Contacts of the strand formed by residues 150 - 156 (chain B) in PDB entry 3ZXR
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 GLY 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ARG* 2.9 45.6 + - - +
148B ALA 3.5 2.6 + - - -
149B ASN* 1.3 82.3 + - - +
151B SER* 1.3 62.6 + - - -
472B PHE* 6.5 1.6 - - - -
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Residues in contact with SER 151 (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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145B ASP* 2.6 29.6 + - - -
146B SER* 3.7 12.8 + - - -
147B ARG* 3.7 4.0 - - - +
150B GLY* 1.3 74.4 - - - -
152B PHE* 1.3 64.9 + - - +
467B PRO 5.3 8.7 - - - -
469B PRO* 4.5 19.9 - - - +
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Residues in contact with PHE 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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143B SER* 3.5 27.6 - - - -
144B PHE* 3.1 35.3 - - - +
145B ASP* 3.1 51.1 + - - +
147B ARG* 4.6 5.4 - - - +
151B SER* 1.3 80.6 + - - +
153B TYR* 1.3 75.1 + - - +
154B GLU* 4.2 8.1 - - + -
469B PRO* 5.6 4.5 - - - -
165C GLY* 3.6 23.6 - - - -
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Residues in contact with TYR 153 (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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142B VAL* 6.0 1.6 - - + -
143B SER 3.2 7.6 - - - +
144B PHE* 3.8 14.6 - - + -
152B PHE* 1.3 83.5 - - - +
154B GLU* 1.3 73.9 + - - +
155B VAL* 4.4 13.2 - - + -
266B PRO* 4.1 21.7 + - + -
268B PHE* 4.9 13.7 + - - +
469B PRO* 6.2 5.6 - - + -
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Residues in contact with GLU 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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141B SER* 4.0 4.0 + - - +
142B VAL* 3.3 6.3 - - - +
143B SER* 2.9 37.0 + - - +
152B PHE* 4.5 11.2 - - + -
153B TYR* 1.3 79.5 - - - +
155B VAL* 1.3 73.2 + - - +
156B ASP* 4.3 18.3 - - - +
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Residues in contact with VAL 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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139B PHE* 3.7 35.2 - - + -
141B SER 3.4 3.6 - - - +
142B VAL* 3.9 20.0 - - + -
153B TYR* 4.4 14.5 - - + -
154B GLU* 1.3 83.5 - - - +
156B ASP* 1.3 64.7 + - - +
162B TRP* 4.2 10.2 + - + -
261B THR* 5.9 0.7 - - + -
263B MET* 6.2 2.5 - - - -
266B PRO* 4.1 13.2 - - + +
267B LEU* 3.5 31.9 - - + -
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Residues in contact with ASP 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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139B PHE* 3.5 5.2 - - - +
140B ASP* 2.6 35.4 + - + -
141B SER* 2.9 30.0 + - - +
154B GLU* 4.3 13.4 - - - +
155B VAL* 1.3 75.4 - - - +
157B ALA* 1.3 64.7 + - - +
162B TRP* 2.8 29.4 + - - -
163B ASN* 3.0 17.3 + - - +
170B ALA* 5.9 3.1 - - - +
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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