Contacts of the strand formed by residues 161 - 167 (chain B) in PDB entry 5IXC
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 LEU 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B ARG 3.5 1.4 + - - +
160B GLU* 1.3 81.2 - - - +
162B SER* 1.3 64.2 + - - +
210B HIS* 4.4 7.4 - - + -
211B TYR 3.6 17.0 - - - +
212B MET* 4.1 5.8 - - + +
213B ALA* 4.7 1.8 - - - -
273B GLY* 4.3 3.6 - - - -
274B CYS* 3.8 31.2 + - + +
507B PHE* 3.5 35.4 - - + -
508B MET* 3.8 22.2 - - + -
510B ARG* 3.4 51.7 - - - +
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Residues in contact with SER 162 (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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160B GLU* 5.8 0.7 - - - -
161B LEU* 1.3 75.2 - - - +
163B CYS* 1.3 60.2 + - - +
210B HIS* 3.7 0.2 - - - -
211B TYR* 2.8 63.9 + - - +
213B ALA* 3.8 18.3 - - - +
271B ALA* 5.3 2.0 - - - -
272B GLU 3.2 17.9 - - - -
273B GLY* 5.2 0.4 - - - -
274B CYS* 3.4 8.5 - - - -
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Residues in contact with CYS 163 (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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162B SER* 1.3 74.4 - - - +
164B LEU* 1.3 61.0 + - - +
165B ASP* 4.0 1.0 + - - +
208B ARG* 3.6 20.4 - - - +
209B PHE 3.1 3.4 - - - -
210B HIS* 3.2 29.4 - - - -
211B TYR* 4.1 2.7 - - - -
270B LYS 3.7 0.9 - - - +
271B ALA* 3.2 3.5 - - - -
272B GLU* 2.9 33.1 + - + +
273B GLY 4.2 9.4 - - - +
274B CYS* 2.2 45.5 - - - -
275B PRO* 4.0 7.0 - - + -
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Residues in contact with LEU 164 (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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163B CYS* 1.3 73.4 - - - +
165B ASP* 1.3 59.3 + - - +
166B VAL* 3.1 36.3 - - + -
189B LEU* 4.2 7.2 - - + -
207B PHE 3.7 1.2 - - - +
208B ARG* 3.4 6.7 - - - -
209B PHE* 2.8 44.2 + - + -
211B TYR* 3.7 19.9 - - + +
219B LEU* 4.3 23.3 - - + -
244B LEU* 4.6 16.2 - - + -
269B LEU* 4.3 10.3 - - + -
270B LYS* 3.4 29.6 - - - +
271B ALA* 3.9 10.3 - - + +
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Residues in contact with ASP 165 (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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163B CYS* 5.2 1.1 - - - +
164B LEU* 1.3 73.7 - - - +
166B VAL* 1.3 68.8 + - - +
167B HIS* 4.7 5.0 - - + -
206B ALA* 5.0 2.3 - - - +
207B PHE 3.5 8.4 + - - +
208B ARG* 2.8 37.5 + - - +
268B GLN 3.3 1.4 - - - +
269B LEU* 3.2 7.6 - - - +
270B LYS* 2.8 45.0 + - + +
272B GLU* 6.5 0.9 - - + -
902B BA 2.8 25.1 - - - -
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Residues in contact with VAL 166 (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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164B LEU* 3.1 33.7 - - + +
165B ASP* 1.3 75.0 + - - +
167B HIS* 1.3 71.0 + - - +
187B LEU* 4.0 25.8 - - + -
206B ALA* 3.1 6.9 - - - -
207B PHE* 2.9 50.0 + - + +
209B PHE* 4.8 6.1 - - + -
219B LEU* 4.7 4.3 - - + -
267B LEU* 4.1 13.9 - - + -
268B GLN 3.2 2.2 - - - -
269B LEU* 4.1 21.5 - - + -
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Residues in contact with HIS 167 (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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165B ASP* 4.7 4.3 - - + -
166B VAL* 1.3 77.2 - - - +
168B LEU* 1.3 59.1 + - - +
169B ASP 3.8 1.8 - - - +
204B ALA 6.1 0.4 - - - -
205B SER 3.7 5.5 + - - -
206B ALA* 4.5 12.0 - - + +
207B PHE* 5.8 0.9 - - - -
267B LEU* 3.2 33.9 - - - +
268B GLN* 2.9 37.4 + - + +
902B BA 3.2 25.5 - - - -
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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