Contacts of the helix formed by residues 200 - 207 (chain B) in PDB entry 1XAI
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 ASP 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B PHE 3.6 1.2 - - - -
199B LYS* 1.3 90.9 - - - +
201B ARG* 1.3 68.5 + - + +
202B GLU* 3.6 16.0 + - + +
203B ILE* 2.9 37.6 + - - +
204B LEU* 3.3 7.8 + - - +
290B GLN* 4.0 20.1 + - + +
291B LEU* 4.2 8.1 - - - +
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Residues in contact with ARG 201 (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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169B PHE* 3.5 33.6 - - + +
200B ASP* 1.3 72.6 - - + +
202B GLU* 1.3 61.8 + - + +
204B LEU* 3.1 3.5 + - - +
205B GLN* 2.7 74.1 + - - +
290B GLN 2.9 21.0 + - - +
291B LEU* 3.5 13.4 - - - +
292B GLY* 4.5 12.6 + - - -
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Residues in contact with GLU 202 (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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200B ASP* 3.2 11.4 + - - +
201B ARG* 1.3 85.7 - - + +
203B ILE* 1.3 60.6 + - + +
205B GLN* 4.0 9.9 - - - +
206B SER* 3.0 29.5 + - - -
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Residues in contact with ILE 203 (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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197B HIS* 3.4 29.8 - - + +
198B PHE* 3.8 19.0 - - + -
199B LYS* 4.0 14.1 - - + +
200B ASP* 2.9 39.2 + - - +
202B GLU* 1.3 76.0 - - + +
204B LEU* 1.3 66.1 + - - +
206B SER* 2.5 25.3 + - - +
207B LEU* 3.0 6.9 + - - -
208B ASN* 3.9 5.9 + - + +
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Residues in contact with LEU 204 (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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169B PHE* 3.7 10.1 - - + -
172B ILE* 3.0 28.9 - - + -
173B LEU* 3.6 30.7 - - + -
176B TYR* 4.0 28.3 - - + -
198B PHE* 3.8 13.8 - - + +
200B ASP 3.3 6.4 + - - +
201B ARG* 3.1 7.7 + - - +
203B ILE* 1.3 78.3 - - - +
205B GLN* 1.3 55.7 + - - +
207B LEU* 2.6 39.2 + - - +
210B MET* 3.6 23.3 - - + -
291B LEU* 4.2 20.9 - - + +
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Residues in contact with GLN 205 (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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169B PHE* 3.3 36.6 - - + +
172B ILE* 4.9 4.9 - - - +
201B ARG* 2.7 66.7 + - - +
202B GLU* 4.0 10.5 - - - +
204B LEU* 1.3 73.1 - - - +
206B SER* 1.3 61.2 + - - +
207B LEU* 4.1 6.6 - - - +
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Residues in contact with SER 206 (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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202B GLU 3.0 16.5 + - - -
203B ILE* 2.5 22.9 + - - +
204B LEU 2.9 1.2 + - - -
205B GLN* 1.3 77.4 - - - +
207B LEU* 1.3 67.8 + - - +
208B ASN* 3.5 16.0 + - - +
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Residues in contact with LEU 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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126B ILE* 4.2 2.9 - - + -
164B LEU* 3.7 43.5 - - + +
165B LYS* 5.5 0.9 - - - -
172B ILE* 3.7 34.5 - - + -
198B PHE* 4.7 2.5 - - - -
203B ILE 3.0 4.5 + - - -
204B LEU 2.6 27.0 + - - +
205B GLN 4.1 5.2 - - - +
206B SER* 1.3 74.8 - - - +
208B ASN* 1.3 64.5 + - - +
209B GLY 3.4 0.3 + - - -
210B MET* 3.2 41.3 + - + +
211B ASP* 4.7 1.4 + - - -
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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