Contacts of the helix formed by residues 218 - 224 (chain B) in PDB entry 1XVI
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 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ASP* 3.2 33.3 - - + +
15B ASP* 5.0 2.0 - - - +
188B LYS* 4.5 3.6 + - - -
213B GLY* 3.3 9.9 - - - -
214B ASP* 3.0 31.9 + - - +
215B GLY* 3.4 17.9 + - - +
216B PRO 3.2 1.2 - - - -
217B ASN* 1.3 81.4 + - - +
219B ALA* 1.3 63.8 + - - +
220B PRO* 3.3 3.1 - - - -
221B LEU* 3.5 7.1 + - + +
222B LEU* 3.1 40.6 + - + +
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Residues in contact with ALA 219 (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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215B GLY 4.7 0.4 + - - -
216B PRO 3.4 17.5 + - - +
217B ASN 4.7 0.2 - - - -
218B ASP* 1.3 78.1 - - - +
220B PRO* 1.4 60.0 - - + +
222B LEU* 3.5 6.1 - - - +
223B GLU* 2.7 53.4 + - + +
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Residues in contact with PRO 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS* 5.7 3.4 - - + +
189B ASP* 3.6 32.8 - - + +
217B ASN* 3.5 13.5 - - - +
218B ASP 3.5 4.5 - - - -
219B ALA* 1.4 94.3 - - + +
221B LEU* 1.3 63.1 - - - +
223B GLU* 3.2 18.3 + - + +
224B VAL* 3.7 3.5 + - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.4 16.2 - - + +
13B ASP* 3.7 27.4 - - + +
46B CYS* 3.7 30.5 - - + -
69B ILE* 4.9 0.2 - - + -
188B LYS* 3.8 22.1 - - + +
189B ASP* 4.2 9.9 - - - +
192B ALA* 3.7 18.4 - - + -
218B ASP* 3.5 8.9 + - - +
220B PRO* 1.3 77.0 - - - +
222B LEU* 1.3 74.0 + - + +
223B GLU 3.4 0.5 + - - -
224B VAL* 3.4 7.8 + - - +
225B MET* 3.4 39.3 - - + +
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Residues in contact with LEU 222 (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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211B GLY* 3.6 34.1 - - - +
212B LEU 3.8 5.8 - - - +
213B GLY* 3.9 15.7 - - - +
218B ASP* 3.1 30.7 + - + +
219B ALA* 3.8 5.2 - - - +
221B LEU* 1.3 89.4 - - + +
223B GLU* 1.3 65.6 + - - +
225B MET* 3.2 20.8 + - - +
228B ALA* 3.7 23.0 - - + +
229B VAL 4.0 5.2 - - - +
230B ILE* 3.7 30.1 - - + -
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Residues in contact with GLU 223 (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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219B ALA* 2.7 43.5 + - + +
220B PRO* 3.2 10.3 + - + +
222B LEU* 1.3 76.4 - - - +
224B VAL* 1.3 64.2 + - + +
225B MET 3.4 5.7 + - - +
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Residues in contact with VAL 224 (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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189B ASP* 3.9 25.1 - - + +
192B ALA* 4.2 11.4 - - + -
193B ASN* 3.7 30.1 - - - +
196B ILE* 4.7 7.7 - - + +
209B THR* 4.3 2.9 + - - -
220B PRO 4.0 2.9 - - - +
221B LEU 3.4 15.5 + - - +
222B LEU 3.2 0.4 - - - -
223B GLU* 1.3 79.2 - - + +
225B MET* 1.3 78.4 + - + +
226B ASP* 3.9 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