Contacts of the strand formed by residues 160 - 166 (chain C) in PDB entry 4BQ7
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 TYR 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C TYR* 4.9 6.6 - - - -
158C PRO* 3.7 33.6 - - + +
159C SER* 1.4 75.4 - - - +
161C LEU* 1.3 65.2 + - - +
162C PHE* 3.6 21.9 - - + -
277D GLY* 3.3 26.0 + - - -
294D ARG* 3.5 56.5 + - + +
295D MET 3.6 1.6 - - - -
296D PRO* 3.9 24.9 - - + -
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C SER 4.3 0.2 + - - -
160C TYR* 1.3 76.1 - - - +
162C PHE* 1.3 61.7 + - - +
174D PHE* 3.4 41.3 - - + +
293D ILE 3.6 0.9 - - - +
294D ARG* 3.5 2.8 - - - -
295D MET 2.8 36.4 + - - +
297D GLU* 3.7 49.4 - - + +
300D ALA* 3.8 13.0 - - + -
301D MET* 3.7 26.0 - - + -
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Residues in contact with PHE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C TYR* 3.6 24.7 - - + -
161C LEU* 1.3 77.2 - - - +
163C CYS* 1.3 62.4 + - - +
172D ARG* 3.5 38.4 + - - +
173D THR 3.3 21.0 - - - +
174D PHE* 3.4 8.8 + - - +
176D ASP* 4.5 0.4 + - - +
293D ILE 3.1 6.5 - - - +
294D ARG* 3.6 39.5 - - + -
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Residues in contact with CYS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C PHE* 1.3 77.0 - - - +
164C GLY* 1.3 62.3 + - - +
171D LEU* 4.0 9.9 - - - -
172D ARG* 3.4 13.0 - - - -
173D THR* 4.5 0.4 - - - -
174D PHE* 3.6 17.5 - - + -
189D LEU* 5.0 1.3 - - - -
291D LEU 4.0 0.2 - - - +
292D ALA* 3.4 4.3 - - - +
293D ILE* 2.8 42.7 + - + +
312D CYS* 2.0 56.5 - - + -
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Residues in contact with GLY 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C CYS* 1.3 76.2 - - - +
165C LEU* 1.3 60.3 + - - -
166C PHE* 4.1 10.5 - - - -
171D LEU* 3.4 10.4 - - - +
172D ARG* 2.9 42.9 + - - +
189D LEU* 5.7 0.7 - - - -
291D LEU* 3.2 10.1 - - - -
292D ALA* 4.6 1.3 - - - -
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLY* 1.3 71.3 - - - -
166C PHE* 1.3 65.3 + - - +
169D PRO* 4.2 17.7 - - + +
170D HIS 3.3 14.4 - - - +
171D LEU* 4.0 24.7 - - + -
181D CYS* 6.5 0.4 - - + -
183D VAL* 5.8 0.9 - - + -
189D LEU* 3.9 26.7 - - + -
199D VAL* 3.7 31.9 - - + -
201D ASN* 4.2 4.0 - - - +
213D THR* 3.4 26.9 - - + +
216D ILE* 6.1 0.2 - - + -
289D LEU 4.4 1.7 - - - +
290D THR* 3.4 3.6 - - - -
291D LEU* 3.0 38.9 + - + +
311D LEU* 5.4 5.2 - - + -
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLY* 4.1 15.9 - - - -
165C LEU* 1.3 84.2 - - - +
167C GLY* 1.3 71.1 + - - +
169D PRO* 3.4 6.7 - - - +
170D HIS* 2.8 59.9 + + + +
171D LEU 5.1 0.4 - - - -
172D ARG* 4.6 15.7 - - + -
178D PHE* 5.1 11.7 - + - -
213D THR* 6.1 0.2 - - - -
289D LEU 4.7 3.1 - - - -
290D THR* 3.7 22.0 - - + +
291D LEU 5.3 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