Contacts of the helix formed by residues 250 - 263 (chain B) in PDB entry 2P1N
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 ARG 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B GLU* 6.2 0.2 - - - -
248B GLU* 2.9 44.6 + - - +
249B VAL* 1.3 82.3 - - - +
251B PRO* 1.3 67.9 - - + +
252B ASP* 3.4 32.8 + - - +
253B VAL* 3.4 17.3 + - + +
254B TYR* 3.1 26.8 + - - +
280B TYR* 3.1 5.7 + - - -
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Residues in contact with PRO 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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249B VAL* 4.5 2.9 - - + +
250B ARG* 1.3 85.8 - - + +
252B ASP* 1.3 67.4 - - - +
254B TYR* 4.5 5.2 - - + -
255B SER* 2.9 26.3 + - - -
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Residues in contact with ASP 252 (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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250B ARG* 3.4 36.9 + - - +
251B PRO* 1.3 78.1 - - - +
253B VAL* 1.3 76.5 + - - +
255B SER* 3.8 4.6 - - - -
256B GLY* 3.1 19.8 + - - -
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Residues in contact with VAL 253 (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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224B LEU* 5.4 5.4 - - + +
225B GLU* 4.4 33.7 - - + +
247B ALA* 4.9 3.6 - - + -
248B GLU 5.2 0.9 - - - +
250B ARG* 3.4 21.7 + - + +
251B PRO 3.2 0.8 - - - -
252B ASP* 1.3 93.1 + - - +
254B TYR* 1.3 59.1 + - - +
256B GLY* 3.6 1.0 + - - -
257B LEU* 3.1 28.2 + - + +
280B TYR* 3.6 27.6 - - + +
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Residues in contact with TYR 254 (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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250B ARG 3.1 14.7 + - - +
251B PRO* 4.0 5.4 - - + +
253B VAL* 1.3 76.1 - - - +
255B SER* 1.3 72.1 + - - +
257B LEU* 3.2 4.8 + - - +
258B SER* 3.0 30.8 + - - -
279B ALA 3.9 23.3 - - - -
280B TYR* 3.9 20.6 - + + -
282B PRO* 3.4 17.5 + - + +
283B ALA* 3.3 45.7 + - + -
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Residues in contact with SER 255 (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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251B PRO 2.9 21.8 + - - -
252B ASP* 3.8 5.4 - - - -
254B TYR* 1.3 79.7 - - - +
256B GLY* 1.3 62.8 + - - +
258B SER* 3.1 5.9 + - - -
259B VAL* 3.1 33.2 + - - +
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Residues in contact with GLY 256 (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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228B ALA* 3.9 9.5 - - - +
252B ASP 3.1 13.8 + - - -
253B VAL* 4.0 1.6 - - - -
255B SER* 1.3 72.1 - - - +
257B LEU* 1.3 67.1 + - - +
258B SER 2.9 2.0 + - - -
259B VAL* 3.4 6.7 + - - +
260B ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 257 (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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224B LEU* 4.1 25.4 - - + +
227B LEU* 3.9 30.1 - - + -
228B ALA* 4.2 13.7 - - + +
231B LEU* 5.2 1.3 - - + -
245B TYR* 4.0 12.6 - - - +
253B VAL* 3.1 16.0 + - + +
254B TYR 3.6 7.6 - - - +
256B GLY* 1.3 73.2 - - - +
258B SER* 1.3 58.1 + - - +
260B ALA* 3.3 2.3 + - - +
261B LEU* 3.0 56.7 + - + +
280B TYR* 4.1 21.1 - - + -
283B ALA* 3.8 20.0 - - + -
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Residues in contact with SER 258 (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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254B TYR* 3.0 28.6 + - - -
255B SER* 3.8 4.7 + - - -
256B GLY 2.9 1.4 - - - -
257B LEU* 1.3 77.4 - - - +
259B VAL* 1.3 68.2 + - - +
261B LEU* 3.3 1.9 + - - +
262B SER* 3.2 24.4 + - - -
283B ALA* 3.9 32.0 - - - +
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Residues in contact with VAL 259 (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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232B GLN* 4.5 11.0 - - - +
255B SER* 3.1 26.2 + - - +
256B GLY* 4.1 6.3 - - - +
258B SER* 1.3 76.7 + - - +
260B ALA* 1.3 58.4 + - - +
262B SER* 3.2 8.3 + - - +
263B GLY* 2.9 26.9 + - - -
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Residues in contact with ALA 260 (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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228B ALA* 3.8 32.3 - - + +
231B LEU* 4.2 13.3 - - + +
232B GLN* 4.0 20.4 + - + +
256B GLY 3.1 18.1 + - - +
257B LEU 3.5 4.3 - - - +
259B VAL* 1.3 77.8 - - - +
261B LEU* 1.3 64.5 + - - +
262B SER 3.5 0.2 + - - -
263B GLY* 3.6 7.9 + - - -
264B CYS* 3.6 15.4 - - - -
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Residues in contact with LEU 261 (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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227B LEU* 5.1 2.5 - - + -
231B LEU* 3.9 23.6 - - + -
240B LEU* 4.0 17.3 - - + -
245B TYR* 5.0 1.6 - - + +
257B LEU* 3.0 40.8 + - + +
258B SER 3.3 3.6 + - - +
259B VAL 3.2 0.2 - - - -
260B ALA* 1.3 80.6 - - - +
262B SER* 1.3 58.1 + - - +
264B CYS* 2.9 22.1 + - - +
267B LEU* 4.4 7.2 - - + -
270B LEU* 5.3 1.8 - - + -
283B ALA* 3.7 28.9 - - + +
284B VAL* 4.1 19.7 - - + -
286B SER* 5.3 0.7 - - - +
287B VAL* 3.5 34.4 - - + +
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Residues in contact with SER 262 (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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258B SER 3.2 13.3 + - - -
259B VAL* 3.3 12.1 + - - +
261B LEU* 1.3 78.4 - - - +
263B GLY* 1.3 59.5 + - - +
264B CYS 3.3 1.5 + - - -
265B LYS* 3.0 29.1 + - - +
286B SER* 3.0 31.0 - - - -
287B VAL* 5.1 0.7 - - - -
290B ARG* 4.9 5.2 + - - +
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Residues in contact with GLY 263 (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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232B GLN* 6.3 0.7 - - - -
235B PRO* 3.8 18.4 - - - +
259B VAL 2.9 14.4 + - - -
260B ALA* 3.7 8.1 - - - -
262B SER* 1.3 73.6 + - - +
264B CYS* 1.3 60.3 + - - -
265B LYS* 3.2 15.7 + - - +
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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