Contacts of the strand formed by residues 198 - 208 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D SER 5.2 1.7 - - - +
190D LEU 5.3 1.2 - - - +
192D SER* 3.4 21.1 + - - +
194D ARG* 2.9 67.1 + - + +
195D GLY* 3.7 6.1 - - - +
196D SER 3.1 7.8 + - - +
197D ASP* 1.3 108.9 - - - +
199D LEU* 1.3 62.7 + - - +
200D MET 3.9 0.5 + - - -
222D GLU* 4.4 17.5 - - + -
223D MET 3.1 19.1 - - - +
224D HIS* 3.4 31.7 - + + -
225D LYS* 3.8 7.2 - - - +
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D SER* 4.1 17.7 - - - +
188D SER 4.3 15.0 - - - +
192D SER* 4.4 0.9 - - - -
198D TYR* 1.3 73.5 - - - +
200D MET* 1.3 59.2 + - - +
222D GLU* 3.4 1.6 - - - -
223D MET* 2.5 66.8 + - + +
225D LYS* 3.9 32.4 - - + +
3402D ADP 3.7 44.4 - - + +
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Residues in contact with MET 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLN* 3.9 5.2 - - - +
187D SER* 2.9 23.4 - - - -
188D SER* 3.0 20.1 + - - +
190D LEU* 3.7 40.4 + - + +
191D LEU 4.9 1.6 - - - +
192D SER* 3.6 18.8 - - - +
193D PRO* 3.5 22.9 - - + -
198D TYR 3.9 1.6 + - - -
199D LEU* 1.3 74.1 - - - +
201D ALA* 1.3 62.0 + - - +
202D LEU* 4.7 5.2 - - + -
220D ARG* 2.9 55.0 - - + +
221D MET 3.1 13.9 - - - +
222D GLU* 4.6 1.3 - - + -
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D VAL* 5.6 2.9 - - + -
185D ILE* 3.2 10.3 - - - +
186D THR* 3.3 25.6 - - - +
200D MET* 1.3 73.8 - - - +
202D LEU* 1.3 62.7 + - - +
220D ARG* 3.4 2.3 - - - -
221D MET* 2.7 56.2 + - + +
223D MET* 3.9 15.3 - - + -
237D PHE* 6.3 1.1 - - + -
260D VAL* 5.8 1.8 - - + -
3402D ADP 5.2 0.2 - - - +
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLN* 4.0 18.6 - - + +
168D ALA* 3.5 32.5 - - + -
169D LEU* 4.6 2.7 - - + +
172D MET* 3.2 25.0 - - + +
184D VAL* 3.4 3.8 - - - +
185D ILE* 2.7 44.9 + - + +
188D SER* 5.9 0.4 - - - +
190D LEU* 4.1 8.7 - - + -
200D MET* 4.7 4.7 - - - -
201D ALA* 1.3 74.3 - - - +
203D GLY* 1.3 57.4 + - - +
219D ILE 3.4 2.9 - - - +
220D ARG* 3.1 43.5 - - + -
221D MET* 5.1 1.3 - - - -
312D LEU* 4.2 11.9 - - + -
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Residues in contact with GLY 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D MET* 4.2 1.3 - - - -
183D VAL 3.3 7.0 - - - -
184D VAL* 4.2 9.9 - - - -
202D LEU* 1.3 75.0 - - - +
204D SER* 1.3 58.0 + - - -
218D ARG* 3.7 2.2 - - - -
219D ILE* 2.8 49.2 + - - +
221D MET* 4.8 1.6 - - - +
252D LEU* 3.3 19.1 - - - +
256D CYS* 5.2 1.1 - - - -
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D MET* 3.8 23.4 - - - -
173D ASP* 4.7 0.3 + - - -
176D HIS* 2.6 30.9 + - - -
182D THR* 3.4 1.6 - - - -
183D VAL 2.6 41.6 + - - +
203D GLY* 1.3 73.2 - - - -
205D GLN* 1.3 63.3 + - - +
216D THR* 5.0 3.1 - - - +
217D GLN 3.4 5.0 + - - -
218D ARG* 3.7 26.2 + - - +
252D LEU* 3.4 3.8 - - - +
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Residues in contact with GLN 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D HIS* 4.1 1.6 - - - -
181D ASP* 3.2 5.2 - - + +
182D THR* 3.5 27.1 + - + +
204D SER* 1.3 77.3 + - - +
206D ARG* 1.3 68.4 + - - +
207D THR* 4.7 9.5 + - - +
215D VAL 4.1 0.6 - - - +
216D THR* 3.5 4.7 - - - +
217D GLN* 2.7 71.6 + - + +
245D THR* 6.1 3.4 - - - +
249D PRO* 2.9 27.0 + - - +
250D ASN* 4.2 0.6 - - - -
252D LEU* 3.4 31.5 + - + +
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Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ASP* 5.9 4.9 + - - +
176D HIS* 4.2 31.7 - - + +
181D ASP* 2.7 44.1 + - - +
205D GLN* 1.3 77.5 - - - +
207D THR* 1.3 68.0 + - - +
208D ARG* 6.0 2.7 - - + +
214D VAL* 3.6 34.0 - - + +
215D VAL 3.7 4.5 - - - -
216D THR* 4.0 17.0 + - + +
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Residues in contact with THR 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D GLN* 4.7 12.3 + - - +
206D ARG* 1.3 76.5 + - - +
208D ARG* 1.3 73.7 + - - +
209D ALA* 4.4 2.2 - - - +
214D VAL* 3.1 7.1 - - - +
215D VAL* 2.7 58.3 + - + +
217D GLN* 5.3 2.1 + - - -
250D ASN* 3.9 20.4 + - - +
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ARG* 6.0 4.1 - - + +
207D THR* 1.3 80.7 - - - +
209D ALA* 1.3 68.3 + - - +
210D PRO* 3.8 1.0 - - - +
212D GLY* 3.4 29.1 + - - -
213D SER 3.5 1.3 - - - -
214D VAL* 3.4 24.2 - - + +
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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