Contacts of the helix formed by residues 215 - 225 (chain B) in PDB entry 2PY5
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 SER 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A ARG* 6.1 0.2 - - - -
323A ILE* 5.9 7.0 - - - -
346A GLU* 2.4 34.3 + - - -
213B THR 4.1 0.6 + - - -
214B LEU* 1.3 76.2 - - - +
216B LEU* 1.3 59.2 + - - +
218B LEU* 3.2 21.5 + - - +
219B ASP* 2.9 25.6 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ARG* 3.7 45.2 - - - +
346A GLU* 4.2 0.6 + - - -
348A ILE* 5.2 0.7 - - - -
214B LEU 4.9 0.4 - - - +
215B SER* 1.3 74.3 - - - +
217B GLY* 1.3 57.5 + - - +
219B ASP* 4.3 0.2 - - - -
220B LYS* 3.0 12.8 + - - +
397B PRO* 4.0 17.3 - - + -
421B THR* 4.0 22.0 - - + +
422B LYS 4.5 1.3 - - - +
423B ASP* 5.5 0.2 - - - -
424B PRO* 3.9 27.8 - - + -
8006B EDO 2.6 41.0 + - - +
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Residues in contact with GLY 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ARG* 4.7 0.2 - - - +
346A GLU* 3.0 27.3 + - - -
348A ILE* 3.8 22.5 - - - +
216B LEU* 1.3 79.0 - - - +
218B LEU* 1.3 61.0 + - - +
220B LYS* 3.3 6.5 + - - +
221B GLU* 3.1 28.6 + - - +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A GLU* 3.7 6.4 + - - +
214B LEU* 4.5 15.9 - - + -
215B SER* 3.2 30.0 + - - +
217B GLY* 1.3 71.9 - - - +
219B ASP* 1.3 61.0 + - - +
221B GLU* 3.2 22.2 + - - +
222B VAL* 2.9 34.4 + - - +
268B PRO* 4.6 17.0 - - + +
270B VAL* 4.4 12.6 - - + -
351B LEU* 3.7 27.3 - - + +
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU* 4.4 11.1 - - + +
215B SER 2.9 18.5 + - - +
216B LEU 4.3 0.2 - - - -
218B LEU* 1.3 74.8 - - - +
220B LYS* 1.3 57.3 + - - +
222B VAL* 3.4 7.8 + - - +
223B ARG* 2.8 38.9 + - - +
397B PRO* 3.6 4.0 - - - +
424B PRO* 3.5 28.6 - - + +
427B THR* 2.7 30.8 + - - +
8006B EDO 2.7 35.4 + - - -
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU* 4.0 8.3 + - - -
287A HIS* 5.0 4.4 + - - -
348A ILE* 3.3 35.3 - - + +
349A SER* 4.5 7.9 + - - -
216B LEU 3.0 18.1 + - - +
217B GLY* 3.5 7.2 - - - +
219B ASP* 1.3 77.2 - - - +
221B GLU* 1.3 61.3 + - + +
223B ARG* 3.2 6.0 + - + +
224B TYR* 3.1 52.7 + - + +
8006B EDO 3.6 20.6 - - - +
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Residues in contact with GLU 221 (chain B).
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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347A TYR 5.3 4.5 - - - +
217B GLY 3.1 15.6 + - - +
218B LEU* 3.2 28.8 + - - +
220B LYS* 1.3 73.5 - - + +
222B VAL* 1.3 66.6 + - - +
224B TYR* 3.1 33.8 + - + +
225B ALA* 3.8 1.7 + - - +
327B TRP* 3.5 52.1 - - + +
351B LEU* 4.3 7.7 - - + +
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Residues in contact with VAL 222 (chain B).
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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214B LEU* 4.3 9.0 - - + -
218B LEU* 2.9 22.1 + - + +
219B ASP* 3.6 6.1 - - - +
221B GLU* 1.3 75.3 - - - +
223B ARG* 1.3 58.4 + - - +
225B ALA* 2.9 25.6 + - - +
285B ILE* 3.9 16.4 - - + -
351B LEU* 3.7 21.8 - - + -
353B PHE* 4.3 2.9 - - + -
427B THR* 3.8 7.0 - - + -
428B PRO* 3.5 48.2 - - + -
431B VAL* 3.5 15.3 - - + +
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Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ASP* 2.8 34.7 + - - +
220B LYS* 3.5 9.4 - - + +
221B GLU 3.2 0.4 - - - -
222B VAL* 1.3 72.5 - - - +
224B TYR* 1.3 66.4 + - + +
226B TYR* 2.9 25.5 + - + +
394B ALA* 2.8 25.7 + - - +
395B SER 3.2 22.2 + - - -
396B ASN* 3.8 14.2 + - - +
397B PRO* 3.4 5.3 - - - +
427B THR* 3.4 22.2 + - + +
8006B EDO 2.7 20.3 + - - -
5E T 4.3 0.8 + - - -
6E T 3.0 39.6 + - - +
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Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU* 2.4 42.4 + - + +
273A GLY 5.2 0.2 + - - -
348A ILE 4.0 7.4 + - - -
220B LYS* 3.1 40.8 + - + +
221B GLU* 3.1 35.6 + - + +
223B ARG* 1.3 76.5 - - - +
225B ALA* 1.3 51.9 + - - +
227B ARG* 2.7 29.3 + - - -
327B TRP* 3.4 47.0 + + + +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLU 3.8 0.4 + - - -
222B VAL 2.9 13.6 + - - +
224B TYR* 1.3 78.3 - - - +
226B TYR* 1.3 59.1 + - - +
227B ARG* 3.6 10.4 + - - +
285B ILE* 3.8 23.8 - - + -
327B TRP* 3.3 22.4 - - + +
328B LEU* 4.3 1.3 - - - +
329B SER 4.3 6.0 + - - +
332B ASP* 4.7 9.2 - - - +
431B VAL* 3.6 25.4 - - + +
438B ARG* 4.7 2.1 + - - -
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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