Contacts of the strand formed by residues 171 - 177 (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 HIS 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A PHE* 3.6 22.8 - + + -
138B SER* 3.4 22.8 + - - +
139B LEU 3.1 21.7 + - - -
169B ALA* 3.7 4.5 - - - +
170B ASP* 1.3 97.1 + - + +
172B VAL* 1.3 67.8 + - - +
173B PHE* 3.6 14.6 - + + -
204B LEU* 4.0 19.0 - - + +
215B ALA* 5.3 0.2 - - + -
216B TYR 3.2 8.5 - - - +
217B THR* 2.7 42.4 + - + -
218B PHE* 4.6 1.1 - - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.3 11.4 - - + +
141B ILE* 3.6 30.7 - - + -
159B LEU* 5.7 0.9 - - + -
160B LEU* 4.2 20.9 - - + -
163B ALA* 3.5 31.9 - - + -
169B ALA* 4.8 0.2 - - + -
171B HIS* 1.3 79.5 - - - +
173B PHE* 1.3 63.6 + - - +
195B PHE* 3.5 14.0 - - + -
215B ALA* 3.5 2.3 - - - -
216B TYR* 2.9 36.5 + - + -
218B PHE* 3.7 16.8 - - + -
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Residues in contact with PHE 173 (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* 3.8 18.2 - + - -
138B SER* 3.6 17.3 - - - -
139B LEU 2.6 14.9 + - - +
140B TYR* 3.4 37.9 - + + -
141B ILE* 2.8 36.4 + - - +
171B HIS* 3.6 24.2 - - + -
172B VAL* 1.3 77.2 - - - +
174B ILE* 1.3 63.1 + - - +
175B CYS* 3.9 5.4 - - - -
198B VAL* 4.3 3.4 - - + -
204B LEU* 3.8 24.2 - - + -
205B VAL* 4.0 28.9 - - + -
213B PHE* 5.1 2.0 - - + -
214B MET 3.3 13.5 - - - +
215B ALA* 3.7 16.6 - - + -
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Residues in contact with ILE 174 (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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141B ILE* 4.0 5.6 - - + -
143B ILE* 3.6 17.9 - - + -
156B PHE* 3.4 38.1 - - + -
172B VAL 4.2 0.2 + - - -
173B PHE* 1.3 79.0 - - - +
175B CYS* 1.3 61.3 + - - +
176B PHE* 3.6 26.9 - - + -
190B PHE* 3.6 28.7 - - + -
195B PHE* 3.5 24.0 - - + -
212B CYS 3.5 0.7 - - - +
213B PHE* 3.1 9.0 - - - +
214B MET* 2.9 41.8 + - + +
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Residues in contact with CYS 175 (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* 3.8 33.7 - - - -
141B ILE 3.1 15.0 + - - +
142B GLU* 3.8 7.1 - - + +
143B ILE* 3.1 24.8 + - - +
173B PHE* 4.1 4.0 - - - -
174B ILE* 1.3 77.1 - - - +
176B PHE* 1.3 61.2 + - - +
211B ALA* 6.0 0.9 - - + -
212B CYS 3.5 4.5 - - - -
213B PHE* 3.5 33.2 - - + -
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Residues in contact with PHE 176 (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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143B ILE* 3.8 25.8 - - + +
174B ILE* 3.6 27.4 - - + -
175B CYS* 1.3 74.2 - - - +
177B HIS* 1.3 75.4 + - - +
180B ARG* 4.0 4.0 - - - +
183B ARG* 4.0 19.5 - - + -
186B LEU* 3.8 40.6 - - + -
187B LEU* 3.9 24.9 - - + -
190B PHE* 5.2 0.4 - + - -
211B ALA* 3.3 8.4 - - - +
212B CYS* 2.9 63.0 + - + +
214B MET* 4.7 6.3 - - + -
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Residues in contact with HIS 177 (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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143B ILE 5.1 1.6 + - - -
176B PHE* 1.3 77.9 - - - +
178B LYS* 1.3 65.6 + - - +
179B ASN* 3.3 49.4 + - + +
180B ARG* 3.2 31.7 - - + +
208B ARG* 5.5 3.0 + - - -
210B ASP* 3.8 31.9 + - + -
211B ALA* 4.6 0.9 - - - +
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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