Contacts of the helix formed by residues 211 - 219 (chain B) in PDB entry 5XVO
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 PHE 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.3 34.8 - + - -
72B LEU* 3.8 35.9 - - + -
73B PRO* 4.4 4.3 - - + -
184B LEU* 4.1 22.0 - - + -
188B ALA* 3.8 23.6 - - + -
198B THR* 3.3 18.4 - - - -
209B ASN* 2.6 21.4 + - - +
210B ASP* 1.3 84.3 - - + +
212B ASN* 1.3 64.1 + - - +
213B LEU 3.1 3.1 - - - -
214B ALA* 2.9 23.4 + - + -
215B SER* 3.0 11.8 + - - -
5R C 4.5 8.3 - - - -
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Residues in contact with ASN 212 (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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87A SER* 3.9 3.2 + - - -
198B THR 3.1 3.2 + - - -
199B GLN 3.3 20.2 + - - +
201B GLY* 3.9 2.7 - - - +
204B HIS* 3.3 36.1 - - + +
205B ALA* 3.7 5.3 - - - +
206B ASN* 3.0 43.8 + - - +
209B ASN* 3.2 33.2 + - - +
211B PHE* 1.3 75.2 - - - +
213B LEU* 1.3 62.6 + - - +
215B SER* 3.1 4.5 + - - -
216B ASP* 3.0 25.6 + - - -
7R T 4.0 0.2 + - - -
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Residues in contact with LEU 213 (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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93B GLN* 3.8 9.0 - - - +
96B TRP* 4.2 12.8 - - + -
191B LEU* 3.7 28.0 - - + -
196B CYS* 4.4 2.5 - - + -
197B PHE 3.5 18.8 - - - +
198B THR* 2.9 17.7 + - - +
200B LEU 3.7 21.1 - - - +
201B GLY* 3.8 3.3 - - - -
202B LEU* 3.8 36.8 - - + +
212B ASN* 1.3 75.7 - - - +
214B ALA* 1.3 67.3 + - - +
216B ASP* 3.4 4.5 + - + +
217B LEU* 3.1 28.3 + - + +
276B LEU* 5.4 1.3 - - + -
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Residues in contact with ALA 214 (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 LEU* 3.6 18.4 - - + +
187B PHE* 4.2 4.5 - - - +
188B ALA* 3.8 32.8 - - - +
191B LEU* 3.6 12.9 - - + +
198B THR* 4.3 2.3 + - + -
211B PHE* 2.9 16.6 + - + +
213B LEU* 1.3 80.1 - - - +
215B SER* 1.3 61.6 + - - +
217B LEU* 3.2 2.9 + - - +
218B MET* 3.0 25.8 + - - +
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Residues in contact with SER 215 (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 LEU* 3.7 12.7 - - - +
204B HIS* 3.7 24.2 - - - -
209B ASN* 3.2 23.0 + - - -
211B PHE 3.0 7.3 + - - -
212B ASN 3.1 7.8 + - - -
214B ALA* 1.3 75.7 - - - +
216B ASP* 1.3 63.9 + - - +
218B MET* 3.1 26.2 - - - +
219B GLU* 3.3 14.9 - - - +
222B ARG* 4.1 3.3 + - - -
5R C 4.0 11.1 - - - +
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Residues in contact with ASP 216 (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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105B TRP* 3.6 24.7 + - + +
108B ILE* 3.6 12.9 - - - +
109B ILE* 5.0 0.2 - - - +
201B GLY* 3.6 1.0 - - - -
202B LEU* 2.8 41.8 + - + -
203B LYS 3.4 1.0 + - - -
204B HIS* 2.2 46.8 + - - +
212B ASN 3.0 13.4 + - - +
213B LEU* 3.5 9.4 - - + +
214B ALA 3.2 0.2 - - - -
215B SER* 1.3 76.4 - - - +
217B LEU* 1.3 63.5 + - + +
219B GLU* 3.2 24.6 + - - +
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Residues in contact with LEU 217 (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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108B ILE* 4.2 13.7 - - + -
187B PHE* 4.1 12.9 - - + -
191B LEU* 3.8 19.3 - - + -
202B LEU* 4.9 3.6 - - + -
213B LEU* 3.1 26.7 + - + +
214B ALA* 3.2 4.9 + - - +
216B ASP* 1.3 82.6 - - + +
218B MET* 1.3 60.9 + - - +
219B GLU 3.1 1.8 + - - -
220B PRO* 3.4 12.1 - - - +
221B PHE* 4.0 3.8 - - - -
268B TYR* 3.7 17.6 - - + -
269B THR* 3.6 42.6 - - + +
272B VAL* 3.8 33.9 - - + -
273B VAL* 5.4 0.7 - - + -
276B LEU* 5.6 0.9 - - + -
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Residues in contact with MET 218 (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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180B TYR* 3.5 26.7 - - + +
183B LEU* 3.8 15.7 - - + +
184B LEU* 3.7 35.4 - - - -
187B PHE* 3.7 27.8 - - + -
214B ALA 3.0 12.4 + - - +
215B SER* 3.1 18.8 - - - +
217B LEU* 1.3 75.3 - - - +
219B GLU* 1.3 65.1 + - - +
220B PRO* 3.4 1.6 - - - -
221B PHE* 2.9 19.0 + - - +
222B ARG* 3.5 50.0 + - + +
5R C 5.1 0.7 - - - +
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Residues in contact with GLU 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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105B TRP* 5.7 0.7 + - - -
108B ILE* 4.2 1.6 - - + -
109B ILE* 3.4 29.1 - - + +
112B LYS* 3.4 25.8 + - + +
148B GLU* 3.3 14.0 - - - +
204B HIS* 3.7 10.3 - - + -
215B SER 3.3 7.9 - - - +
216B ASP* 3.2 21.1 - - - +
217B LEU 3.1 0.2 - - - -
218B MET* 1.3 78.0 - - - +
220B PRO* 1.3 70.5 - - + +
221B PHE 3.0 1.4 + - - -
222B ARG* 3.0 49.9 + - - +
223B PRO* 4.0 0.2 - - - +
6R G 3.2 22.5 + - - -
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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