Contacts of the helix formed by residues 248 - 259 (chain B) in PDB entry 4LGD
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 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B GLU* 2.7 32.4 + - - -
247B TRP* 1.3 74.0 - - - +
249B ASP* 1.3 60.2 + - - +
250B ASP* 3.5 7.4 + - - +
251B PHE* 3.0 18.6 + - - +
252B THR* 2.8 32.8 + - - -
277B PHE* 4.7 0.5 - - - -
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Residues in contact with ASP 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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247B TRP 5.1 1.0 - - - +
248B SER* 1.3 74.3 - - - +
250B ASP* 1.3 61.2 + - - +
252B THR* 3.7 4.6 - - - -
253B ASP* 2.8 34.8 + - - +
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Residues in contact with ASP 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 SER* 3.3 7.5 + - - +
249B ASP* 1.3 82.9 - - - +
251B PHE* 1.3 56.8 + - - +
253B ASP* 4.7 0.9 - - - -
254B PHE* 2.8 26.3 + - - +
275B HIS* 3.2 14.6 - - - -
276B PRO* 3.7 29.8 - - - +
277B PHE* 3.8 23.8 + - + +
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Residues in contact with PHE 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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120B GLU* 3.5 22.2 - - + +
123B ILE* 4.2 19.1 - - + -
211B SER* 4.0 30.1 - - - -
215B ALA* 4.1 7.0 - - + -
241B PHE* 3.8 25.4 - + - -
247B TRP* 3.9 19.3 - + + -
248B SER* 3.0 21.2 + - - +
250B ASP* 1.3 73.8 - - - +
252B THR* 1.3 65.4 + - - +
254B PHE* 3.0 4.3 + + - +
255B VAL* 3.0 36.6 + - + +
277B PHE* 3.3 43.6 - + + -
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Residues in contact with THR 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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240B THR* 5.8 2.5 - - - +
241B PHE* 3.6 28.6 - - + -
244B PRO* 4.6 7.8 + - + +
247B TRP* 3.9 11.4 + - - +
248B SER 2.8 27.5 + - - -
249B ASP* 3.7 4.7 - - - +
251B PHE* 1.3 74.9 - - - +
253B ASP* 1.3 63.5 + - - +
255B VAL* 3.3 4.9 + - - +
256B LYS* 3.1 20.8 + - + +
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Residues in contact with ASP 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 ASP 2.8 21.9 + - - +
250B ASP* 3.7 3.4 - - - +
252B THR* 1.3 71.5 - - - +
254B PHE* 1.3 67.7 + - - +
256B LYS* 2.8 32.1 + - - +
257B LYS* 2.9 40.2 + - - +
275B HIS* 2.8 25.3 + - + +
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Residues in contact with PHE 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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127B LEU* 3.8 12.3 - - + -
131B LEU* 4.2 7.9 - - + -
207B LEU* 4.3 16.4 - - + -
211B SER* 3.6 23.6 - - - -
250B ASP 2.8 14.8 + - - +
251B PHE* 3.3 9.4 - + - +
253B ASP* 1.3 76.3 - - - +
255B VAL* 1.3 69.4 + - + +
257B LYS* 3.1 13.3 + - - +
258B CYS* 3.3 31.7 + - - -
272B LEU* 3.9 26.0 - - + -
275B HIS* 3.4 22.4 + + + -
277B PHE* 3.7 20.9 - + + -
278B ILE* 3.8 35.0 - - + -
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Residues in contact with VAL 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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208B GLY* 4.6 4.0 - - - +
211B SER* 4.2 13.2 - - - -
212B ILE* 4.2 18.4 - - + -
239B PRO 4.7 4.3 - - - +
240B THR* 5.5 1.6 - - - -
241B PHE* 3.5 28.0 - - + -
251B PHE* 3.0 35.2 + - + +
252B THR 3.5 8.3 - - - +
253B ASP 3.2 0.2 - - - -
254B PHE* 1.3 79.2 - - + +
256B LYS* 1.3 60.0 + - - +
258B CYS* 3.5 5.5 + - - +
259B LEU* 3.2 45.2 + - + +
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Residues in contact with LYS 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 THR* 3.1 13.9 + - + +
253B ASP* 2.8 28.5 + - - +
255B VAL* 1.3 78.7 - - - +
257B LYS* 1.3 69.2 + - + +
258B CYS 3.5 0.2 + - - -
259B LEU* 3.7 10.7 + - - +
260B VAL* 3.6 14.2 - - - +
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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 ASP* 2.9 43.8 + - - +
254B PHE 3.1 7.2 + - - +
256B LYS* 1.3 86.6 - - + +
258B CYS* 1.3 62.3 + - - +
260B VAL* 3.3 18.6 - - + +
267B ALA* 3.9 24.1 + - + +
272B LEU* 4.1 16.6 - - + -
275B HIS* 4.1 16.3 - - + -
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Residues in contact with CYS 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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204B ILE* 3.5 27.6 - - - +
205B TRP* 3.8 7.2 - - - -
207B LEU* 4.9 2.9 - - - -
208B GLY* 3.7 18.8 - - - -
254B PHE* 3.3 37.1 + - - -
255B VAL 3.9 4.5 - - - +
256B LYS 3.3 0.2 - - - -
257B LYS* 1.3 78.2 - - - +
259B LEU* 1.3 58.9 + - - +
260B VAL 3.0 8.1 + - - -
266B ARG* 3.3 23.2 + - - -
272B LEU* 3.8 26.5 - - - -
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Residues in contact with LEU 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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205B TRP* 3.4 50.8 - - + +
208B GLY* 3.7 12.8 - - - -
209B ILE* 3.8 9.4 - - + +
212B ILE* 4.2 7.2 - - + -
238B PRO* 3.1 34.6 - - + +
239B PRO* 3.7 39.5 - - + +
255B VAL* 3.2 32.7 + - + +
256B LYS* 3.7 7.1 + - - +
257B LYS 3.5 0.4 - - - -
258B CYS* 1.3 75.4 - - - +
260B VAL* 1.3 60.4 + - - +
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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