Contacts of the strand formed by residues 251 - 261 (chain B) in PDB entry 4ZCH
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 ASN 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B ILE 3.4 1.1 + - - -
90B ARG* 3.6 17.4 - - - +
91B SER* 2.9 43.0 + - - +
208B LEU* 3.5 4.9 - - - +
209B TYR* 3.1 38.8 + - - +
242B GLN* 3.3 28.8 - - + +
243B ASN 4.0 12.3 - - - +
244B MET* 3.8 15.1 - - - +
245B PRO* 4.1 8.1 - - - +
250B ASN* 1.4 75.4 - - - +
252B SER* 1.3 58.5 + - - +
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Residues in contact with SER 252 (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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88B CYS* 3.5 13.5 - - - -
89B ILE 2.8 36.6 + - - -
90B ARG* 2.8 31.2 + - - -
206B GLN* 4.0 12.8 + - - -
207B VAL 3.3 8.7 - - - -
208B LEU* 3.5 5.0 - - - +
242B GLN* 3.7 4.6 + - - -
251B ASN* 1.3 72.2 - - - +
253B CYS* 1.3 59.2 + - - +
254B TYR 4.1 0.8 + - - -
284B VAL* 4.0 22.7 - - - -
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Residues in contact with CYS 253 (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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90B ARG* 5.7 0.2 - - - +
206B GLN* 3.2 2.3 - - - -
207B VAL 2.8 29.3 + - - -
209B TYR* 3.5 26.2 - - + -
218B HIS* 3.0 8.6 - - + -
240B CYS* 2.0 48.2 - - + -
241B ILE* 3.4 15.0 - - - -
242B GLN* 3.3 26.0 - - + -
252B SER* 1.3 74.0 - - - +
254B TYR* 1.3 58.9 + - - +
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Residues in contact with TYR 254 (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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90B ARG* 5.8 1.6 - - - +
104B TYR* 3.6 44.6 + + - +
105B SER* 4.3 0.9 - - - -
106B ALA* 3.5 44.0 - - + +
202B PHE* 4.0 8.3 - - - -
204B TYR* 3.5 21.2 - + + +
205B GLY 3.4 13.2 - - - -
206B GLN* 3.6 26.9 - - + +
240B CYS* 3.4 9.5 - - - -
252B SER 4.1 1.4 + - - -
253B CYS* 1.3 74.1 - - - +
255B SER* 1.3 62.6 + - - +
256B ALA* 3.4 28.7 - - + +
286B PHE* 4.5 0.4 - + - -
357B GLN* 4.1 0.3 - - - +
405B TYR* 3.6 31.2 + + - +
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Residues in contact with SER 255 (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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204B TYR* 3.5 1.2 - - - +
205B GLY 3.1 30.7 + - - +
218B HIS* 5.0 3.6 - - - -
220B ILE* 3.8 7.8 - - - +
238B PHE* 4.0 8.4 - - - +
239B ARG 3.8 14.6 + - - -
240B CYS* 4.0 11.3 - - - +
254B TYR* 1.3 77.6 - - - +
256B ALA* 1.4 63.1 + - - +
357B GLN* 2.8 32.8 + - - -
405B TYR* 4.3 1.8 - - - -
437B PHE* 3.5 10.6 - - - -
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Residues in contact with ALA 256 (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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202B PHE* 3.7 12.8 - - + -
203B ILE 3.2 16.6 - - - +
204B TYR* 3.6 4.7 - - + +
238B PHE* 4.3 10.3 - - - +
254B TYR* 3.4 23.3 - - + +
255B SER* 1.4 77.7 + - - +
257B GLY* 1.3 58.4 + - - +
355B TYR* 4.4 1.4 - - - -
405B TYR* 3.6 20.6 - - - +
437B PHE* 3.1 26.4 - - - -
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Residues in contact with GLY 257 (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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201B PHE 3.8 0.3 - - - +
202B PHE* 3.6 6.8 - - - -
203B ILE* 2.8 33.6 + - - +
238B PHE* 3.3 25.2 - - - -
256B ALA* 1.3 76.3 - - - +
258B ILE* 1.3 61.6 + - - -
307B GLN* 3.9 4.0 - - - -
355B TYR* 4.4 11.0 - - - -
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Residues in contact with ILE 258 (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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200B TYR* 4.1 11.7 - - + -
201B PHE 3.3 11.2 - - - +
202B PHE* 4.3 17.5 - - + -
238B PHE* 3.8 4.6 - - - -
257B GLY* 1.3 75.5 - - - +
259B ALA* 1.4 64.7 + - - +
292B LEU* 3.9 19.1 - - + -
305B CYS* 4.2 15.3 - - + -
307B GLN* 2.8 35.4 + - - +
331B PHE* 3.5 27.7 - - + -
355B TYR* 3.7 26.2 - - + +
441B LEU* 4.1 31.2 - - + -
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Residues in contact with ALA 259 (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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200B TYR* 3.5 5.3 - - - -
201B PHE 3.1 29.7 + - - +
203B ILE* 4.0 17.3 - - + -
222B ARG* 5.9 0.2 - - - -
237B LEU* 3.7 31.9 - - + -
238B PHE* 4.7 2.9 - - + -
257B GLY 4.3 0.4 + - - -
258B ILE* 1.4 76.3 - - - +
260B LYS* 1.3 63.5 + - - +
261B LEU* 3.5 11.2 + - + +
331B PHE* 5.4 2.7 - - - -
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Residues in contact with LYS 260 (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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198B THR* 3.8 26.9 - - - +
199B GLY* 3.6 12.6 - - - +
200B TYR* 3.7 45.2 - - + +
222B ARG* 3.5 25.1 + - - -
259B ALA* 1.3 73.0 - - - +
261B LEU* 1.3 60.1 + - - +
262B GLU* 3.5 20.9 + - - +
331B PHE* 6.0 0.8 - - - -
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Residues in contact with LEU 261 (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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195B VAL* 3.9 25.8 - - + -
198B THR* 3.1 4.5 - - - +
199B GLY 2.8 34.0 + - - +
201B PHE* 3.5 39.0 - - + -
203B ILE* 3.9 12.3 - - + -
222B ARG* 3.7 34.3 - - + +
237B LEU* 4.5 0.7 - - + -
259B ALA* 4.0 15.5 - - + +
260B LYS* 1.3 78.6 - - - +
262B GLU* 1.3 62.3 + - - +
265B ASP* 3.7 7.0 - - + +
267B LEU* 4.0 21.5 - - + -
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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