Contacts of the helix formed by residues 185 - 190 (chain B) in PDB entry 1XKH
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 ILE 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ASN* 1.3 68.9 + - - +
186B ASP* 1.3 70.5 + - - +
188B VAL* 2.4 37.1 + - + +
189B MSE 3.0 36.2 + - + +
207B TYR* 3.6 16.4 - - + +
217B PHE* 5.4 3.4 - - + -
235B ASN 4.0 6.7 - - - +
237B LEU* 3.8 12.1 - - - +
238B SER* 2.9 30.8 + - - +
240B MSE 3.7 23.3 - - + -
246B VAL* 4.8 2.9 - - + -
266B ILE* 5.2 6.5 - - + -
268B LEU* 4.3 16.6 - - + -
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Residues in contact with ASP 186 (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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184B ASN* 2.4 32.2 + - - +
185B ILE* 1.3 73.7 - - - +
187B ASP* 1.3 51.8 + - - +
188B VAL 2.6 12.3 + - - -
189B MSE 2.9 12.0 + - - +
190B ARG* 2.9 27.7 + - + +
197B VAL* 5.2 1.3 - - + +
205B ASN* 3.6 22.7 - - - +
207B TYR* 2.4 36.3 + - - -
236B THR* 2.7 30.2 + - - +
237B LEU* 4.3 4.2 - - - +
327B ARG* 5.3 4.7 + - - -
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Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY 4.9 3.1 - - - -
182B LEU* 3.0 45.5 - - + +
183B ASN* 3.8 8.1 + - - +
184B ASN* 2.6 44.4 + - - +
186B ASP* 1.3 77.2 - - - +
188B VAL* 1.3 57.1 + - - +
190B ARG* 4.4 15.6 + - - +
191B HIS* 3.4 11.1 + - + -
318B LYS* 5.6 0.9 + - - -
782B ASN* 5.3 4.3 - - - +
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Residues in contact with VAL 188 (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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172B VAL* 4.0 13.9 - - + -
177B MSE 4.4 7.0 - - + -
182B LEU* 4.2 14.8 - - + -
184B ASN 3.9 1.6 - - - +
185B ILE* 2.4 30.6 + - + +
186B ASP 2.6 0.8 + - - -
187B ASP* 1.3 76.4 - - - +
189B MSE 1.3 52.1 + - - +
190B ARG 3.0 1.1 - - - -
191B HIS* 2.7 6.5 + - - +
192B THR* 2.6 44.4 + - - +
240B MSE 3.8 35.0 - - + -
246B VAL* 3.3 30.5 - - + -
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Residues in contact with MSE 189 (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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185B ILE* 3.0 30.4 + - + -
186B ASP 2.9 4.1 + - - +
188B VAL* 1.3 79.5 - - - +
190B ARG* 1.3 65.4 + - - +
192B THR* 3.2 29.5 + - - +
195B ILE* 3.4 34.1 - - + +
197B VAL* 3.8 6.7 - - + +
207B TYR* 3.4 42.2 - - + -
214B ILE* 3.5 14.6 - - + -
246B VAL* 5.8 2.7 - - - -
248B VAL* 4.8 2.2 - - + -
266B ILE* 2.7 41.3 - - + -
735B ARG* 4.3 2.3 + - - -
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Residues in contact with ARG 190 (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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186B ASP* 2.9 25.5 + - - +
187B ASP* 4.7 14.3 + - - -
189B MSE 1.3 77.8 - - - +
191B HIS* 1.3 70.6 + - + +
192B THR 3.9 0.2 - - - +
197B VAL* 3.1 51.1 + - + +
199B ALA* 5.8 0.8 - - - +
205B ASN* 3.9 14.9 + - - +
716B TYR* 4.1 7.4 + - - -
735B ARG* 3.1 26.2 + - - +
789B TYR* 5.0 9.0 + - - -
791B THR* 5.0 9.9 + - - -
803B ASP* 4.0 22.7 + - - -
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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