Contacts of the strand formed by residues 156 - 163 (chain B) in PDB entry 4BNR
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 GLN 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.6 28.6 - - + +
19B GLY* 3.7 14.6 + - - +
20B THR* 3.4 15.0 - - - -
21B ASP* 2.7 29.3 + - - +
22B ALA 4.9 0.7 - - - -
139B THR* 3.2 9.1 - - - +
140B GLY 3.1 32.2 + - - +
144B THR* 4.6 12.0 - - + +
152B PRO* 3.7 24.4 - - + +
154B VAL* 3.0 22.8 + - - +
155B LEU* 1.3 81.0 + - - +
157B LYS* 1.3 60.1 + - - +
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Residues in contact with LYS 157 (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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16B ILE* 4.2 1.3 - - - -
19B GLY* 3.0 4.7 - - - -
20B THR* 2.8 58.7 + - - +
21B ASP 3.9 12.5 + - - +
26B GLU* 2.8 34.3 + - - +
27B PHE* 3.7 16.6 - - + -
137B ILE* 4.4 5.4 - - + -
138B VAL 3.5 5.6 - - - -
139B THR* 3.7 16.4 - - + -
156B GLN* 1.3 74.6 - - - +
158B VAL* 1.3 62.2 + - - +
159B THR* 6.1 0.9 - - - +
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Residues in contact with VAL 158 (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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16B ILE* 3.6 19.5 - - + -
17B VAL 4.0 3.8 - - - +
18B GLY 3.6 23.6 - - - +
19B GLY* 4.0 0.4 - - - -
136B VAL 3.7 0.5 - - - +
137B ILE* 3.4 4.6 - - - -
138B VAL* 2.9 52.1 + - + +
157B LYS* 1.3 77.2 - - - +
159B THR* 1.3 65.1 + - - +
160B VAL* 4.1 10.9 + - + -
188B LYS* 3.7 29.6 - - + -
189B ASP* 4.4 11.9 - - - +
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Residues in contact with THR 159 (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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135B ASP* 3.8 30.1 - - + +
136B VAL 3.4 11.9 - - - +
137B ILE* 3.9 17.4 - - + +
157B LYS* 6.1 1.0 - - - +
158B VAL* 1.3 74.3 - - - +
160B VAL* 1.3 68.3 + - - +
188B LYS* 2.9 31.5 + - - +
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Residues in contact with VAL 160 (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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135B ASP* 4.3 4.3 - - - -
136B VAL* 2.9 41.1 + - + +
138B VAL* 4.5 12.1 - - + -
158B VAL* 4.2 11.0 - - + +
159B THR* 1.3 80.9 - - - +
161B PRO* 1.3 73.0 - - + +
183B ALA* 3.6 28.3 - - + +
184B GLY* 3.9 10.3 - - - +
188B LYS* 3.7 39.7 - - + +
189B ASP* 4.8 1.6 - - - +
229B TYR* 5.3 1.8 - - - +
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Residues in contact with PRO 161 (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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134B GLY 3.9 2.5 - - - +
135B ASP* 3.6 21.7 - - - +
159B THR 4.8 0.2 - - - +
160B VAL* 1.3 85.8 - - + +
162B LEU* 1.3 67.8 + - - +
163B VAL* 5.7 0.4 - - + -
183B ALA* 3.5 1.2 - - - -
184B GLY 3.1 37.3 + - - +
185B VAL* 3.5 27.8 - - + -
186B PRO* 5.6 2.2 - - + -
188B LYS* 5.7 0.4 - - - +
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Residues in contact with LEU 162 (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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130B ALA* 3.4 47.6 - - + +
131B THR* 3.5 8.7 - - - +
134B GLY* 3.0 22.9 + - - +
136B VAL* 3.5 35.9 - - + -
160B VAL 3.6 0.4 + - - -
161B PRO* 1.3 79.9 - - - +
163B VAL* 1.3 62.4 + - - +
164B SER 4.5 0.3 + - - -
181B ILE* 3.5 23.8 - - + -
182B CYS 3.6 12.3 - - - +
183B ALA* 4.1 4.9 - - + +
199B LEU* 4.3 8.5 - - + -
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Residues in contact with VAL 163 (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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161B PRO* 4.0 2.5 - - + +
162B LEU* 1.3 81.1 - - - +
164B SER* 1.3 77.3 + - - +
165B ASP* 3.8 1.4 + - - +
167B ASP* 3.7 20.2 - - + +
168B CYS* 3.8 13.9 - - + +
171B ASP* 5.0 1.8 - - - +
181B ILE* 4.6 6.1 - - - +
182B CYS* 2.8 32.5 + - + +
183B ALA* 4.4 0.7 - - - -
184B GLY 3.7 29.2 - - - +
225B PRO* 4.4 12.8 - - + -
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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