Contacts of the helix formed by residues 247 - 262 (chain B) in PDB entry 3L43
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 ASP 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLY 5.5 1.2 - - - +
55B ASP* 5.7 0.4 - - - -
237B ARG* 4.3 0.4 + - - -
245B LYS 3.7 3.0 + - - -
246B LYS* 1.3 78.8 - - - +
248B ILE* 1.4 78.0 + - - +
249B LYS* 3.3 22.4 + - - +
250B ALA* 3.7 16.8 - - + +
251B ALA* 3.1 22.0 + - - +
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Residues in contact with ILE 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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49B GLU* 4.0 19.3 - - + +
50B ASN* 3.5 36.1 - - - +
53B GLY* 3.7 43.3 - - - +
54B ARG* 4.1 2.7 - - - +
55B ASP* 3.4 17.8 + - - +
237B ARG* 3.4 28.9 - - - +
246B LYS 4.0 0.2 + - - -
247B ASP* 1.4 76.0 + - - +
249B LYS* 1.4 57.3 + - - +
251B ALA* 3.3 6.1 + - - +
252B MET* 3.0 34.8 + - + +
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASP* 3.3 18.6 + - - +
248B ILE* 1.4 77.0 - - - +
250B ALA* 1.4 55.3 + - - +
252B MET* 3.3 8.5 + - - +
253B LEU* 3.1 31.7 + - + +
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Residues in contact with ALA 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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246B LYS* 3.7 24.8 - - + -
247B ASP* 3.4 21.5 + - + +
249B LYS* 1.4 77.3 - - - +
251B ALA* 1.4 57.8 + - - +
253B LEU* 3.4 12.6 - - - +
254B ALA* 3.1 26.2 + - - +
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Residues in contact with ALA 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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50B ASN* 5.3 5.4 - - - +
235B VAL* 4.3 5.8 - - - +
236B ASN* 5.3 2.0 - - - -
237B ARG* 3.5 41.1 - - + +
246B LYS* 4.0 11.1 - - - +
247B ASP 3.1 8.8 + - - +
248B ILE* 3.5 9.6 - - - +
250B ALA* 1.4 75.4 - - - +
252B MET* 1.4 61.7 + - + +
254B ALA* 3.3 3.6 + - - +
255B GLU* 2.9 29.2 + - - +
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Residues in contact with MET 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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50B ASN* 4.3 26.5 - - + +
248B ILE* 3.0 28.7 + - + +
249B LYS* 3.3 8.5 + - - +
251B ALA* 1.4 74.8 - - + +
253B LEU* 1.3 57.3 + - - +
255B GLU* 3.5 24.6 + - - +
256B ARG* 3.1 28.2 + - - +
274B THR* 3.6 32.1 - - + -
275B PRO* 3.8 24.6 - - + +
278B GLN* 4.9 5.2 - - - +
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Residues in contact with LEU 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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249B LYS* 3.1 17.7 + - + +
250B ALA* 3.4 15.5 - - - +
252B MET* 1.3 76.5 - - - +
254B ALA* 1.4 58.5 + - + +
256B ARG* 3.4 6.7 + - - +
257B LYS* 3.1 35.4 + - + +
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Residues in contact with ALA 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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235B VAL* 5.5 4.9 - - + +
246B LYS* 3.7 19.1 - - - +
250B ALA 3.1 17.2 + - - +
251B ALA* 3.3 6.0 + - - +
253B LEU* 1.4 77.3 - - + +
255B GLU* 1.4 57.4 + - - +
257B LYS* 3.5 10.7 + - - +
258B PHE* 2.9 29.0 + - - +
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Residues in contact with GLU 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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50B ASN* 5.2 0.6 + - - -
234B VAL* 3.3 5.9 - - - +
235B VAL* 3.0 47.7 + - + +
236B ASN* 4.7 0.2 - - - +
251B ALA 2.9 17.4 + - - +
252B MET* 3.6 20.5 - - - +
254B ALA* 1.4 75.9 - - - +
256B ARG* 1.4 60.3 + - - +
258B PHE* 3.4 6.5 + - - +
259B PHE* 3.2 40.8 + - + -
273B GLY* 3.6 7.5 - - - -
274B THR* 2.8 43.6 + - - -
275B PRO* 3.8 4.3 - - - +
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Residues in contact with ARG 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 MET 3.1 16.3 + - - +
253B LEU* 3.4 6.0 + - - +
255B GLU* 1.4 71.7 + - - +
257B LYS* 1.4 64.1 + - - +
259B PHE* 3.7 5.2 + - - +
260B LEU* 3.3 53.4 + - + +
269B ALA* 3.2 28.9 + - - +
270B ASP* 3.0 31.7 + - - +
272B MET 5.3 1.0 + - - -
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Residues in contact with LYS 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 LEU* 3.1 24.0 + - + +
254B ALA* 3.6 10.5 - - - +
255B GLU 3.4 0.2 - - - -
256B ARG* 1.4 75.9 - - - +
258B PHE* 1.4 55.1 + - - +
260B LEU* 3.5 6.1 + - - +
261B SER* 2.8 47.1 + - - +
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Residues in contact with PHE 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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207B LEU* 3.4 36.1 - - + -
208B ASP* 3.6 25.4 - - + -
235B VAL* 3.5 24.9 - - + -
254B ALA 2.9 18.1 + - - +
255B GLU* 3.4 9.6 - - - +
256B ARG 3.3 0.4 - - - -
257B LYS* 1.4 75.5 - - - +
259B PHE* 1.4 68.1 + + - +
261B SER* 3.9 3.1 - - - -
262B HIS* 3.0 56.2 + + - +
265B TYR* 4.0 16.6 - + - -
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Residues in contact with PHE 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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207B LEU* 3.7 21.8 - - + -
220B LEU* 5.0 0.2 - - + -
233B GLY 3.3 35.4 - - - -
234B VAL* 3.6 7.9 - - - -
235B VAL* 4.2 6.1 - - + -
255B GLU* 3.2 41.1 + - + +
256B ARG* 3.7 5.6 + - - +
257B LYS 3.5 0.2 - - - -
258B PHE* 1.4 89.5 - + - +
260B LEU* 1.4 61.0 + - - +
262B HIS* 4.0 4.0 - - - +
265B TYR* 3.7 19.1 - + + +
266B ARG* 3.3 24.6 + - - -
269B ALA* 3.6 23.8 - - + +
272B MET* 3.6 29.6 - - + -
273B GLY* 3.8 9.0 - - - -
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Residues in contact with LEU 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 ARG* 3.3 67.8 + - + +
257B LYS* 4.1 5.4 - - - +
258B PHE 3.4 0.2 - - - -
259B PHE* 1.4 76.9 - - - +
261B SER* 1.4 57.8 - - - +
266B ARG* 3.4 32.9 + - + +
269B ALA* 3.9 12.6 - - + -
270B ASP* 4.9 1.8 - - - +
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Residues in contact with SER 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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257B LYS* 2.8 36.8 + - - +
258B PHE* 4.0 3.1 - - - -
260B LEU* 1.4 77.3 - - - +
262B HIS* 1.4 63.0 + - - +
263B PRO* 3.3 9.5 - - - +
266B ARG* 3.8 8.9 + - - +
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Residues in contact with HIS 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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207B LEU 5.4 1.6 + - - -
210B MET* 6.3 0.8 - - - +
214B THR 5.0 5.4 + - - -
215B ASP* 4.2 11.1 - - + +
258B PHE* 3.0 48.1 + + + +
259B PHE 4.0 0.6 + - - +
260B LEU 3.7 0.4 - - - -
261B SER* 1.4 73.5 - - - +
263B PRO* 1.4 69.3 - - + +
264B ALA* 3.2 29.7 + - + +
265B TYR* 3.1 31.7 + + + -
266B ARG* 2.8 31.8 + - - +
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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