Contacts of the strand formed by residues 214 - 224 (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 VAL 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D ARG* 3.6 29.2 - - + +
207D THR 3.1 9.0 - - - +
208D ARG* 3.4 44.6 - - + +
212D GLY 3.8 2.7 - - - +
213D SER* 1.3 74.8 - - - +
215D VAL* 1.3 62.0 + - - +
216D THR* 3.4 8.2 + - - +
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Residues in contact with VAL 215 (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 4.1 0.9 - - - +
206D ARG* 3.7 1.0 - - - -
207D THR* 2.7 65.6 + - + +
209D ALA* 5.1 7.0 - - + +
213D SER* 3.9 3.0 + - - +
214D VAL* 1.3 71.4 - - - +
216D THR* 1.3 66.8 + - - +
217D GLN* 5.2 12.0 - - + +
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Residues in contact with THR 216 (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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204D SER* 5.0 2.9 - - - +
205D GLN 3.5 9.8 + - - +
206D ARG* 4.0 29.4 + - + +
214D VAL* 3.4 8.0 + - - +
215D VAL* 1.3 78.8 + - - +
217D GLN* 1.3 72.9 + - - +
218D ARG* 4.1 20.5 + - + +
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Residues in contact with GLN 217 (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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203D GLY 3.9 1.5 - - - +
204D SER* 3.4 4.9 + - - -
205D GLN* 2.7 68.8 + - + +
207D THR* 5.3 1.9 + - - -
215D VAL* 4.2 11.7 + - + +
216D THR* 1.3 75.4 - - - +
218D ARG* 1.3 63.5 + - - +
219D ILE* 5.6 3.5 - - + +
250D ASN* 3.4 24.8 + - - +
251D ASN* 3.6 3.8 + - - +
252D LEU* 3.3 32.0 - - + +
253D LYS* 4.4 5.3 - - - +
311D VAL* 6.1 1.1 - - - -
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Residues in contact with ARG 218 (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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169D LEU* 3.4 46.2 + - + +
173D ASP* 2.9 40.2 + - - -
203D GLY 3.7 2.5 - - - -
204D SER* 3.7 25.2 + - - +
216D THR* 4.1 17.1 + - + +
217D GLN* 1.3 76.2 - - - +
219D ILE* 1.3 67.4 + - - +
311D VAL* 3.5 9.4 - - - +
312D LEU* 3.0 48.3 + - + +
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Residues in contact with ILE 219 (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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169D LEU* 6.0 0.4 - - - +
201D ALA 3.9 0.5 - - - +
202D LEU* 3.4 4.9 - - - +
203D GLY 2.8 50.9 + - - +
217D GLN* 5.3 3.8 - - + +
218D ARG* 1.3 83.5 - - - +
220D ARG* 1.3 60.4 + - - +
221D MET* 4.1 9.4 - - + -
252D LEU* 3.4 35.4 - - + +
253D LYS* 3.6 28.0 - - + +
256D CYS* 3.7 22.2 - - + -
309D ALA* 4.4 7.4 - - + -
310D THR 3.4 9.9 - - - +
311D VAL* 4.5 11.7 - - + -
312D LEU* 4.4 3.5 - - - +
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Residues in contact with ARG 220 (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* 2.4 31.0 + - - +
193D PRO* 3.0 28.1 - - - +
200D MET* 2.9 36.5 - - + +
201D ALA 3.4 3.8 - - - -
202D LEU* 3.1 23.8 - - + -
219D ILE* 1.3 72.5 - - - +
221D MET* 1.3 71.0 + - - +
222D GLU* 3.5 15.7 + - - -
309D ALA* 3.6 0.2 - - - -
310D THR* 2.9 50.6 + - - +
312D LEU* 3.9 16.9 - - + +
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Residues in contact with MET 221 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184D VAL* 5.8 3.4 - - + -
199D LEU 3.5 0.9 - - - +
200D MET* 3.1 9.3 - - - +
201D ALA* 2.7 62.4 + - + +
202D LEU 5.1 0.7 - - - -
203D GLY* 4.8 3.1 - - - +
219D ILE* 4.1 16.2 - - + +
220D ARG* 1.3 81.6 - - - +
222D GLU* 1.3 63.9 + - - +
223D MET* 3.9 8.3 - - + -
237D PHE* 6.5 0.4 - - + -
256D CYS* 4.0 34.3 - - + -
257D GLU 4.7 0.7 - - - -
260D VAL* 4.1 20.2 - - + -
307D VAL* 4.9 10.8 - - + -
308D GLN 4.8 3.4 - - - +
309D ALA* 3.4 31.4 - - + +
310D THR* 5.0 0.4 - - - -
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Residues in contact with GLU 222 (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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192D SER* 4.2 9.1 - - - +
193D PRO* 3.5 38.9 - - + +
194D ARG* 3.1 45.9 + - - +
198D TYR* 4.4 14.6 - - + -
199D LEU 3.4 4.7 - - - +
200D MET* 4.6 1.1 - - + -
220D ARG* 3.5 16.8 + - - -
221D MET* 1.3 74.7 - - - +
223D MET* 1.3 61.7 + - - +
224D HIS 4.3 0.2 + - - -
307D VAL* 4.4 14.2 - - - +
308D GLN 5.4 2.6 + - - -
310D THR* 5.4 6.2 - - - +
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Residues in contact with MET 223 (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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186D THR 3.4 22.7 - - - +
187D SER* 4.1 3.4 - - - -
198D TYR* 3.1 10.7 - - - +
199D LEU* 2.5 68.6 + - + +
201D ALA* 3.9 13.7 - - + -
221D MET* 4.5 10.3 - - + +
222D GLU* 1.3 78.3 - - - +
224D HIS* 1.3 61.9 + - - +
260D VAL* 3.3 27.8 - - + -
307D VAL* 4.9 7.2 - - + -
3402D ADP 3.0 40.4 - - - +
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Residues in contact with HIS 224 (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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197D ASP* 3.4 19.2 + - + -
198D TYR* 3.4 39.9 - + + -
222D GLU 4.3 0.2 + - - -
223D MET* 1.3 73.0 - - - +
225D LYS* 1.3 69.2 + - - +
226D VAL* 3.6 5.5 + - - +
264D HIS* 4.6 26.9 - - + +
268D GLN* 4.9 9.4 - - - +
3402D ADP 3.1 16.1 - - - -
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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