Contacts of the strand formed by residues 184 - 191 (chain G) in PDB entry 1XFB
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 VAL 184 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16G LEU* 3.2 40.4 - - + +
19G ILE* 3.6 21.5 - - + -
20G ALA* 3.9 11.9 - - + +
23G ILE* 5.2 0.2 - - + -
144G ASP 2.8 13.6 + - - +
145G PHE* 2.9 16.0 - - + +
146G ALA 2.8 26.5 + - - -
183G ILE* 1.3 69.8 - - - +
185G PRO* 1.3 68.6 - - + +
186G ILE* 5.8 0.4 - - + -
226G GLY 3.3 22.7 - - - +
227G THR* 3.9 11.7 - - - +
228G LEU* 4.6 8.5 - - + +
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Residues in contact with PRO 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ALA 3.9 1.6 - - - +
174G TYR* 3.5 24.0 - - + +
175G ALA* 3.8 36.3 - - + +
178G CYS* 3.8 9.2 - - + -
179G GLN* 3.8 9.2 - - + -
183G ILE 3.2 7.6 - - - +
184G VAL* 1.3 85.8 - - - +
186G ILE* 1.3 62.4 + - - +
187G VAL* 3.6 3.1 + - + +
226G GLY 3.2 16.6 - - - +
227G THR* 3.6 12.8 - - + -
228G LEU 3.2 21.7 + - - +
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Residues in contact with ILE 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ILE* 3.8 20.4 - - + -
78G ILE* 4.1 14.6 - - + -
145G PHE* 3.6 36.1 - - + -
146G ALA 2.8 19.1 + - - +
147G LYS* 4.3 4.9 - - + -
148G TRP 3.7 7.3 + - - -
174G TYR* 2.9 18.4 + - - -
184G VAL 5.1 0.9 - - - +
185G PRO* 1.3 71.5 - - - +
187G VAL* 1.3 61.5 + - - +
188G GLU* 3.4 5.0 + - + +
228G LEU* 3.4 24.0 - - + +
230G LYS* 3.4 39.0 - - + +
269G THR* 4.5 4.9 - - - +
301G SER* 4.9 1.1 - - - +
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Residues in contact with VAL 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G LEU* 3.5 38.4 - - + -
174G TYR* 4.4 8.1 - - + -
175G ALA* 4.5 20.0 - - + -
185G PRO 4.3 6.7 - - - +
186G ILE* 1.3 70.4 - - - +
188G GLU* 1.3 57.4 + - - +
189G PRO* 3.1 9.9 - - + +
213G VAL* 3.9 18.2 - - + -
214G TYR* 5.7 1.1 - - - +
217G LEU* 4.4 19.1 - - + -
227G THR* 4.8 7.4 - - - -
228G LEU 2.8 17.0 + - - +
229G LEU* 3.4 8.6 - - + +
230G LYS 3.0 20.8 + - - -
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Residues in contact with GLU 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G LYS* 2.8 36.1 + - + +
148G TRP 3.3 15.0 + - - +
149G ARG* 3.3 31.2 - - + +
150G CYS* 3.0 23.9 + - - +
171G LEU* 4.0 5.3 - - - +
186G ILE* 3.4 6.3 + - + +
187G VAL* 1.3 73.7 - - - +
189G PRO* 1.3 58.9 - - - +
190G GLU* 3.3 14.8 + - + +
230G LYS* 3.3 41.0 - - + +
271G LEU* 3.7 11.1 - - + +
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Residues in contact with PRO 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G CYS* 4.2 7.2 - - + +
152G LEU* 5.6 4.9 - - + -
171G LEU* 3.8 17.9 - - + -
187G VAL* 3.1 16.8 - - + +
188G GLU* 1.3 81.7 - - - +
190G GLU* 1.3 62.3 + - - +
191G ILE* 3.4 9.0 + - - +
209G VAL* 4.2 11.6 - - + +
210G LEU* 4.0 26.7 - - + -
213G VAL* 4.1 14.6 - - + -
229G LEU* 3.8 10.3 - - + -
230G LYS 3.8 7.4 - - - +
231G PRO* 4.5 6.1 - - + +
232G ASN* 3.6 8.3 + - - -
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Residues in contact with GLU 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ARG* 2.4 30.8 + - - +
150G CYS 3.2 16.0 + - - +
151G VAL* 3.4 3.1 - - - +
152G LEU* 2.8 27.5 + - - +
188G GLU* 3.3 17.5 + - - +
189G PRO* 1.3 71.2 - - - +
191G ILE* 1.3 67.7 + - - +
192G LEU* 3.2 23.6 + - + +
193G PRO* 4.7 4.5 - - - +
232G ASN* 4.0 3.4 - - + +
271G LEU* 3.7 39.7 - - + +
273G GLY* 5.0 6.0 - - - -
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Residues in contact with ILE 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G LEU* 3.6 22.4 - - + +
154G ILE* 3.5 38.1 - - + -
189G PRO 4.2 5.4 - - - +
190G GLU* 1.3 74.7 - - - +
192G LEU* 1.3 64.8 + - - +
193G PRO* 3.7 3.3 - - - +
202G CYS* 5.2 5.0 - - - -
205G VAL* 3.7 4.7 - - + -
206G THR* 3.4 41.7 - - + +
209G VAL* 3.6 26.0 - - + -
232G ASN* 2.7 38.4 - - - +
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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