Contacts of the helix formed by residues 242 - 251 (chain B) in PDB entry 3P8P
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 TYR 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ASP* 3.3 37.0 - - + +
218B ILE* 3.2 25.1 - - + +
219B ALA* 3.9 6.7 - - + -
237B ARG* 3.4 48.5 - - + +
238B THR 3.1 11.2 + - - +
241B GLU* 1.3 93.4 - - + +
243B PRO* 1.3 56.2 - - - +
244B GLU 3.1 2.5 - - - -
245B SER* 2.9 18.7 + - - -
246B ALA* 2.6 35.4 + - - +
266B GLU* 2.6 29.6 + - - -
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Residues in contact with PRO 243 (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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239B PRO* 2.9 40.3 - - + +
240B GLU 4.9 0.7 - - - -
241B GLU 3.7 4.9 - - - +
242B TYR* 1.3 85.7 - - - +
244B GLU* 1.3 76.3 + - + +
246B ALA* 3.7 2.5 - - + +
247B LYS* 2.9 38.5 + - - +
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Residues in contact with GLU 244 (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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215B PRO* 3.6 20.5 - - + +
216B ASP* 4.5 4.5 - - - +
242B TYR 3.1 0.8 - - - -
243B PRO* 1.3 94.1 - - + +
245B SER* 1.3 64.7 + - - +
247B LYS* 3.6 32.2 + - - +
248B VAL* 3.2 23.2 + - - +
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Residues in contact with SER 245 (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 VAL* 4.0 5.4 - - - -
215B PRO* 3.3 12.5 - - - +
216B ASP* 2.5 44.7 + - - +
219B ALA* 3.3 26.7 - - - -
242B TYR* 2.9 8.1 + - - -
244B GLU* 1.3 77.1 - - - +
246B ALA* 1.3 61.7 + - - +
248B VAL* 3.2 12.5 + - - +
249B TYR* 2.9 24.0 - - - -
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Residues in contact with ALA 246 (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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236B HIS* 4.7 5.9 - - + +
237B ARG 4.0 10.3 - - - +
239B PRO* 3.6 39.0 - - + -
242B TYR* 2.6 20.0 + - - +
243B PRO 3.7 4.3 - - - +
245B SER* 1.3 71.3 - - - +
247B LYS* 1.3 65.1 + - - +
249B TYR* 3.1 12.5 + - - +
250B GLU* 3.0 26.4 + - + +
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Residues in contact with LYS 247 (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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243B PRO* 2.9 31.3 + - - +
244B GLU* 3.6 32.9 + - - +
245B SER 3.3 0.2 - - - -
246B ALA* 1.3 76.5 - - - +
248B VAL* 1.3 63.0 + - + +
250B GLU* 3.2 20.5 + - + +
251B LYS* 3.3 20.1 + - + +
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Residues in contact with VAL 248 (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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212B LEU* 4.2 25.3 - - + +
213B THR 3.2 24.2 - - - +
214B VAL* 4.3 6.1 - - + -
215B PRO* 3.7 20.0 - - + -
244B GLU 3.2 17.9 - - - +
245B SER* 3.2 11.0 - - - +
246B ALA 3.1 0.6 - - - -
247B LYS* 1.3 80.2 - - + +
249B TYR* 1.3 57.0 + - + +
251B LYS* 3.7 17.5 + - - +
252B LEU* 4.2 7.4 + - - +
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Residues in contact with TYR 249 (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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187B ALA* 4.4 3.5 - - + +
212B LEU* 4.3 11.7 - - + -
214B VAL* 3.9 17.8 - - + +
219B ALA* 2.8 30.8 + - + -
220B ALA* 3.6 12.5 + - - -
222B CYS* 3.9 12.3 - - + +
234B LEU* 3.1 34.3 - - + -
236B HIS* 3.9 39.7 - + + +
237B ARG* 5.4 2.0 - - + -
245B SER* 2.9 33.3 + - - -
246B ALA* 3.1 9.4 + - - +
248B VAL* 1.3 75.0 - - - +
250B GLU* 1.3 65.9 + - - +
251B LYS 2.9 2.7 - - - -
252B LEU* 2.9 29.0 + - + +
257B LEU* 3.3 14.7 - - + +
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B HIS* 4.3 11.4 + - - +
239B PRO* 5.6 8.8 - - + +
246B ALA* 3.0 21.2 + - + +
247B LYS* 3.2 15.5 + - + +
249B TYR* 1.3 76.6 - - - +
251B LYS* 1.3 60.9 + - + +
252B LEU 3.2 4.4 + - - +
253B LYS* 5.3 2.3 - - - +
257B LEU* 3.3 30.4 - - - +
259B PRO* 5.8 2.4 - - - +
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Residues in contact with LYS 251 (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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247B LYS* 3.3 16.8 - - + +
248B VAL* 3.7 12.1 - - - +
249B TYR 2.9 1.2 - - - -
250B GLU* 1.3 77.9 - - + +
252B LEU* 1.3 59.2 + - - +
253B LYS* 3.2 23.7 + - - +
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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