Contacts of the strand formed by residues 198 - 204 (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 SER 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLU* 2.7 25.0 + - - -
157A ILE 3.0 4.6 + - - +
158A ARG* 3.0 25.4 + - - +
159A VAL* 3.0 23.8 + - - +
183B LYS* 3.9 17.5 - - - -
184B PHE 3.3 13.9 - - - -
185B ALA* 4.7 1.8 - - - -
186B ALA 4.1 1.6 - - - +
197B GLY* 1.3 77.6 + - - +
199B VAL* 1.3 68.7 + - - +
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Residues in contact with VAL 199 (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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137A VAL* 3.7 35.0 - - + +
159A VAL* 3.3 16.8 - - + +
161A ASP* 4.9 2.5 - - + -
145B TYR* 3.7 26.9 - - + +
182B VAL 3.5 2.1 - - - +
184B PHE* 2.8 34.6 + - - +
186B ALA* 5.1 8.1 - - + -
189B LEU* 3.7 23.1 - - + -
190B PHE* 4.9 1.3 - - + -
198B SER* 1.3 80.1 - - - +
200B VAL* 1.3 65.2 + - - +
201B VAL* 4.0 9.2 - - + -
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Residues in contact with VAL 200 (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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158A ARG* 3.7 31.2 - - + -
159A VAL 2.8 9.6 + - - +
160A TYR* 3.5 30.5 - - + +
161A ASP* 3.0 28.2 + - - +
168A TYR* 4.5 2.5 + - - +
154B SER* 5.1 5.4 - - - +
181B HIS* 3.6 33.0 - - + -
182B VAL 3.2 9.2 - - - +
183B LYS* 4.0 19.5 - - + -
199B VAL* 1.3 74.2 - - - +
201B VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 201 (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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161A ASP* 4.2 2.7 - - - -
163A THR* 3.5 24.2 - - + +
143B PRO* 4.0 10.8 - - + -
145B TYR* 3.4 33.7 - - + +
146B CYS* 4.4 3.1 - - + -
180B TYR 3.1 2.6 - - - +
181B HIS* 3.6 1.7 - - - -
182B VAL* 2.9 30.7 + - - +
184B PHE* 3.7 28.5 - - + -
199B VAL* 4.0 3.4 - - + -
200B VAL* 1.3 78.1 - - - +
202B ASP* 1.3 60.8 + - - +
203B LEU* 3.5 27.1 + - + +
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Residues in contact with ASP 202 (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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161A ASP 3.8 6.5 + - - +
163A THR* 2.7 32.9 + - - +
164A ALA* 3.4 26.6 + - + +
166A THR* 2.8 40.7 + - - +
168A TYR* 4.2 13.0 + - + +
141B ARG 4.5 1.7 - - - +
179B THR* 2.6 25.6 + - - -
180B TYR 3.4 4.8 + - - +
181B HIS* 3.3 16.8 - - - -
201B VAL* 1.3 68.9 - - - +
203B LEU* 1.3 60.3 + - - +
204B PHE* 4.1 1.0 + - - -
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Residues in contact with LEU 203 (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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131B VAL* 3.8 27.6 - - + -
141B ARG 3.9 17.7 - - - +
142B MET* 4.2 7.9 - - + -
146B CYS* 4.1 11.7 - - - -
179B THR* 3.9 1.8 - - - -
180B TYR* 2.8 42.9 + - - +
182B VAL* 4.0 13.7 - - + -
184B PHE* 4.1 5.6 - - + -
201B VAL* 3.7 36.3 - - + +
202B ASP* 1.3 71.7 + - - +
204B PHE* 1.3 68.9 + - - +
205B GLU 3.5 0.3 + - - -
207B TYR* 3.9 13.7 - - + -
208B LEU* 4.0 18.1 - - + +
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Residues in contact with PHE 204 (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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164A ALA* 3.8 20.0 - - + -
165A GLU* 5.1 5.2 - - + -
141B ARG* 4.8 3.8 - - + -
161B TRP* 3.6 25.8 - + + -
162B PRO 3.6 20.2 - - - -
163B PHE* 4.1 9.2 - + + -
164B PRO* 3.4 36.6 - - + -
177B GLU* 3.5 28.9 - - + +
178B PRO 3.9 3.1 - - - -
179B THR* 3.7 25.4 - - + -
202B ASP 5.2 0.2 - - - -
203B LEU* 1.3 73.8 - - - +
205B GLU* 1.3 65.8 + - - +
207B TYR* 2.9 42.2 + + + +
208B LEU* 3.8 4.7 - - - +
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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