Contacts of the helix formed by residues 249 - 260 (chain B) in PDB entry 3P3W
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 ASN 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B ASN* 3.4 27.6 + - + +
247B ASN 3.2 0.6 - - - -
248B GLU* 1.3 77.0 - - - +
250B PRO* 1.4 73.7 - - - +
251B MET* 2.9 36.2 + - - +
252B VAL* 3.1 25.5 + - + +
253B GLN* 3.1 13.2 + - - +
336B GLN* 5.5 3.8 + - - -
337B GLY 4.2 16.5 + - - -
338B MET 4.9 3.6 + - - +
340B GLY* 5.7 3.6 - - - +
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Residues in contact with PRO 250 (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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248B GLU 3.3 8.7 - - - +
249B ASN* 1.4 91.2 - - - +
251B MET* 1.3 58.2 + - + +
253B GLN* 3.8 10.7 - - + +
254B GLN* 2.9 30.2 + - - +
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Residues in contact with MET 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 ASN* 2.9 15.2 + - - +
250B PRO* 1.3 76.2 - - - +
252B VAL* 1.3 61.1 + - + +
254B GLN* 3.3 22.2 + - - +
255B PHE* 2.9 28.3 + - + +
283B HIS* 6.3 1.8 - - + -
287B LEU* 5.7 3.8 - - - -
336B GLN* 3.5 29.8 - - + +
337B GLY* 4.3 15.3 - - - +
338B MET* 4.9 6.6 - - + +
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Residues in contact with VAL 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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245B VAL* 4.5 12.6 - - + -
246B ASN 3.7 22.2 - - - +
247B ASN* 4.7 10.1 - - - +
249B ASN* 3.1 19.0 + - + +
251B MET* 1.3 75.9 - - - +
253B GLN* 1.3 52.1 + - + +
255B PHE* 3.0 7.4 + - - +
256B ILE* 2.8 50.4 + - + +
338B MET* 3.8 53.2 - - + +
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Residues in contact with GLN 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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247B ASN 2.7 29.9 + - - +
248B GLU* 3.6 19.6 + - - +
249B ASN 3.1 10.4 + - - +
250B PRO* 3.9 8.7 - - + +
252B VAL* 1.3 73.0 - - + +
254B GLN* 1.3 63.1 + - - +
256B ILE* 4.2 7.0 - - - +
257B GLN* 3.2 33.1 + - - +
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Residues in contact with GLN 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 PRO 2.9 21.7 + - - +
251B MET* 3.3 22.8 + - - +
252B VAL 3.2 0.2 - - - -
253B GLN* 1.3 77.8 - - - +
255B PHE* 1.3 60.5 + - - +
257B GLN* 4.0 12.3 + - - +
258B ARG* 2.9 42.8 + - - +
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Residues in contact with PHE 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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22B ALA* 6.0 2.7 - - + -
25B PHE* 3.7 31.4 - + - -
29B LEU* 4.9 4.5 - - + -
251B MET 2.9 13.8 + - - +
252B VAL* 3.0 8.7 + - - +
254B GLN* 1.3 75.7 - - - +
256B ILE* 1.3 72.4 + - + +
258B ARG* 3.2 11.6 + - - +
259B TRP* 3.0 61.6 + + + +
275B LEU* 5.1 7.2 - - + -
279B SER 6.1 0.2 - - - -
280B ALA* 6.3 0.9 - - - -
283B HIS* 4.1 31.4 - + + -
338B MET* 3.7 36.8 - - + -
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Residues in contact with ILE 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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252B VAL* 2.8 36.1 + - + +
253B GLN* 3.6 7.2 + - - +
254B GLN 3.5 0.2 - - - -
255B PHE* 1.3 89.1 - - + +
257B GLN* 1.3 63.9 + - - +
258B ARG 3.1 2.0 - - - -
259B TRP* 2.9 31.4 + - + -
260B VAL* 3.2 28.7 + - + +
275B LEU* 4.9 16.4 - - + -
338B MET* 5.1 0.4 - - + -
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Residues in contact with GLN 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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253B GLN* 3.2 18.8 + - + +
254B GLN* 4.1 8.1 - - - +
255B PHE 3.3 0.2 - - - -
256B ILE* 1.3 80.9 - - - +
258B ARG* 1.3 61.1 + - + +
260B VAL* 4.0 5.5 - - - +
261B ARG* 3.0 50.4 + - - +
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Residues in contact with ARG 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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25B PHE* 4.0 23.9 - - + -
29B LEU* 5.8 5.8 - - - -
254B GLN* 2.9 47.6 + - - +
255B PHE* 3.2 9.9 + - - +
256B ILE 3.1 0.4 - - - -
257B GLN* 1.3 79.2 - - + +
259B TRP* 1.3 63.8 + - - +
260B VAL 3.4 1.1 - - - -
261B ARG* 3.3 21.0 + - - +
262B LEU* 3.3 13.6 - - - +
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Residues in contact with TRP 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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18B GLN* 4.2 30.1 - - + +
21B SER* 3.9 15.0 - - - -
22B ALA* 3.7 41.5 - - + -
25B PHE* 4.2 13.7 - + + -
255B PHE* 3.0 45.0 + + + +
256B ILE* 2.9 26.1 + - + +
258B ARG* 1.3 77.4 - - - +
260B VAL* 1.3 67.9 + - + +
262B LEU* 3.3 31.7 + - + +
267B PHE* 5.8 0.7 - + - -
270B ALA* 3.7 35.1 + - + +
273B ALA 5.2 1.2 + - - -
275B LEU* 4.9 19.2 - - + +
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Residues in contact with VAL 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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256B ILE* 3.2 27.8 + - + +
257B GLN* 4.0 12.6 - - - +
259B TRP* 1.3 83.9 - - + +
261B ARG* 1.3 73.8 + - + +
262B LEU 3.4 4.1 + - - +
270B ALA 4.7 8.0 - - - +
271B LYS* 5.0 12.3 - - - +
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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