Contacts of the strand formed by residues 198 - 208 (chain G) in PDB entry 1RFU
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 TYR 198 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188G SER 5.2 1.6 - - - +
190G LEU 5.3 1.2 - - - +
192G SER* 3.3 21.3 + - - +
194G ARG* 2.8 67.5 + - + +
195G GLY* 3.6 5.7 - - - +
196G SER 3.1 9.0 + - - +
197G ASP* 1.3 108.8 - - - +
199G LEU* 1.3 62.3 + - - +
200G MET 3.9 0.5 + - - -
222G GLU* 4.3 16.6 - - + -
223G MET 3.2 18.8 - - - +
224G HIS* 3.4 30.1 + + + -
225G LYS* 3.9 6.9 - - - +
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Residues in contact with LEU 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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119G GLN* 6.1 0.4 - - - +
187G SER* 4.1 17.3 - - - +
188G SER 4.2 16.2 - - - +
192G SER* 4.4 1.1 - - - -
198G TYR* 1.3 73.7 - - - +
200G MET* 1.3 58.5 + - - +
221G MET 3.4 0.5 - - - +
222G GLU* 3.4 1.7 - - - -
223G MET* 2.6 66.3 + - + +
225G LYS* 4.1 30.1 - - + +
6402G ADP 3.8 45.5 - - + +
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Residues in contact with MET 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G GLN* 4.2 5.2 - - + +
187G SER* 3.0 23.7 - - - -
188G SER* 3.0 22.6 + - - +
190G LEU* 3.6 39.3 - - + +
191G LEU 4.8 2.5 - - - +
192G SER* 3.8 18.6 - - - +
193G PRO* 3.5 23.6 - - + -
198G TYR 3.9 1.0 + - - -
199G LEU* 1.3 75.0 - - - +
201G ALA* 1.3 63.8 + - - +
202G LEU* 4.5 7.0 - - + -
220G ARG* 3.0 52.9 - - + +
221G MET 3.1 10.1 - - - +
222G GLU* 4.8 1.6 - - + -
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Residues in contact with ALA 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G VAL* 5.5 2.7 - - + -
185G ILE* 3.3 9.2 - - - +
186G THR* 3.4 24.0 - - - +
199G LEU 4.1 0.2 + - - -
200G MET* 1.3 72.7 - - - +
202G LEU* 1.3 64.3 + - - +
220G ARG* 3.3 2.4 - - - -
221G MET* 2.7 55.5 + - + +
223G MET* 4.0 16.4 - - + -
237G PHE* 6.3 1.8 - - + -
260G VAL* 5.9 1.6 - - + -
6402G ADP 5.2 0.2 - - - +
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Residues in contact with LEU 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G GLN* 4.2 11.0 - - + +
168G ALA* 3.5 32.1 - - + -
169G LEU* 4.7 3.8 - - + +
172G MET* 3.3 24.8 - - + +
184G VAL* 3.4 4.1 - - - -
185G ILE* 2.8 41.8 + - + +
188G SER* 5.8 0.7 - - - +
190G LEU* 4.1 15.5 - - + -
200G MET* 4.5 7.2 - - + -
201G ALA* 1.3 76.5 - - - +
203G GLY* 1.3 57.9 + - - +
219G ILE 3.3 2.7 - - - +
220G ARG* 3.1 44.4 - - + +
221G MET* 5.2 0.7 - - - -
312G LEU* 4.3 10.8 - - + -
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Residues in contact with GLY 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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172G MET* 4.2 1.6 - - - -
183G VAL 3.4 7.4 - - - -
184G VAL* 4.0 10.1 - - - -
201G ALA 4.3 0.2 - - - -
202G LEU* 1.3 74.5 - - - +
204G SER* 1.3 57.9 + - - -
218G ARG* 3.6 1.5 - - - -
219G ILE* 2.7 50.6 + - - +
221G MET* 4.9 1.2 - - - +
252G LEU* 3.1 19.1 - - - +
256G CYS* 5.0 1.1 - - - -
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Residues in contact with SER 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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172G MET* 3.6 26.8 - - - +
173G ASP* 4.7 0.9 + - - -
176G HIS* 2.7 30.1 + - - -
182G THR* 3.4 2.1 - - - -
183G VAL 2.7 37.6 + - - +
203G GLY* 1.3 73.3 - - - -
205G GLN* 1.3 64.4 + - - +
216G THR* 5.5 1.4 + - - -
217G GLN 3.4 4.9 + - - -
218G ARG* 3.7 22.2 + - - +
252G LEU* 3.5 3.7 - - - +
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Residues in contact with GLN 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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176G HIS* 4.3 2.0 - - - -
181G ASP 3.3 5.8 - - - +
182G THR* 3.6 23.7 + - + +
204G SER* 1.3 76.5 + - - +
206G ARG* 1.3 62.7 + - - +
207G THR* 4.5 12.8 + - - +
215G VAL 4.8 0.2 - - - -
216G THR* 3.7 4.0 + - - -
217G GLN* 2.5 72.6 + - + +
245G THR* 6.1 3.2 - - - +
248G HIS 5.4 0.2 + - - -
249G PRO* 2.8 27.7 + - - +
250G ASN* 4.7 0.2 - - - -
251G ASN 4.1 0.2 + - - -
252G LEU* 3.4 30.8 + - + +
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Residues in contact with ARG 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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173G ASP* 5.6 5.7 + - - +
176G HIS* 4.3 29.8 - - + +
181G ASP* 2.8 45.5 + - - +
205G GLN* 1.3 76.4 - - - +
207G THR* 1.3 68.5 + - - +
208G ARG* 6.0 5.2 - - + +
214G VAL* 3.8 34.6 + - + +
215G VAL 3.7 4.7 + - - +
216G THR* 4.8 13.5 + - - +
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Residues in contact with THR 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 GLN* 4.5 13.5 + - - +
206G ARG* 1.3 77.3 + - - +
208G ARG* 1.3 70.8 + - - +
209G ALA* 4.5 2.0 - - - +
214G VAL* 3.1 6.5 - - - +
215G VAL* 2.7 59.6 + - + +
217G GLN* 5.2 2.3 + - - -
250G ASN* 3.9 20.2 + - - +
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Residues in contact with ARG 208 (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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206G ARG* 6.0 5.3 - - + +
207G THR* 1.3 78.9 - - - +
209G ALA* 1.3 68.0 + - - +
210G PRO* 4.5 1.4 - - - +
212G GLY* 3.3 30.6 + - - -
213G SER 3.5 1.3 - - - -
214G VAL* 3.4 22.9 - - + +
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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