Contacts of the strand formed by residues 179 - 185 (chain B) in PDB entry 2ZPB
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 THR 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ALA* 3.9 7.7 - - + +
165A GLU 5.2 0.2 + - - -
166A THR* 4.3 0.2 + - - -
156B ARG* 3.7 2.8 - - - -
157B THR* 2.9 48.4 + - - +
161B TRP* 4.1 11.8 - - + -
178B PRO* 1.3 78.4 - - - +
180B TYR* 1.3 64.9 + - - +
202B ASP* 2.6 28.3 + - - -
203B LEU 3.4 10.5 - - - -
204B PHE* 3.7 45.1 - - + -
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Residues in contact with TYR 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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122B THR* 3.5 2.4 - - - -
123B PHE* 3.0 48.0 + + + -
153B ILE* 3.8 31.4 - - + -
155B HIS 3.2 13.9 - - - +
156B ARG* 3.5 27.7 - - + -
178B PRO* 4.0 7.4 - - + +
179B THR* 1.3 75.8 - - - +
181B HIS* 1.3 60.5 + - - +
182B VAL* 3.3 4.2 + - + +
201B VAL 3.1 3.8 - - - +
202B ASP* 3.4 4.0 - - - -
203B LEU 2.8 42.5 + - - +
205B GLU* 2.6 49.2 + - + -
208B LEU* 3.7 17.7 - - + -
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Residues in contact with HIS 181 (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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95A VAL* 3.9 13.4 - - + +
160A TYR* 4.7 5.0 - - + -
166A THR* 2.9 34.2 + - + -
168A TYR* 3.2 32.5 + + - -
153B ILE* 3.6 3.1 - - - -
154B SER* 2.8 37.7 + - - -
155B HIS* 3.0 46.6 + + + +
157B THR* 4.7 2.0 - - + +
180B TYR* 1.3 69.8 - - - +
182B VAL* 1.3 57.0 + - - +
183B LYS 4.0 0.2 - - - -
200B VAL* 3.6 15.3 - - + -
201B VAL 3.6 4.0 - - - -
202B ASP* 3.3 18.4 - - + -
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Residues in contact with VAL 182 (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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129B VAL* 3.8 20.6 - - + -
151B GLY* 3.9 15.7 - - - -
152B THR 3.5 3.4 - - - +
153B ILE* 4.1 7.0 - - + -
180B TYR* 3.7 17.3 - - + +
181B HIS* 1.3 73.8 - - - +
183B LYS* 1.3 60.2 + - - +
184B PHE* 3.4 35.7 - - + -
200B VAL* 3.2 3.4 - - - +
201B VAL 2.9 33.4 + - - +
203B LEU* 4.0 14.8 - - + -
208B LEU* 4.1 22.4 - - + -
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Residues in contact with LYS 183 (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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156A GLU* 5.1 0.8 + - - -
158A ARG* 3.5 39.9 - - - +
151B GLY* 3.2 3.6 - - - -
152B THR* 2.8 55.3 + - + +
154B SER* 3.7 19.1 - - - +
181B HIS 3.9 1.4 + - - -
182B VAL* 1.3 71.4 - - - +
184B PHE* 1.3 64.4 + - - +
185B ALA 4.3 0.2 + - - -
198B SER* 3.9 20.2 - - - +
199B VAL 3.6 3.4 - - - -
200B VAL* 4.0 13.0 - - + -
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Residues in contact with PHE 184 (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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129B VAL 5.3 0.2 - - - -
131B VAL* 3.6 21.3 - - + -
146B CYS* 3.9 7.4 - - + -
149B ARG* 3.7 31.6 - - + -
150B VAL 3.3 28.7 - - - +
151B GLY* 3.8 3.6 - - - -
182B VAL* 3.4 38.1 - - + -
183B LYS* 1.3 74.4 - - - +
185B ALA* 1.3 61.4 + - - +
188B GLU* 4.5 1.3 - - + -
189B LEU* 3.8 35.9 - - + -
198B SER* 3.3 6.7 - - - -
199B VAL 2.8 39.5 + - - +
201B VAL* 3.7 25.4 - - + -
203B LEU* 4.1 1.1 - - + -
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Residues in contact with ALA 185 (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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150B VAL 5.2 0.6 + - - -
183B LYS 4.3 0.6 + - - -
184B PHE* 1.3 73.9 - - - +
186B ALA* 1.3 67.5 + - - +
187B GLU* 3.6 29.2 - - + +
188B GLU* 2.9 26.8 + - + +
189B LEU* 3.5 6.6 + - - +
197B GLY 3.9 6.1 - - - +
198B SER* 4.5 2.0 - - - +
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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