Contacts of the strand formed by residues 189 - 196 (chain B) in PDB entry 5ZF6
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 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ASN* 3.7 5.4 - - - -
188B VAL* 1.3 74.8 - - - +
190B ALA* 1.3 60.0 + - - -
219B ALA* 3.2 2.9 - - - -
220B GLY 2.6 39.9 + - - -
252B THR* 3.3 25.4 - - - +
255B ILE* 4.0 11.4 - - - -
256B ILE* 3.6 4.4 - - - +
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Residues in contact with ALA 190 (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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167B VAL* 3.3 5.9 - - - +
170B ILE* 3.6 44.4 - - + -
171B ASN* 2.8 35.9 + - - +
188B VAL* 4.9 1.1 - - + -
189B GLY* 1.3 74.6 - - - +
191B VAL* 1.3 67.9 + - - +
203B ASN* 5.1 0.3 + - - -
217B VAL* 5.2 1.3 - - + -
218B VAL 3.1 11.7 - - - +
219B ALA* 4.3 4.9 - - + -
252B THR* 4.1 0.7 - - - -
255B ILE* 3.6 4.2 - - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.1 13.9 - - + -
167B VAL* 3.8 7.2 - - - -
190B ALA* 1.3 80.4 - - - +
192B ARG* 1.3 67.6 + - - +
193B ILE* 4.4 4.3 - - + -
202B VAL* 4.4 3.8 - - + -
203B ASN* 3.4 12.3 - - - +
216B LEU 3.9 0.2 - - - +
217B VAL* 3.4 5.1 - - - +
218B VAL* 3.1 28.7 + - + +
248B GLY* 3.6 36.3 - - - +
251B TYR* 4.1 22.2 - - + -
252B THR* 4.1 3.8 - - + +
255B ILE* 3.6 19.5 - - + -
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Residues in contact with ARG 192 (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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126B LYS* 5.3 2.8 - - - +
133B ILE* 5.9 3.0 - - - +
164B GLU* 4.2 11.7 - - - +
166B ASP* 2.6 42.7 + - - -
167B VAL* 3.3 20.5 - - + +
191B VAL* 1.3 76.6 - - - +
193B ILE* 1.3 78.8 + - - +
202B VAL* 3.7 0.5 - - - -
203B ASN* 2.8 32.6 + - - +
204B PRO* 3.7 24.5 + - + -
209B MET* 3.9 30.3 - - - +
215B ASN* 2.8 29.0 + - - +
216B LEU 3.2 10.3 - - - +
217B VAL* 3.5 20.8 - - + +
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Residues in contact with ILE 193 (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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191B VAL* 4.4 6.1 - - + +
192B ARG* 1.3 88.0 - - - +
194B GLY* 1.3 69.0 + - - +
200B TYR* 4.6 6.3 - - + -
201B VAL 3.3 11.4 - - - +
202B VAL* 4.3 9.9 - - + -
214B LEU* 3.5 9.7 - - + +
215B ASN* 4.0 0.9 - - - -
216B LEU* 2.7 45.6 + - + +
218B VAL* 5.3 0.9 - - + -
244B ALA* 3.7 33.7 - - + +
247B VAL* 3.7 27.6 - - + -
248B GLY* 3.7 24.5 - - - -
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Residues in contact with GLY 194 (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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193B ILE* 1.3 77.1 - - - +
195B ILE* 1.3 67.7 + - - +
196B ILE* 4.1 1.3 - - - -
200B TYR* 3.4 2.6 - - - -
201B VAL* 2.8 37.6 + - - +
204B PRO* 4.0 16.0 - - - +
212B SER* 3.3 12.1 - - - -
214B LEU* 3.4 6.5 - - - -
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Residues in contact with ILE 195 (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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194B GLY* 1.3 78.6 - - - +
196B ILE* 1.3 58.3 + - - +
197B ASP 4.0 0.9 + - - -
198B GLY* 3.9 27.4 - - - +
199B GLU 3.1 4.3 - - - +
200B TYR* 3.8 33.0 - - + -
211B SER 4.0 1.0 - - - +
212B SER* 2.8 12.1 + - - -
213B THR* 3.0 39.9 + - + +
214B LEU* 3.7 30.6 + - + +
236B ILE* 4.1 17.0 - - + -
240B ASP* 4.5 8.3 - - + -
244B ALA* 4.6 0.9 - - + -
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Residues in contact with ILE 196 (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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194B GLY 4.4 0.9 - - - -
195B ILE* 1.3 72.3 - - - +
197B ASP* 1.3 86.7 + - + +
199B GLU* 2.9 28.6 + - + +
201B VAL* 3.6 27.6 - - + -
204B PRO* 4.4 4.5 - - + -
208B GLU* 3.3 48.9 - - + +
211B SER* 3.7 23.3 - - - +
212B SER* 3.5 14.8 - - - +
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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