Contacts of the strand formed by residues 151 - 155 (chain B) in PDB entry 2B2T
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 TYR 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ILE* 3.5 37.7 - - + -
138B ALA 3.4 5.8 - - - +
139B HIS* 3.3 29.8 - + + -
148B TYR* 5.7 3.2 - + - -
149B PRO* 3.5 36.7 - - + +
150B ASP* 1.3 71.7 - - - +
152B TYR* 1.3 59.3 + - - +
153B CYS* 3.5 9.6 - - - -
164B SER 3.4 2.1 - - - +
165B TRP* 3.4 6.5 - - - -
166B GLU 2.9 33.3 + - - +
168B GLY* 4.0 20.0 - - - -
171B ILE* 4.1 9.4 - - + -
172B SER* 5.5 3.6 - - - -
179B ILE* 3.8 31.6 - - + +
182B TYR* 4.8 1.1 - + - -
183B PHE* 3.8 17.2 - + - -
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Residues in contact with TYR 152 (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 LYS* 3.1 32.4 - - - +
100A GLU* 3.9 16.6 - - + +
101A THR* 4.2 11.7 + - - -
104A TRP* 4.0 23.6 - + - -
136B ILE* 3.6 3.1 - - - -
137B ILE* 2.8 43.0 + - + +
138B ALA* 2.9 27.6 + - + +
151B TYR* 1.3 70.7 - - - +
153B CYS* 1.3 60.0 + - - +
160B TYR* 6.1 0.4 - + - -
163B CYS* 3.3 29.6 - - + +
164B SER* 3.5 17.0 - - - -
165B TRP* 3.3 46.3 - + + -
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Residues in contact with CYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 4.3 11.4 - - + -
135B ARG 3.6 3.4 - - - -
136B ILE* 4.6 4.5 - - - +
137B ILE* 5.7 0.2 - - - -
151B TYR* 3.5 24.0 - - - -
152B TYR* 1.3 76.1 - - - +
154B LYS* 1.3 60.8 + - - +
155B TRP* 3.9 19.8 + - + -
163B CYS* 3.0 29.7 - - - +
164B SER 2.9 14.5 + - - +
166B GLU* 4.1 6.1 - - - -
171B ILE* 2.9 37.9 - - + -
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Residues in contact with LYS 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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115A TYR* 4.9 8.6 + - + +
119A GLN* 3.8 31.2 + - - +
123A THR* 5.2 1.0 - - - +
133B VAL* 3.7 2.6 - - - -
134B GLY* 2.7 32.7 + - - -
135B ARG* 2.7 27.3 + - + +
137B ILE* 4.3 8.0 - - + +
153B CYS* 1.3 73.6 - - - +
155B TRP* 1.3 67.0 + - - +
156B GLN* 4.8 1.4 - - - +
157B GLY 4.7 3.0 - - - +
158B LEU 2.7 30.0 + - - +
159B PRO 4.5 2.2 - - - +
160B TYR* 3.4 50.5 - - + +
163B CYS* 4.1 12.1 - - - -
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Residues in contact with TRP 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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68B SER* 3.6 23.8 - - - -
70B ILE* 4.0 20.4 - - + -
130B TYR 3.2 25.1 - - - +
131B GLN 3.7 13.5 - - - -
132B ILE 3.2 23.6 - - - -
133B VAL* 3.5 34.1 - - + -
134B GLY* 4.4 0.4 - - - -
153B CYS* 3.9 15.9 + - + -
154B LYS* 1.3 89.7 + - - +
156B GLN* 1.3 65.1 + - - +
158B LEU* 3.1 38.0 + - + +
159B PRO 5.5 1.6 + - - -
162B GLU 3.3 22.6 + - - -
163B CYS* 5.3 0.8 - - - +
164B SER* 2.8 20.4 + - - -
166B GLU* 3.7 17.5 - - + -
171B ILE* 4.5 6.7 - - + -
175B PHE* 4.9 0.9 - + - -
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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
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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