Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 4ZGY
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 ALA 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B CYS* 6.0 0.4 - - + -
176B PHE 3.3 15.5 - - - +
177B HIS* 5.0 0.7 - - - -
178B LYS* 3.5 19.2 + - - +
208B ARG* 3.2 24.4 + - + +
209B PRO 3.2 2.2 + - - -
210B ASP* 1.3 86.8 - - - +
212B CYS* 1.3 60.5 + - - +
213B PHE* 3.6 31.5 - - + -
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Residues in contact with CYS 212 (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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323A TYR* 5.7 2.7 - - - -
363A LEU* 4.1 6.5 - - - -
174B ILE 3.5 2.8 - - - +
175B CYS* 3.5 2.3 - - - -
176B PHE* 2.9 59.0 + - + -
178B LYS* 3.8 33.8 - - - +
183B ARG* 3.9 22.0 - - - -
187B LEU* 4.8 10.1 - - + -
197B ILE* 6.4 2.0 - - + -
211B ALA* 1.3 73.4 - - - +
213B PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 213 (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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140B TYR* 5.2 0.7 - + - -
173B PHE* 5.1 4.3 - - + -
174B ILE 3.1 4.0 - - - +
175B CYS* 3.5 41.5 - - + -
187B LEU* 5.7 0.4 - - - +
197B ILE* 4.0 4.2 - - - +
198B VAL* 2.9 34.9 + - + +
205B VAL* 3.5 41.5 - - + -
206B PRO* 3.9 33.9 - - + -
208B ARG* 4.2 13.2 - - + -
211B ALA* 3.6 35.7 - - + -
212B CYS* 1.3 76.8 - - - +
214B MET* 1.3 67.8 + - - +
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Residues in contact with MET 214 (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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331A TYR* 4.0 9.4 - - - +
173B PHE* 3.3 7.4 - - - -
174B ILE* 2.9 38.0 + - + +
176B PHE* 4.7 6.5 - - + -
186B LEU 4.5 0.4 - - - +
187B LEU* 3.5 56.1 - - + +
190B PHE* 3.7 17.5 - - - -
191B SER 3.9 1.8 - - - +
195B PHE* 3.6 42.2 - - + +
196B GLU 3.2 14.8 - - - +
197B ILE* 4.0 8.1 - - + +
198B VAL* 3.8 1.8 - - - -
213B PHE* 1.3 78.8 - - - +
215B ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 215 (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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397A PHE* 3.7 22.9 - - + -
171B HIS* 5.3 0.9 - - + -
172B VAL 3.5 4.7 - - - +
173B PHE* 3.7 20.0 - - + -
194B GLY 4.1 0.9 - - - +
195B PHE* 3.2 7.0 - - - -
196B GLU* 2.9 38.7 + - + +
198B VAL* 3.7 17.2 - - + +
214B MET* 1.3 75.1 - - - +
216B TYR* 1.3 61.7 + - - +
217B THR* 4.3 0.8 + - - -
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Residues in contact with TYR 216 (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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112A ASN* 4.9 4.3 + - - -
114A CYS 4.4 4.9 + - - -
116A GLN* 2.7 30.6 + - - -
119A GLN* 4.6 8.5 + - - -
160B LEU* 4.1 14.8 - - + -
171B HIS* 3.2 7.2 - - - +
172B VAL* 2.9 34.9 + - + +
193B LEU 3.6 20.9 - - - -
194B GLY* 3.9 24.0 - - - -
195B PHE* 3.4 30.3 - + + -
215B ALA* 1.3 73.5 - - - +
217B THR* 1.3 72.8 + - - +
218B PHE* 3.6 38.9 + + - -
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Residues in contact with THR 217 (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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119A GLN* 5.7 0.5 + - - -
397A PHE* 4.0 12.1 - - - -
170B ASP 3.8 5.8 - - - +
171B HIS* 2.7 36.2 + - + +
194B GLY 5.5 0.2 + - - -
196B GLU* 5.0 4.4 + - - -
215B ALA 4.3 1.1 + - - -
216B TYR* 1.3 84.7 + - - +
218B PHE* 1.3 75.5 + - - +
219B GLU* 3.9 7.7 + - + +
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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