Contacts of the strand formed by residues 198 - 207 (chain G) in PDB entry 4BEI
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 ALA 198 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164G LEU* 4.3 19.1 - - + -
192G ASN* 3.4 21.3 - - + +
194G ARG* 3.5 26.9 - - - +
197G GLU* 1.3 73.4 - - - +
199G ASN* 1.3 63.1 + - - +
200G VAL* 3.9 2.8 + - + -
222G TRP 3.5 2.3 - - - +
223G VAL* 3.6 1.7 - - - -
224G ILE* 2.9 38.0 + - + +
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Residues in contact with ASN 199 (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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194G ARG* 4.8 2.4 - - - +
197G GLU* 3.9 22.7 + - - +
198G ALA* 1.3 73.1 - - - +
200G VAL* 1.3 66.4 + - - +
222G TRP 3.4 2.9 - - - +
223G VAL* 3.3 28.8 - - - +
255G ASP* 3.5 7.1 + - - +
256G ILE* 2.9 44.7 + - + -
257G VAL* 4.7 19.2 - - + +
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Residues in contact with VAL 200 (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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161G LEU* 4.6 0.2 - - + -
164G LEU* 3.3 31.2 - - + -
190G LEU* 4.5 9.4 - - + -
198G ALA* 4.7 2.7 - - + -
199G ASN* 1.3 83.2 - - - +
201G GLU* 1.3 59.2 + - - +
202G PHE* 5.2 2.0 - - + -
220G GLU 3.9 0.3 - - - +
221G LYS* 3.5 2.1 - - - -
222G TRP* 2.8 58.5 + - + +
224G ILE* 4.1 16.4 - - + -
253G VAL* 3.8 17.5 - - + -
254G VAL 3.1 11.9 - - - +
255G ASP* 4.3 7.6 - - + -
256G ILE* 3.5 9.9 - - - +
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Residues in contact with GLU 201 (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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200G VAL* 1.3 74.9 - - - +
202G PHE* 1.3 64.7 + - - +
203G TRP* 3.7 21.8 - - + -
219G ARG* 3.8 30.0 + - + +
220G GLU 3.2 15.3 - - - +
221G LYS* 4.0 16.0 + - + +
252G GLN 4.1 0.3 - - - +
253G VAL* 3.4 4.2 - - - +
254G VAL* 2.8 36.0 + - + +
256G ILE* 3.8 7.7 - - + +
92H ALA* 5.5 2.1 - - - +
121H PRO* 4.1 3.8 - - - +
123H TYR* 2.6 43.7 + - + +
124H MET* 3.8 8.1 - - - +
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Residues in contact with PHE 202 (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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168G ILE* 4.5 4.3 - - + -
188G VAL* 4.0 24.0 - - + -
190G LEU* 4.4 15.7 - - + -
200G VAL* 5.2 3.1 - - + -
201G GLU* 1.3 77.2 - - - +
203G TRP* 1.3 70.5 + - - +
204G MET* 3.8 37.7 - - + -
217G ASN* 3.7 27.6 - - - -
218G ALA 3.4 2.4 - - - +
219G ARG* 3.5 0.5 - - - -
220G GLU* 2.8 45.5 + - + +
222G TRP* 5.2 3.1 - + + -
230G TYR* 4.3 24.2 - + - -
232G LYS* 4.6 1.6 - - - -
251G ALA* 4.5 8.7 - - + -
252G GLN 3.4 12.6 - - - +
253G VAL* 3.8 17.3 - - + -
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Residues in contact with TRP 203 (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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201G GLU* 3.7 25.1 - - + -
202G PHE* 1.3 87.7 - - - +
204G MET* 1.3 72.7 - - - +
205G THR* 4.8 0.4 - - + -
217G ASN* 3.5 15.0 - - - +
218G ALA 4.0 1.1 - - - +
219G ARG* 3.6 30.5 - - + -
250G ASN 5.5 0.2 - - - -
251G ALA* 3.4 0.2 - - - -
252G GLN* 2.8 67.5 + - + +
254G VAL* 3.3 31.6 - - + -
261G ARG* 4.5 2.2 - - - -
86H ILE* 5.3 0.9 - - + -
87H TYR 2.9 27.2 + - - -
88H PHE* 3.5 20.8 - + + +
89H PRO* 4.1 4.0 - - + -
124H MET* 3.5 27.1 - - + -
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Residues in contact with MET 204 (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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168G ILE* 4.3 14.8 - - + -
186G PHE* 4.5 13.2 - - + -
188G VAL* 4.2 13.5 - - - -
202G PHE* 3.8 22.2 - - + -
203G TRP* 1.3 83.5 - - - +
205G THR* 1.3 67.4 + - - +
215G PRO* 4.0 1.2 - - - +
216G VAL* 2.9 21.2 + - + -
217G ASN* 2.9 44.4 + - + +
234G ARG* 4.5 8.1 - - - +
249G ILE* 4.0 26.2 - - + -
250G ASN 3.2 5.6 - - - +
251G ALA* 3.7 23.3 - - + -
266G MET* 5.2 0.2 - - + -
89H PRO* 4.1 0.3 - - - +
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Residues in contact with THR 205 (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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203G TRP* 4.8 0.6 - - + -
204G MET* 1.3 78.5 - - - +
206G ALA* 1.3 58.3 + - - +
207G VAL* 3.9 9.7 - - - +
213G ILE* 3.9 22.7 - - + -
214G ILE 3.2 11.0 - - - +
215G PRO* 4.7 2.2 - - + -
216G VAL* 3.7 6.9 - - - +
248G THR 3.7 0.2 - - - +
249G ILE* 3.6 2.9 - - - +
250G ASN* 2.7 44.5 + - - +
79H SER* 5.7 0.2 - - - +
87H TYR* 3.7 33.4 - - - +
88H PHE* 4.1 2.2 - - - -
89H PRO* 4.1 21.8 - - + -
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Residues in contact with ALA 206 (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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205G THR* 1.3 72.4 - - - +
207G VAL* 1.3 65.4 + - - +
208G GLY 3.6 2.4 + - - -
212G LEU 3.7 0.5 - - - +
213G ILE* 3.7 0.6 - - - -
214G ILE* 2.7 45.3 + - + +
216G VAL* 3.7 11.7 - - + -
236G ILE* 4.0 11.2 - - + -
247G TYR* 4.5 12.0 - - + -
248G THR 3.5 4.7 - - - +
249G ILE* 3.5 26.5 - - + -
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Residues in contact with VAL 207 (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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205G THR* 3.9 11.9 - - - +
206G ALA* 1.3 72.0 - - - +
208G GLY* 1.3 60.7 + - - +
212G LEU 3.5 9.9 - - - +
213G ILE* 4.5 4.5 - - + +
246G GLU 3.8 1.0 - - - +
247G TYR* 3.5 0.8 - - - -
248G THR* 2.7 43.2 + - - +
250G ASN* 4.9 1.8 - - + -
1272G O4B 3.9 37.9 - - - +
87H TYR* 3.6 46.7 - - + +
1272H O4B 4.3 14.1 - - - -
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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