Contacts of the strand formed by residues 206 - 212 (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 ALA 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B ASP* 5.0 5.8 - - - +
166B VAL 3.1 12.1 - - - +
167B HIS* 4.5 18.4 - - + +
204B ALA 5.2 0.7 - - - +
205B SER* 1.3 77.0 - - - +
207B PHE* 1.3 78.0 + - - +
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Residues in contact with PHE 207 (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 3.7 0.9 - - - +
165B ASP* 3.5 8.1 - - - +
166B VAL* 2.9 47.3 + - + +
167B HIS 5.8 0.4 - - - -
168B LEU* 5.1 4.0 - - + -
185B LEU* 3.8 24.9 - - + -
187B LEU* 3.6 21.8 - - + -
197B GLN* 3.7 31.9 - - + +
198B THR* 4.7 5.2 - - - -
199B SER* 3.4 41.5 - - - -
205B SER* 4.2 15.5 - - - -
206B ALA* 1.3 88.8 - - - +
208B ARG* 1.3 61.9 + - - +
209B PHE* 4.6 4.0 - - + -
267B LEU* 5.7 0.4 - - + -
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Residues in contact with ARG 208 (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* 3.6 28.2 - - - +
164B LEU 3.4 5.4 - - - -
165B ASP* 2.8 29.4 + - - -
194B GLU* 3.5 10.4 - - - +
197B GLN* 2.8 22.5 + - - +
207B PHE* 1.3 75.7 - - - +
209B PHE* 1.3 58.5 + - - +
210B HIS* 3.4 26.5 + - + -
275B PRO* 3.6 32.6 - - - +
276B GLU* 4.7 2.4 + - - -
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Residues in contact with PHE 209 (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* 3.1 6.6 - - - -
164B LEU* 2.8 51.3 + - + -
166B VAL* 4.8 3.4 - - + -
187B LEU* 3.7 44.9 - - + -
189B LEU* 3.6 35.7 - - + -
192B SER* 3.6 18.6 - - - -
194B GLU* 3.4 11.7 - - - -
195B ASP 3.9 21.5 - - - -
197B GLN* 3.5 33.2 - - + -
207B PHE* 4.6 3.6 - - + -
208B ARG* 1.3 75.6 - - - +
210B HIS* 1.3 61.4 + - - +
211B TYR* 3.7 2.8 - - + -
219B LEU* 4.3 7.6 - - + -
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Residues in contact with HIS 210 (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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161B LEU* 4.4 10.1 - - + -
162B SER 3.7 3.6 - - - -
163B CYS* 3.2 24.8 - - - -
192B SER* 3.1 4.9 - - - -
193B TYR* 3.0 27.8 + - + +
194B GLU* 2.7 35.5 + - - +
208B ARG* 3.4 25.2 + - + +
209B PHE* 1.3 71.9 - - - +
211B TYR* 1.3 61.3 + - - +
274B CYS* 3.9 3.8 - - - -
276B GLU* 3.0 32.0 + - - -
507B PHE* 4.1 20.3 - - + -
510B ARG* 5.6 0.4 - - - -
512B MET* 3.3 24.0 - - + +
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Residues in contact with TYR 211 (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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161B LEU* 3.6 10.1 - - - +
162B SER* 2.8 54.7 + - - +
164B LEU* 3.7 32.4 - - + +
189B LEU* 3.8 18.2 - - + -
191B GLY 4.0 6.5 - - - +
192B SER* 3.8 18.8 - - - +
209B PHE 3.7 4.3 - - - -
210B HIS* 1.3 80.1 - - - +
212B MET* 1.3 81.2 + - - +
213B ALA* 5.2 1.1 - - - -
215B LEU* 4.6 4.3 - - + -
217B THR* 4.6 13.7 - - + -
244B LEU* 3.9 30.1 - - + +
271B ALA* 3.7 24.1 - - - +
507B PHE* 4.7 2.9 - - - -
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Residues in contact with MET 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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53B THR 3.7 25.6 - - - +
55B PRO* 4.0 19.3 - - + +
159B ARG* 3.8 35.7 - - + -
160B GLU 3.3 6.5 - - - +
161B LEU* 4.1 9.7 - - + +
191B GLY 4.7 6.8 + - - +
211B TYR* 1.3 89.3 - - - +
213B ALA* 1.3 63.3 + - - +
214B ALA* 3.2 6.4 + - + +
215B LEU* 3.5 41.6 + - + +
507B PHE* 5.3 9.8 - - + -
508B MET* 5.2 4.9 - - + +
608B GLY* 5.5 4.3 - - - +
610B GLN* 3.7 15.3 - - - +
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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