Contacts of the strand formed by residues 164 - 168 (chain D) in PDB entry 6CAJ
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 VAL 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C C7B 3.6 47.6 - - + +
163D GLU* 1.3 73.5 - - - +
165D ILE* 1.3 64.8 + - - +
188D HIS* 3.6 7.2 - - + +
190D ILE* 3.8 30.3 - - + -
228D ARG* 3.4 22.7 - - + +
229D VAL* 3.8 6.7 - - + -
230D ASN* 3.3 40.4 + - - +
231D LYS 3.4 9.0 + - - +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 3.9 3.1 - - + -
163D GLU* 3.5 33.4 - - + +
164D VAL* 1.3 79.2 - - - +
166D MET* 1.3 63.2 + - - +
167D THR* 5.5 0.7 - - - -
178D LEU* 4.1 13.2 - - + -
187D PHE* 4.0 20.2 - - + -
188D HIS 2.8 18.6 + - - +
189D VAL* 3.8 12.1 - - + -
190D ILE* 2.4 38.6 + - - +
231D LYS* 3.8 10.1 - - + +
233D ILE* 3.7 44.6 - - + +
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Residues in contact with MET 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ILE* 1.3 77.5 - - - +
167D THR* 1.3 67.7 + - - +
190D ILE* 3.3 17.5 - - + +
192D ALA* 3.8 17.7 - - + -
217D MET* 4.9 2.0 - - - -
222D ILE* 3.8 44.0 - - + -
225D VAL* 3.9 14.6 - - + -
226D MET* 4.3 4.7 - - - +
229D VAL* 3.7 37.9 - - + -
231D LYS 3.3 6.8 + - - +
232D VAL* 3.7 8.9 - - + +
233D ILE 3.1 23.7 + - - -
254D LEU* 3.7 23.8 - - + -
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Residues in contact with THR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ILE* 5.0 1.1 - - - +
166D MET* 1.3 74.8 - - - +
168D ILE* 1.3 75.8 + - - +
171D SER* 5.7 0.3 + - - -
174D VAL* 3.8 7.8 - - - +
178D LEU* 5.3 1.8 - - - -
189D VAL* 4.3 12.3 - - + -
190D ILE 3.0 12.0 + - - +
191D VAL* 3.9 15.5 - - + -
192D ALA* 3.2 27.9 + - - +
203D MET* 3.8 36.6 - - + +
233D ILE 3.2 20.0 + - - -
234D ILE* 4.4 4.4 - - - -
235D GLY 5.3 0.2 + - - -
254D LEU* 4.7 2.5 - - - +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D THR* 1.3 83.2 + - - +
169D GLY* 1.3 68.7 + - - +
170D PHE 3.8 1.4 + - - -
171D SER* 5.5 2.4 + - - -
192D ALA* 3.3 26.2 - - + +
193D GLU 3.4 20.9 - - - +
194D CYS* 3.9 10.1 - - + +
203D MET* 5.0 0.3 - - - +
219D ASP* 3.6 13.5 - - - +
222D ILE* 5.0 6.5 - - + -
234D ILE* 3.7 17.6 - - + +
235D GLY 5.2 6.7 + - - +
247D ALA* 5.9 0.2 - - + -
248D VAL* 3.8 19.0 - - + +
249D THR 4.5 8.7 - - - +
250D GLY 5.1 2.0 - - - +
251D THR* 3.7 29.6 - - - +
254D LEU* 4.3 9.2 - - + -
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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