Contacts of the helix formed by residues 269 - 282 (chain B) in PDB entry 3P9K
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 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B TRP* 1.3 77.9 - - - +
270B ASP* 1.3 59.2 + - - +
271B GLN* 3.5 9.7 + - - +
272B HIS* 3.1 25.3 + - - -
273B CYS* 2.9 25.6 + - - -
322B PRO 3.2 8.4 + - - -
323B GLY* 3.5 24.7 - - - -
325B ARG* 5.8 0.7 - - - +
327B ARG* 3.5 2.0 - - - +
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Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG* 5.3 6.4 + - - -
269B SER* 1.3 72.7 - - - +
271B GLN* 1.3 65.4 + - + +
273B CYS* 3.1 5.9 + - - +
274B ALA* 2.9 25.3 + - - +
325B ARG* 4.4 10.6 - - - +
327B ARG* 2.9 33.0 + - - +
331B GLU* 5.4 3.7 - - - +
335B LEU* 4.2 17.7 - - + +
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Residues in contact with GLN 271 (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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269B SER* 3.3 9.3 + - - +
270B ASP* 1.3 77.1 - - + +
272B HIS* 1.3 65.9 + - + +
274B ALA* 3.3 7.5 + - - +
275B THR* 3.2 24.0 + - - -
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Residues in contact with HIS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 3.2 28.8 - + + -
268B TRP* 3.5 41.8 - + + -
269B SER* 3.1 24.7 + - - +
271B GLN* 1.3 81.0 - - + +
273B CYS* 1.3 62.7 + - - +
275B THR* 3.2 5.8 + - - -
276B LEU 3.0 18.5 + - - -
322B PRO* 3.7 15.9 + - - +
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Residues in contact with CYS 273 (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 PHE* 5.3 0.2 - - - -
265B LEU* 3.4 50.3 - - + -
268B TRP* 3.7 10.8 - - - -
269B SER 2.9 19.9 + - - +
270B ASP* 3.1 5.8 + - - +
272B HIS* 1.3 76.7 - - - +
274B ALA* 1.3 58.3 + - - +
276B LEU* 3.8 6.1 - - - +
277B LEU* 2.8 38.0 + - + +
327B ARG* 3.7 10.5 - - - -
335B LEU* 4.1 18.2 - - + -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASP 2.9 16.1 + - - +
271B GLN* 3.6 7.9 - - - +
273B CYS* 1.3 73.7 - - - +
275B THR* 1.3 66.8 + - - +
277B LEU* 3.4 6.0 + - - +
278B LYS* 2.9 25.5 + - - +
335B LEU* 4.9 8.7 - - + +
338B GLY* 6.2 4.5 - - - -
339B ALA* 4.8 4.7 - - - +
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Residues in contact with THR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 3.6 35.9 - - + +
271B GLN 3.2 11.6 + - - -
272B HIS* 3.2 10.7 + - - -
274B ALA* 1.3 80.3 - - - +
276B LEU* 1.3 62.0 + - - +
278B LYS* 3.3 5.9 + - - +
279B ASN* 3.1 26.5 + - - +
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Residues in contact with LEU 276 (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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204B VAL* 4.4 3.4 - - + -
249B MET* 3.7 62.6 - - + +
250B PHE* 3.8 11.6 - - + -
253B VAL* 4.1 4.7 - - + -
261B MET* 3.9 23.6 - - + -
264B ILE* 3.9 8.3 - - + -
265B LEU* 4.2 11.0 - - + -
268B TRP* 5.2 2.2 - - + -
272B HIS 3.0 15.9 + - - +
273B CYS* 3.8 5.4 - - - +
275B THR* 1.3 79.3 - - - +
277B LEU* 1.3 61.6 + - - +
279B ASN* 3.2 7.2 + - - +
280B CYS* 3.0 30.7 + - - -
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Residues in contact with LEU 277 (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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261B MET* 3.8 25.4 - - + -
265B LEU* 4.0 20.2 - - + -
273B CYS* 2.8 26.0 + - + +
274B ALA* 4.0 2.7 - - - +
276B LEU* 1.3 73.4 - - - +
278B LYS* 1.3 58.3 + - - +
280B CYS* 3.5 4.0 + - - +
281B TYR* 3.0 27.4 + - - +
290B VAL* 4.7 4.5 - - + -
335B LEU* 3.7 39.7 - - + +
336B ALA* 4.8 0.4 - - - -
339B ALA* 3.5 18.6 - - + +
341B PHE* 3.9 9.2 - - + -
358B PHE* 4.2 24.9 - - + -
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Residues in contact with LYS 278 (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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274B ALA 2.9 18.2 + - - +
275B THR* 3.5 7.4 - - - +
276B LEU 3.1 0.2 - - - -
277B LEU* 1.3 75.0 - - - +
279B ASN* 1.3 68.6 + - - +
281B TYR* 3.1 18.1 + - + +
282B ASP* 2.9 57.0 + - - +
338B GLY 5.9 0.2 - - - +
339B ALA* 3.9 22.9 + - + +
340B GLY* 5.8 0.8 - - - -
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Residues in contact with ASN 279 (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 MET 2.9 27.7 + - - +
250B PHE* 3.0 25.9 + - - +
251B LYS 3.4 17.3 + - - +
252B GLU* 4.2 8.2 - - - -
253B VAL* 3.8 8.2 + - + +
275B THR* 3.1 22.8 + - - +
276B LEU 3.6 6.3 - - - +
278B LYS* 1.3 78.2 - - - +
280B CYS* 1.3 61.7 + - - +
282B ASP* 3.3 10.8 + - - +
283B ALA* 3.1 22.3 + - - +
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Residues in contact with CYS 280 (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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204B VAL* 4.9 0.4 - - - -
253B VAL* 4.0 8.1 - - - -
259B ILE* 3.8 32.3 - - + -
261B MET* 4.0 27.6 - - - -
276B LEU* 3.0 32.5 + - - -
277B LEU* 3.5 9.9 - - - +
279B ASN* 1.3 74.2 - - - +
281B TYR* 1.3 58.9 - - - +
283B ALA* 2.8 22.2 + - - +
284B LEU* 3.1 18.3 + - - +
290B VAL* 4.0 14.8 - - + -
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Residues in contact with TYR 281 (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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277B LEU 3.0 11.3 + - - +
278B LYS* 3.3 18.2 - - + +
280B CYS* 1.3 80.0 - - - +
282B ASP* 1.3 73.4 + - - +
283B ALA 3.3 0.5 + - - -
284B LEU* 3.3 1.4 + - - -
339B ALA 3.3 21.3 - - - +
340B GLY* 3.1 35.5 + - - -
341B PHE* 3.9 21.7 - + + -
360B LYS* 2.8 70.7 + - + +
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LYS* 2.9 56.0 + - - +
279B ASN* 3.6 10.4 - - - +
281B TYR* 1.3 82.0 - - - +
283B ALA* 1.3 58.6 + - - +
284B LEU 3.4 3.0 - - - +
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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