Contacts of the helix formed by residues 184 - 189 (chain B) in PDB entry 2XAR
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 ASN 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ILE* 3.6 8.6 - - + +
181B GLY* 3.3 14.1 + - - +
182B LYS 3.3 0.8 - - - -
183B GLU* 1.3 87.5 - - - +
185B MET* 1.3 54.7 + - - +
186B LEU 2.8 12.9 + - - -
187B LYS* 3.0 27.3 + - - +
316B GLU* 2.4 36.0 + - - +
424B LYS* 5.8 3.4 - - - +
427B ILE* 3.7 35.5 - - + +
428B SER* 5.8 0.3 - - - -
431B ASN* 4.1 4.3 + - - -
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Residues in contact with MET 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.5 36.7 - - + +
47A ASN* 3.1 36.6 - - - +
132A ASN* 2.9 26.0 - - - +
133A ALA* 3.7 24.7 - - + +
177B SER 5.4 3.6 - - - +
180B ILE* 3.9 28.5 - - - +
181B GLY 3.3 9.4 - - - +
182B LYS 3.7 2.7 - - - +
183B GLU 3.3 3.0 + - - -
184B ASN* 1.3 74.7 - - - +
186B LEU* 1.3 59.9 + - - +
187B LYS 3.2 0.9 - - - -
188B THR* 3.4 29.7 - - - +
189B SER 4.5 0.2 + - - -
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 4.5 9.8 - - + +
183B GLU 4.6 1.7 + - - +
184B ASN 2.8 1.8 + - - -
185B MET* 1.3 74.5 - - - +
187B LYS* 1.3 60.2 + - - +
188B THR 3.0 7.3 + - - -
189B SER* 3.1 28.0 + - - +
190B VAL* 3.2 20.2 + - + +
195B MET* 4.6 1.3 - - - +
427B ILE* 4.3 9.9 - - + -
430B TYR* 4.2 27.4 - - + -
431B ASN* 3.5 26.7 - - - +
434B GLN* 4.6 9.2 - - + -
435B LYS* 4.6 12.8 - - - +
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Residues in contact with LYS 187 (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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174B LEU* 4.3 0.9 - - - +
175B PRO* 3.2 32.7 - - + +
180B ILE* 3.9 25.4 - - + -
184B ASN* 3.0 17.8 + - - +
186B LEU* 1.3 78.6 - - - +
188B THR* 1.3 59.9 + - - +
189B SER 3.4 0.2 - - - -
190B VAL 3.6 10.9 - - - +
195B MET* 3.9 19.0 - - + +
314B ASP* 3.0 29.2 + - - +
316B GLU* 3.4 18.7 + - - +
423B ASP* 2.6 40.3 + - - +
427B ILE* 3.8 23.5 - - + +
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Residues in contact with THR 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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47A ASN* 3.3 47.0 + - + +
174B LEU* 3.1 23.7 - - - +
175B PRO* 4.1 16.6 + - - +
176B THR* 5.2 3.2 - - - -
180B ILE* 4.8 8.1 - - - +
185B MET* 3.4 26.1 + - - +
186B LEU 3.0 0.2 - - - -
187B LYS* 1.3 80.5 - - - +
189B SER* 1.3 57.4 + - - +
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Residues in contact with SER 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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46A ARG 3.5 14.2 + - - -
47A ASN 3.5 19.9 + - - -
48A ASP 5.5 1.2 - - - -
174B LEU* 3.3 20.7 - - - +
185B MET 4.6 0.3 + - - -
186B LEU* 3.1 15.6 + - - +
188B THR* 1.3 79.5 - - - +
190B VAL* 1.3 68.4 + - - +
191B SER 3.9 0.7 + - - -
215B LEU* 4.9 3.1 - - - +
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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