Contacts of the helix formed by residues 181 - 186 (chain D) in PDB entry 3UYS
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 SER 181 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D TYR 3.7 2.0 + - - -
180D ALA* 1.3 76.1 - - - +
182D ILE* 1.3 62.5 + - - +
183D ASN 3.6 1.5 + - - -
184D THR* 3.1 30.7 + - - -
185D HIS* 3.3 10.4 + - - -
194D ASP* 3.0 31.3 + - - -
197D GLU* 2.9 39.7 - - - -
198D SER* 4.3 3.2 + - - -
201D TYR* 4.2 2.0 - - - -
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Residues in contact with ILE 182 (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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233A MET 5.7 0.9 - - - +
180D ALA 3.9 0.2 + - - -
181D SER* 1.3 73.3 - - - +
183D ASN* 1.3 66.0 + - - +
185D HIS* 2.9 19.1 + - + +
186D LEU* 3.0 23.1 + - + +
197D GLU* 3.2 9.0 + - - +
201D TYR* 4.0 10.8 - - - +
232D LYS* 3.5 31.6 - - + +
233D MET* 4.0 34.1 - - + -
256D ARG* 3.4 36.6 - - - +
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Residues in contact with ASN 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PRO* 4.6 13.4 - - - +
238A GLU* 5.5 0.2 - - - -
181D SER* 3.2 6.8 + - - +
182D ILE* 1.3 79.9 - - - +
184D THR* 1.3 54.6 + - - +
186D LEU* 2.8 36.4 + - - +
187D GLY 3.1 9.4 + - - -
188D ILE* 3.2 27.9 + - + +
193D ARG* 3.1 44.0 - - - +
194D ASP* 3.9 10.8 + - - +
197D GLU* 4.7 6.0 + - - -
256D ARG* 5.9 0.8 + - - +
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Residues in contact with THR 184 (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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171D LYS 4.7 5.2 - - - +
173D LEU* 3.5 43.2 - - + +
180D ALA* 3.9 10.0 - - + -
181D SER* 3.1 24.5 + - - -
183D ASN* 1.3 76.9 - - - +
185D HIS* 1.3 61.1 + - - +
187D GLY* 3.2 11.4 + - - -
188D ILE 4.0 8.5 + - - -
190D GLN* 3.2 37.0 - - + +
194D ASP* 4.6 2.1 - - - +
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Residues in contact with HIS 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 3.9 20.9 - - + +
177D ALA* 3.6 9.6 + - + -
180D ALA* 3.7 5.6 - - + +
181D SER 3.3 22.1 + - - -
182D ILE* 2.9 14.1 + - + +
184D THR* 1.3 77.3 - - - +
186D LEU* 1.3 62.5 + - + +
187D GLY 3.2 1.2 + - - -
225D TYR* 3.8 9.3 + - - +
228D ILE* 3.6 22.9 - - + -
229D SER* 3.4 38.2 + - - +
232D LYS* 2.9 41.2 + - + +
233D MET* 5.7 0.2 - - - -
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Residues in contact with LEU 186 (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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233A MET 4.1 15.5 - - - +
234A SER* 4.0 37.7 - - - +
236A PRO* 4.5 10.3 - - + -
169D GLU* 4.8 2.9 - - - +
182D ILE* 3.0 25.3 + - + +
183D ASN* 2.8 26.0 + - - +
185D HIS* 1.3 81.5 - - - +
187D GLY* 1.3 56.5 + - - +
188D ILE* 3.2 15.9 + - + +
229D SER* 5.7 0.7 - - - +
233D MET* 4.7 13.5 - - + -
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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