Contacts of the strand formed by residues 217 - 225 (chain D) in PDB entry 1PYB
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 LEU 217 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C LEU* 5.2 11.7 - - + -
98C ILE* 6.1 1.1 - - + -
212D PHE* 4.5 19.1 - - + -
215D VAL* 3.5 21.5 + - + +
216D ASP* 1.3 74.6 - - - +
218D ARG* 1.3 65.4 + - - +
267D VAL* 4.5 2.2 - - + -
268D ILE 3.6 7.0 - - - +
269D VAL* 3.5 40.6 - - + -
287D LEU* 3.7 22.0 - - + -
309D LYS* 3.3 7.3 - - - +
310D LEU* 2.9 53.9 + - + +
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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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216D ASP* 5.3 6.3 - - + +
217D LEU* 1.3 81.0 - - - +
219D VAL* 1.3 60.8 + - - +
241D LEU* 3.8 34.4 + - + -
244D GLU* 5.0 11.4 + - - -
246D ARG* 6.2 0.2 - - - -
267D VAL* 3.6 3.1 - - - +
268D ILE* 2.8 41.5 + - - +
270D ALA* 4.3 21.3 - - + +
307D GLY* 3.1 28.3 + - - +
308D ALA 3.3 10.5 - - - +
309D LYS* 3.7 22.4 - - + +
310D LEU* 3.7 5.4 - - - -
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Residues in contact with VAL 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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89C ALA* 4.3 12.8 - - + -
218D ARG* 1.3 72.7 - - - +
220D ALA* 1.3 70.0 + - - +
221D LYS* 6.3 0.2 - - + -
241D LEU* 4.2 2.6 - - - +
265D LYS* 4.5 13.7 - - + -
266D ILE 3.5 13.0 - - - +
267D VAL* 4.3 11.2 - - + -
300D PRO* 4.9 5.8 - - + -
304D VAL* 3.8 36.8 - - + +
305D LYS 4.6 2.7 - - - +
306D GLU* 3.7 1.7 - - - -
307D GLY* 3.1 26.9 + - - -
308D ALA* 2.7 17.9 + - + +
310D LEU* 3.7 21.5 - - + -
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Residues in contact with ALA 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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219D VAL* 1.3 76.6 - - - +
221D LYS* 1.3 64.2 + - - +
222D VAL* 5.3 0.5 - - - +
239D LEU* 4.3 4.6 - - + +
240D SER 3.4 30.1 - - - +
241D LEU* 3.5 21.5 - - + -
264D LYS 3.7 0.5 - - - +
265D LYS* 3.5 2.2 - - - -
266D ILE* 3.0 32.8 + - - +
268D ILE* 4.1 13.7 - - + +
306D GLU* 4.6 3.6 - - - +
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Residues in contact with LYS 221 (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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219D VAL* 6.3 0.2 - - + -
220D ALA* 1.3 78.0 - - - +
222D VAL* 1.3 64.3 + - - +
223D LEU* 3.3 3.1 + - + -
238D THR 3.7 0.2 - - - +
239D LEU* 4.0 1.5 - - - -
240D SER* 2.9 37.3 + - - +
263D GLY* 4.0 17.9 - - - +
264D LYS 3.5 5.4 - - - -
265D LYS* 3.0 42.0 - - + +
304D VAL 3.1 18.4 + - - +
305D LYS* 4.4 3.5 - - - +
306D GLU* 3.6 33.7 - - + +
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Residues in contact with VAL 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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220D ALA 5.3 0.4 - - - +
221D LYS* 1.3 71.5 - - - +
223D LEU* 1.3 62.6 + - - +
224D SER* 3.4 20.4 - - - +
237D LEU* 3.3 42.4 - - + -
238D THR 3.8 4.7 - - - +
239D LEU* 4.7 7.0 - - + +
261D LEU* 2.9 27.1 - - + +
262D VAL* 3.5 0.8 - - + +
263D GLY* 2.7 29.5 + - - +
264D LYS 3.1 14.2 + - - +
266D ILE* 3.8 25.6 - - + -
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Residues in contact with LEU 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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221D LYS* 3.3 2.2 + - + +
222D VAL* 1.3 70.6 - - - +
224D SER* 1.3 66.6 + - - +
238D THR* 3.0 34.8 + - + +
239D LEU 4.8 2.0 - - - +
240D SER* 3.9 31.2 - - - +
245D GLU* 4.1 21.1 - - + +
262D VAL* 3.2 22.7 - - - +
306D GLU* 5.6 2.0 - - - +
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Residues in contact with SER 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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222D VAL* 3.4 11.9 - - - +
223D LEU* 1.3 82.0 - - - +
225D ALA* 1.3 65.3 + - - +
226D GLU* 5.9 1.0 - - - +
227D ARG* 4.7 6.5 - - - -
237D LEU* 3.6 0.3 - - - -
238D THR* 2.6 37.4 + - - +
262D VAL* 4.2 15.3 - - - -
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Residues in contact with ALA 225 (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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224D SER* 1.3 81.3 - - - +
226D GLU* 1.3 61.2 + - - +
227D ARG* 2.8 46.3 + - - +
234D LEU* 4.6 3.1 - - + +
235D LEU* 4.5 7.4 - - + -
236D LYS 3.5 13.2 - - - +
237D LEU* 4.1 18.2 - - + -
258D PRO* 4.8 15.3 - - + +
262D VAL* 5.2 0.8 - - - +
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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