Contacts of the strand formed by residues 242 - 254 (chain D) in PDB entry 5E6J
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 PHE 242 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D LEU* 3.7 48.5 - - + -
125D GLU 4.7 4.7 - - - +
126D VAL* 4.9 9.0 - - + -
170D MET* 5.2 0.4 - - + -
174D LEU* 4.1 26.0 - - + -
179D LEU* 4.6 13.9 - - + -
206D VAL* 3.5 37.6 - - + +
240D SER* 2.5 28.3 + - - -
241D SER* 1.3 96.5 - - - +
243D VAL* 1.3 74.6 + - - +
244D MET* 4.4 15.3 - - + -
305D PHE* 4.4 3.4 - + - -
306D TYR 3.2 14.1 - - - +
307D LYS* 4.8 1.3 - - - -
308D GLU 3.7 3.8 - - - +
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Residues in contact with VAL 243 (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 ARG* 3.2 27.8 - - - +
206D VAL 3.5 5.6 - - - +
214D TYR* 3.5 34.8 - - + +
238D GLN* 3.6 21.5 - - + +
240D SER* 3.8 1.8 - - - +
242D PHE* 1.3 86.7 - - - +
244D MET* 1.3 63.6 + - - +
245D MET* 4.0 20.6 - - + -
305D PHE* 3.3 4.3 - - - +
306D TYR* 2.7 46.6 + - + +
308D GLU* 4.1 5.4 - - + -
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Residues in contact with MET 244 (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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166D VAL* 4.4 1.8 - - + -
167D ARG* 4.1 18.8 - - + -
170D MET* 4.1 24.5 - - + -
174D LEU* 5.6 0.4 - - - -
206D VAL 2.7 14.5 + - - +
207D MET* 3.5 21.5 - - + +
208D TYR 3.3 22.9 + - - +
242D PHE* 4.2 6.7 - - + -
243D VAL* 1.3 72.3 - - - +
245D MET* 1.3 62.3 + - - +
246D SER* 3.5 23.4 + - - +
303D ASP* 3.5 23.1 - - + +
304D VAL 3.7 4.3 - - - +
305D PHE* 3.3 42.0 - - + -
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Residues in contact with MET 245 (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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208D TYR* 3.6 28.5 - - + -
211D THR* 3.4 34.5 - - + +
212D LEU* 3.2 26.3 - - - +
213D SER 4.2 2.0 - - - +
214D TYR* 4.1 13.5 - - + -
217D LEU* 3.7 32.8 - - + -
243D VAL* 4.0 16.6 - - + -
244D MET* 1.3 71.9 - - - +
246D SER* 1.3 58.2 + - - +
303D ASP* 3.6 0.7 - - - -
304D VAL* 2.8 41.9 + - - +
306D TYR* 3.5 21.1 - - + -
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Residues in contact with SER 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ARG* 3.5 26.6 - - - +
208D TYR 2.9 16.8 + - - +
209D MET* 3.8 2.2 - - - -
210D GLY 2.9 21.7 + - - -
211D THR 3.1 8.1 - - - +
212D LEU* 3.9 0.7 - - - -
244D MET* 3.5 17.9 + - - +
245D MET* 1.3 75.7 - - - +
247D ALA* 1.3 62.3 + - - +
302D THR 3.3 4.5 - - - -
303D ASP* 2.5 27.5 + - - -
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Residues in contact with ALA 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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209D MET* 3.7 10.4 - - - +
210D GLY 3.6 4.7 - - - +
211D THR* 3.5 26.0 - - - +
212D LEU* 3.5 12.7 - - + +
246D SER* 1.3 78.3 - - - +
248D PRO* 1.3 81.8 - - + +
302D THR* 3.0 28.9 + - - +
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Residues in contact with PRO 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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209D MET* 3.7 20.6 - - + -
210D GLY* 4.8 9.9 - - - +
212D LEU* 5.5 0.5 - - - +
247D ALA* 1.3 92.4 - - + +
249D PRO* 1.3 76.8 - - + +
250D ALA* 3.0 11.6 + - - +
269D TYR* 4.4 9.4 - - - +
301D VAL 4.1 1.7 - - - +
70E VAL* 4.3 17.0 - - + -
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Residues in contact with PRO 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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247D ALA 3.5 2.2 - - - +
248D PRO* 1.3 83.2 - - + -
250D ALA* 1.3 59.3 + - - +
265D TYR* 3.9 41.7 - - + +
267D GLY 5.8 1.8 - - - +
269D TYR* 4.0 14.8 - - + +
300D PRO* 5.0 6.3 - - + +
301D VAL 3.5 12.6 - - - +
302D THR* 4.3 7.6 - - - -
73E LEU* 3.9 23.1 - - + -
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Residues in contact with ALA 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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212D LEU* 4.8 4.2 - - + +
248D PRO 3.0 9.5 + - - +
249D PRO* 1.3 75.9 - - - +
251D GLU* 1.3 69.4 + - - +
252D TYR* 3.3 2.6 + - - +
300D PRO* 3.9 5.8 - - - -
301D VAL* 2.8 28.7 + - - +
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Residues in contact with GLU 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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250D ALA* 1.3 77.9 - - - +
252D TYR* 1.3 63.3 + - - +
298D LYS* 4.3 3.6 - - - +
299D GLY* 3.3 25.6 + - - -
300D PRO* 3.9 17.2 - - - +
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Residues in contact with TYR 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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212D LEU* 3.7 38.8 - - + -
213D SER* 3.5 30.5 + - - -
216D ASN* 6.0 0.7 - - - -
251D GLU* 1.3 78.0 - - - +
253D LYS* 1.3 71.1 + - - +
254D LEU* 3.7 32.3 + - + -
297D TYR* 4.4 0.2 - - - -
298D LYS* 3.3 2.4 - - - -
299D GLY 2.7 34.1 + - - +
301D VAL* 3.7 24.4 - - + +
304D VAL* 4.7 3.6 - - + -
306D TYR* 4.3 5.8 + - - -
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Residues in contact with LYS 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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252D TYR* 1.3 85.6 - - - +
254D LEU* 1.3 61.6 + - - +
255D GLN* 3.5 18.4 + - + +
297D TYR 3.1 10.5 - - - +
298D LYS* 4.0 10.8 - - + +
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Residues in contact with LEU 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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252D TYR* 3.7 27.7 + - + -
253D LYS* 1.3 70.3 - - - +
255D GLN* 1.3 60.5 + - - +
259D PHE* 3.9 31.2 - - + -
262D ALA* 3.7 28.9 - - + -
277D ILE* 3.7 33.9 - - + -
283D LEU* 3.9 3.8 - - + +
296D GLU* 3.8 5.2 - - - +
297D TYR* 2.5 51.2 + - + +
301D VAL* 4.1 12.3 - - + -
304D VAL* 4.4 9.2 - - + -
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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