Contacts of the helix formed by residues 240 - 250 (chain D) in PDB entry 3PII
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 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238D ALA 3.1 8.2 + - - -
239D VAL* 1.3 74.9 - - - +
241D LYS* 1.3 67.6 + - - +
242D PRO* 3.2 15.5 - - - +
243D ALA* 3.2 14.3 + - - +
244D PHE 3.1 17.7 + - - -
265D GLU* 5.7 2.5 - - - -
267D MET* 3.6 6.9 - - - +
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Residues in contact with LYS 241 (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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240D SER* 1.3 71.1 - - - +
242D PRO* 1.4 66.4 - - + +
244D PHE* 3.3 3.3 + - - +
245D GLN* 3.0 29.3 + - - +
265D GLU* 3.9 25.4 + - - +
266D GLU 3.5 20.8 + - - -
267D MET* 3.8 28.5 - - + +
268D PRO* 4.2 21.2 - - + +
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Residues in contact with PRO 242 (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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240D SER* 3.3 15.9 - - - +
241D LYS* 1.4 91.9 - - + +
243D ALA* 1.3 59.1 + - - +
245D GLN* 3.3 6.3 + - + +
246D SER* 2.9 31.3 + - - -
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Residues in contact with ALA 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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171D TYR* 3.7 17.8 - - + -
236D VAL* 4.2 10.8 - - + -
238D ALA 3.6 23.8 - - - +
240D SER* 3.2 14.0 + - - +
242D PRO* 1.3 77.6 - - - +
244D PHE* 1.3 59.4 + - - +
246D SER* 3.3 4.3 + - - -
247D ALA* 2.8 32.2 + - - +
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Residues in contact with PHE 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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269A ILE* 4.5 3.1 - - + -
271A ILE* 4.3 9.9 - - + -
236D VAL* 4.5 5.7 - - + +
239D VAL* 4.2 10.3 - - + -
240D SER 3.1 11.9 + - - +
241D LYS 3.5 8.5 - - - +
243D ALA* 1.3 77.5 - - - +
245D GLN* 1.3 65.5 + - - +
247D ALA* 3.2 4.9 + - - +
248D TYR* 2.7 54.3 + + + -
257D CYS* 4.6 9.9 - - - -
259D LEU* 4.4 16.6 - - + -
267D MET* 3.6 43.1 - - + -
268D PRO 5.1 2.2 - - - -
269D ILE* 3.5 28.0 - - + -
281D ILE* 4.2 14.4 - - + -
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Residues in contact with GLN 245 (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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266A GLU* 4.6 8.5 + - - +
241D LYS 3.0 17.3 + - - +
242D PRO* 4.0 6.1 - - + +
244D PHE* 1.3 79.8 - - - +
246D SER* 1.3 61.9 + - - +
248D TYR* 3.6 12.8 + - - +
249D ASN* 2.6 49.8 + - - +
268D PRO* 4.1 13.8 - - + +
270D PRO* 4.0 32.9 - - - +
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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
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171D TYR* 2.6 32.8 + - - -
215D PRO* 5.0 6.3 - - - +
219D ASP* 5.5 0.7 + - - -
220D ALA* 3.5 18.0 + - - +
221D ALA* 4.2 6.2 + - - +
242D PRO 2.9 18.0 + - - -
243D ALA* 3.7 3.8 - - - -
245D GLN* 1.3 75.6 - - - +
247D ALA* 1.3 65.4 + - - +
249D ASN* 3.1 5.7 + - - +
250D SER* 2.9 21.1 + - - -
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Residues in contact with ALA 247 (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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171D TYR* 3.2 24.3 + - + -
234D ALA* 4.2 6.1 - - + -
236D VAL* 3.7 28.9 - - + -
243D ALA 2.8 18.3 + - - +
244D PHE* 3.5 4.0 - - - +
246D SER* 1.3 75.1 - - - +
248D TYR* 1.3 64.7 + - - +
250D SER* 2.7 18.8 + - - -
251D ILE* 3.3 14.6 + - - +
257D CYS* 4.3 3.6 - - - -
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Residues in contact with TYR 248 (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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244D PHE* 2.7 44.4 + + + +
245D GLN* 3.7 15.9 - - - +
247D ALA* 1.3 73.5 - - - +
249D ASN* 1.3 76.8 + - - +
250D SER 3.7 0.2 + - - -
251D ILE* 3.8 22.9 - - - +
257D CYS* 4.4 5.0 - - - -
269D ILE* 4.8 1.1 - - + -
270D PRO* 3.8 23.9 + - + -
273D ASP* 3.6 13.8 - - + +
274D THR* 2.8 45.4 + - - -
277D ASN* 6.1 0.9 - - - -
279D ILE* 3.7 34.5 - - + +
281D ILE* 4.1 12.1 - - + -
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Residues in contact with ASN 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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221D ALA* 3.7 22.7 - - + +
245D GLN* 2.6 48.1 + - - +
246D SER* 3.1 1.5 + - - +
248D TYR* 1.3 85.6 - - - +
250D SER* 1.3 62.7 + - - +
251D ILE 3.5 5.0 - - - +
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Residues in contact with SER 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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171D TYR* 3.8 5.7 + - - -
221D ALA* 3.9 16.6 - - - +
224D MET* 3.6 36.0 - - - +
230D GLY* 3.3 10.4 - - - -
231D VAL* 3.2 25.7 + - - +
234D ALA* 4.7 1.2 - - - +
246D SER 2.9 11.3 + - - -
247D ALA* 2.7 24.4 + - - -
249D ASN* 1.3 78.1 - - - +
251D ILE* 1.3 63.7 + - - +
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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