Contacts of the strand formed by residues 245 - 254 (chain D) in PDB entry 5E5R
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 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D LEU* 4.4 9.2 - - + -
239D ALA* 4.2 19.1 - - + -
243D SER* 3.7 2.9 - - - +
244D THR* 1.3 74.4 - - - +
246D ARG* 1.3 61.2 + - - +
247D LEU* 3.9 24.2 - - + -
282D LEU 3.7 1.0 - - - +
283D GLU* 3.7 0.3 - - - -
284D ILE* 2.7 45.9 + - + +
287D PHE* 3.5 40.2 - - + -
312D LEU* 4.0 16.6 - - + -
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Residues in contact with ARG 246 (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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237D LEU* 5.1 2.4 - - - +
244D THR* 3.4 37.4 + - + +
245D VAL* 1.3 78.1 - - - +
247D LEU* 1.3 65.4 + - - +
281D MET* 3.4 34.6 - - - +
282D LEU 3.5 4.3 - - - -
283D GLU* 4.3 22.1 + - + -
401D MLI 2.6 38.3 + - - +
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Residues in contact with LEU 247 (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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233D PHE* 3.7 24.9 - - + -
237D LEU* 3.6 31.0 - - + -
245D VAL* 3.9 9.6 - - + -
246D ARG* 1.3 72.9 - - - +
248D GLU* 1.3 62.2 + - - +
261D TRP* 3.7 17.4 - - + -
281D MET* 3.1 6.3 - - - -
282D LEU* 2.8 45.2 + - + +
284D ILE* 4.2 10.8 - - + -
295D TYR* 4.0 39.5 - - + -
312D LEU* 3.8 16.8 - - + -
401D MLI 3.7 2.2 - - - -
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Residues in contact with GLU 248 (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 PHE* 3.9 19.2 - - + -
174D VAL 4.5 0.3 - - - +
175D SER* 2.5 33.3 + - - -
176D GLN* 2.9 28.1 + - - +
177D GLU* 3.7 5.8 - - - +
231D VAL* 4.5 6.5 - - + +
232D GLN* 3.2 6.1 - - - +
233D PHE* 3.1 27.6 + - - +
247D LEU* 1.3 75.7 - - - +
249D CYS* 1.3 67.1 + - - +
277D LYS* 6.2 0.4 - - + +
280D GLY 3.4 4.3 - - - +
281D MET* 4.8 9.2 - - + -
401D MLI 3.0 43.3 - - + +
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Residues in contact with CYS 249 (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 PHE* 5.0 0.2 - - - -
229D ILE* 3.9 27.1 - - - -
231D VAL 3.4 6.3 - - - -
232D GLN* 4.6 1.1 - - - -
233D PHE* 4.8 0.4 - - + -
248D GLU* 1.3 78.8 - - - +
250D PHE* 1.3 63.4 + - - +
259D ILE* 3.8 10.8 - - - +
261D TRP* 3.4 13.7 - - + -
280D GLY* 2.8 31.5 + - - -
297D CYS* 2.0 50.5 - - + -
308D ALA* 4.5 4.5 - - - -
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Residues in contact with PHE 250 (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 ASP 4.6 2.7 - - - -
170D SER* 3.3 31.2 - - - -
171D ARG 3.8 16.2 - - - -
173D PHE* 3.5 43.5 - + + -
182D TYR* 3.6 38.1 - + + -
184D ALA* 4.0 9.6 - - + -
229D ILE* 3.6 3.5 - - - -
230D GLU* 2.9 24.6 + - - +
231D VAL* 3.1 20.7 + - + +
249D CYS* 1.3 77.8 - - - +
251D ALA* 1.3 87.0 + - - +
252D LEU* 4.6 1.6 - - + -
259D ILE* 4.4 9.6 - - + -
277D LYS 6.0 0.2 - - - -
278D PHE 6.2 0.7 - - - -
280D GLY* 5.0 4.7 - - - -
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Residues in contact with ALA 251 (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 ALA* 3.5 8.1 - - - +
227D PRO* 4.1 1.8 - - + -
228D LYS 3.1 18.8 - - - +
229D ILE* 4.0 2.5 - - + -
230D GLU 5.0 0.2 - - - -
250D PHE* 1.3 95.3 - - - +
252D LEU* 1.3 64.1 + - - +
257D PRO* 4.0 20.0 - - + +
259D ILE* 4.3 4.1 - - + +
299D ALA* 3.7 30.1 - - + -
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Residues in contact with LEU 252 (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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297C LYS* 5.2 0.9 - - + +
298C SER 5.6 0.4 - - - -
299C VAL* 3.5 31.9 - - + +
139D GLY* 3.7 22.4 - - - +
140D VAL* 3.7 8.7 - - - +
141D VAL* 4.1 17.5 - - + -
182D TYR* 4.4 12.6 - - + -
183D ILE 3.4 31.6 - - - +
184D ALA* 3.9 3.6 - - - +
225D TYR* 4.2 2.7 - - - +
227D PRO* 3.4 3.1 - - - +
228D LYS* 2.7 37.7 + - + +
230D GLU* 4.0 23.6 - - + +
251D ALA* 1.3 76.7 - - - +
253D GLY* 1.3 58.9 + - - +
257D PRO* 4.1 1.8 - - - -
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Residues in contact with GLY 253 (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 ALA 3.0 19.8 + - - +
185D LYS* 3.8 4.0 - - - +
225D TYR* 3.5 17.4 + - - -
227D PRO* 4.4 1.6 - - - -
252D LEU* 1.3 76.3 - - - +
254D ASN* 1.3 61.0 + - - +
255D PRO 3.0 17.1 - - - +
256D VAL* 3.4 4.7 + - - -
257D PRO* 3.5 15.3 - - - +
301D ASN* 4.4 4.0 - - - -
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Residues in contact with ASN 254 (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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137D GLY* 3.6 25.2 + - - +
185D LYS* 3.1 25.8 - - + +
222D MET 3.7 8.3 + - - -
223D GLY 2.9 25.7 + - - +
224D GLU* 3.3 12.9 - - - +
225D TYR* 3.0 42.3 + - + +
253D GLY* 1.3 74.7 - - - +
255D PRO* 1.3 70.1 + - - +
256D VAL 4.0 0.2 - - - +
301D ASN* 3.7 2.2 - - - -
303D ARG* 4.3 0.3 - - - +
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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