Contacts of the helix formed by residues 211 - 219 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78I LEU* 4.4 18.2 - - + -
79I PRO 3.8 16.8 - - - -
80I PHE* 3.2 35.2 - + + -
82I GLY 5.9 0.7 - - - -
184J LEU* 3.6 34.8 - - + -
188J ALA* 5.4 3.6 - - + -
198J THR* 3.3 11.0 - - - +
209J ASN* 2.9 42.8 - - + -
210J ASP* 1.3 82.8 - - + +
212J ASN* 1.3 66.8 + - - +
213J LEU 3.2 3.1 - - - -
214J ALA* 3.0 17.7 + - + +
215J SER* 3.0 18.9 + - - -
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Residues in contact with ASN 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198J THR 3.2 2.4 + - - -
199J GLN 3.9 7.9 - - - +
201J GLY* 3.9 6.5 - - - -
204J HIS* 3.5 38.9 + - - +
206J ASN 3.7 8.7 - - - +
207J GLN 3.9 8.3 - - - +
208J PHE* 4.1 4.2 - - - +
209J ASN* 2.6 39.6 + - - +
210J ASP 3.7 0.6 - - - -
211J PHE* 1.3 76.6 - - - +
213J LEU* 1.3 62.5 + - - +
215J SER* 3.2 11.6 + - - -
216J ASP* 3.0 28.4 + - - +
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Residues in contact with LEU 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J GLN* 3.8 14.6 - - - +
96J TRP* 4.2 12.3 - - + -
191J LEU* 3.7 29.3 - - + +
196J CYS* 4.4 2.2 - - + -
197J PHE 3.5 19.1 - - - +
198J THR* 3.0 19.4 + - - +
200J LEU 3.7 17.7 - - - +
201J GLY* 3.8 5.5 - - - -
202J LEU* 3.8 35.2 - - + +
212J ASN* 1.3 77.7 - - - +
214J ALA* 1.3 61.8 + - - +
216J ASP* 3.4 5.5 + - + +
217J LEU* 3.1 28.9 + - + +
276J LEU* 5.4 1.1 - - + -
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Residues in contact with ALA 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J LEU* 3.6 18.6 - - + +
187J PHE* 4.2 4.5 - - - +
188J ALA* 3.8 35.0 - - + +
191J LEU* 3.6 12.2 - - + +
198J THR* 4.3 3.0 + - - -
211J PHE* 3.0 13.9 + - + +
213J LEU* 1.3 77.3 - - - +
215J SER* 1.3 65.1 + - - +
217J LEU* 3.2 2.8 + - - +
218J MET* 3.0 25.5 + - - +
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Residues in contact with SER 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184J LEU* 3.6 13.3 - - - +
209J ASN* 4.2 4.2 + - - -
211J PHE* 3.0 23.9 + - - -
212J ASN* 3.5 13.0 + - - -
214J ALA* 1.3 76.6 - - - +
216J ASP* 1.3 65.8 + - - +
218J MET* 3.1 26.5 - - - +
219J GLU* 3.2 20.9 - - - +
222J ARG* 5.1 2.7 - - - -
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Residues in contact with ASP 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J TRP* 3.5 29.1 + - + +
108J ILE* 3.6 13.1 - - + +
201J GLY* 3.6 6.9 - - - -
202J LEU* 2.8 44.5 + - + +
203J LYS* 3.8 5.4 + - - +
204J HIS 5.0 0.9 + - - +
212J ASN* 3.0 16.4 + - - +
213J LEU* 3.5 9.9 - - + +
215J SER* 1.3 78.5 - - - +
217J LEU* 1.3 62.4 + - + +
219J GLU* 3.2 24.4 + - - +
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Residues in contact with LEU 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J ILE* 4.1 13.9 - - + -
187J PHE* 4.0 13.3 - - + -
191J LEU* 3.8 19.3 - - + -
202J LEU* 4.9 3.4 - - + -
213J LEU* 3.1 29.3 + - + +
214J ALA* 3.2 4.0 + - - +
216J ASP* 1.3 79.1 - - + +
218J MET* 1.3 60.1 + - - +
219J GLU 3.2 1.8 + - - -
220J PRO* 3.3 12.1 - - - +
221J PHE* 4.0 3.5 - - - -
268J TYR* 3.7 17.2 - - + -
269J THR* 3.6 42.4 - - + +
272J VAL* 3.8 34.1 - - + -
273J VAL* 5.4 0.4 - - + -
276J LEU* 5.6 0.7 - - + -
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Residues in contact with MET 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J TYR* 3.5 26.0 - - + +
183J LEU* 3.8 16.2 - - + +
184J LEU* 3.8 34.8 - - - -
187J PHE* 3.8 28.0 - - + -
214J ALA 3.0 11.7 + - - +
215J SER* 3.1 23.1 - - - +
217J LEU* 1.3 76.8 - - - +
219J GLU* 1.3 65.3 + - - +
220J PRO* 3.4 1.3 - - - -
221J PHE* 2.9 19.5 + - - +
222J ARG* 3.5 49.8 + - + +
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Residues in contact with GLU 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J TRP* 5.9 1.8 - - - +
108J ILE* 4.1 7.0 - - + -
109J ILE* 4.8 12.3 - - + +
112J LYS* 3.0 49.0 + - + +
148J GLU* 3.3 17.3 - - - +
215J SER* 3.2 13.1 - - - +
216J ASP* 3.2 21.0 - - - +
217J LEU 3.2 0.4 - - - -
218J MET* 1.3 76.0 - - - +
220J PRO* 1.3 70.9 - - + +
221J PHE 3.0 1.2 + - - -
222J ARG* 2.6 46.9 + - - +
223J PRO* 4.0 0.2 - - - +
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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