - - -
152B GLY 5.3 4.0 + - - -
179B ARG* 1.3 77.9 - - - +
181B LYS* 1.3 64.6 + - - +
182B LYS* 3.1 25.9 + - - +
187B LEU* 3.5 18.6 - - - +
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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