Contacts of the strand formed by residues 153 - 160 (chain B) in PDB entry 4BR6
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 LEU 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ALA* 4.2 12.3 - - + -
131B LYS 3.7 2.2 - - - +
132B ASP* 3.7 29.8 - - + +
137B ASN 5.5 0.2 - - - +
139B ALA* 5.8 7.4 - - + -
141B VAL* 3.7 30.5 - - + -
143B ARG* 4.3 12.6 - - - +
149B VAL* 3.7 23.7 - - + +
150B THR* 3.7 19.3 + - - +
151B GLY 3.9 2.2 + - - +
152B GLN* 1.3 94.3 - - + +
154B VAL* 1.3 63.8 + - - +
155B PRO* 4.1 0.2 - - - +
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Residues in contact with VAL 154 (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* 3.2 3.2 - - - -
131B LYS* 2.9 39.7 + - + +
133B LYS* 4.2 20.9 - - + -
149B VAL* 4.1 0.2 - - - -
151B GLY 5.2 2.2 - - - +
153B LEU* 1.3 77.8 - - - +
155B PRO* 1.3 79.3 - - + +
156B LEU* 4.0 3.6 - - + +
193B ARG* 6.3 0.2 - - + -
197B ALA* 3.7 32.3 - - + -
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Residues in contact with PRO 155 (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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72B LEU* 5.6 4.9 - - + -
76B LEU* 3.7 22.4 - - + +
128B TRP* 3.5 29.8 - - + -
129B LEU 4.0 4.5 - - - +
130B ALA* 4.3 1.1 - - + -
149B VAL* 3.5 40.2 - - + +
153B LEU 4.1 0.2 - - - +
154B VAL* 1.3 94.4 - - + +
156B LEU* 1.3 65.4 + - - +
193B ARG* 4.1 10.8 + - - +
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Residues in contact with LEU 156 (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 LEU* 5.0 1.3 - - + -
128B TRP* 5.2 0.2 - - - -
129B LEU* 2.9 24.1 + - + +
131B LYS* 3.9 21.3 - - + +
138B LEU* 3.9 10.3 - - + -
154B VAL* 4.0 11.4 - - + +
155B PRO* 1.3 83.0 - - - +
157B MET* 1.3 63.0 + - - +
190B VAL* 3.6 23.4 - - + +
193B ARG* 2.7 64.0 + - + +
194B PHE* 3.8 32.8 - - + +
197B ALA* 4.4 7.4 - - + -
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Residues in contact with MET 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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80B ASN* 3.6 12.6 - - - -
110B PHE* 4.2 4.3 - - + -
114B MET* 3.7 33.2 - - + +
128B TRP* 3.3 5.9 - - - -
129B LEU* 2.8 41.5 + - + -
156B LEU* 1.3 82.6 - - - +
158B GLY* 1.3 75.5 + - - +
159B ILE* 3.9 15.5 - - + -
182B TRP* 4.0 18.8 - - + -
185B ILE* 3.9 19.7 - - + -
187B TRP* 4.1 9.2 - - + -
190B VAL* 3.7 27.4 - - + -
193B ARG* 4.0 0.2 - - - +
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Residues in contact with GLY 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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77B PHE* 3.4 14.3 - - - -
80B ASN* 3.1 28.3 + - - -
126B TRP* 4.6 1.3 - - - -
127B ALA 3.4 4.5 - - - -
128B TRP* 3.4 29.6 - - - -
157B MET* 1.3 74.3 - - - +
159B ILE* 1.3 68.2 + - - +
185B ILE* 4.9 0.2 - - - +
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Residues in contact with ILE 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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77B PHE* 3.9 2.7 - - - -
114B MET* 4.2 4.0 - - + -
118B LEU* 3.6 35.8 - - + +
126B TRP* 3.6 4.3 - - - -
127B ALA 2.9 32.9 + - - +
157B MET* 3.9 19.5 - - + -
158B GLY* 1.3 79.5 - - - +
160B ASP* 1.3 70.7 + - - +
161B ALA 3.6 0.2 + - - -
177B TYR* 4.0 15.5 - - + +
178B PHE* 4.8 0.2 - - + -
181B ILE* 4.0 33.7 - - + -
182B TRP* 4.0 28.0 - - + -
185B ILE* 4.6 4.9 - - + -
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Residues in contact with ASP 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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26B HIS* 2.8 12.8 + - - -
77B PHE* 3.8 19.2 - - + -
126B TRP* 3.4 33.0 - - + -
159B ILE* 1.3 73.2 - - - +
161B ALA* 1.3 67.2 + - - +
162B TRP* 3.1 26.3 + - - -
164B HIS* 3.7 0.7 + - - -
165B ALA* 3.7 11.2 - - + +
177B TYR* 3.0 29.3 + - - -
301B MN3 2.2 32.8 + - - -
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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