Contacts of the helix formed by residues 243 - 259 (chain B) in PDB entry 5ID3
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 GLU 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU* 3.8 24.6 - - - +
231B ARG* 4.7 0.4 - - - +
242B VAL* 1.4 81.0 - - + +
244B PRO* 1.4 64.2 - - - +
245B VAL* 3.5 5.6 + - - -
246B THR* 3.9 7.8 + - - -
247B TYR* 3.5 22.4 + - + +
242C VAL 4.9 2.1 - - - +
243C GLU* 3.2 22.1 - - - +
247C TYR* 3.1 62.7 + - + +
243D GLU* 5.7 0.3 - - - +
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Residues in contact with PRO 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 4.6 20.9 - - + +
227B GLY 6.2 1.8 - - - -
228B LEU* 4.5 10.1 - - + -
231B ARG* 3.6 19.7 - - - +
241B ILE* 3.6 11.0 - - + +
242B VAL 3.1 11.2 - - - +
243B GLU 1.4 87.4 - - - +
245B VAL* 1.4 64.3 + - + +
246B THR 3.6 0.2 + - - -
247B TYR* 3.6 25.3 - - + +
248B PHE* 3.5 28.9 + - + -
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA 5.7 1.8 - - - +
224B VAL* 4.3 18.8 - - + +
225B GLN* 5.4 12.3 - - + -
228B LEU* 4.7 26.2 - - + -
243B GLU* 5.2 2.2 - - - -
244B PRO* 1.4 84.4 - - + +
246B THR* 1.4 65.8 + - - +
248B PHE* 3.6 2.4 + - - +
249B ALA* 3.1 29.7 + - + +
247C TYR* 6.3 0.4 - - + -
248C PHE* 5.0 8.1 - - + -
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Residues in contact with THR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLU* 3.9 3.6 + - - -
244B PRO 3.6 1.2 - - - -
245B VAL* 1.4 78.3 - - - +
247B TYR* 1.4 58.2 + - - +
249B ALA* 3.2 8.0 + - + +
250B THR* 2.9 27.7 + - - -
247C TYR* 3.3 47.5 - - + +
248C PHE* 2.9 53.8 - - + -
251C TYR* 4.6 11.8 - - + -
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Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL* 5.7 1.0 - - - +
243A GLU* 3.0 63.5 + - + +
246A THR* 3.6 36.6 + - + -
247A TYR* 5.5 5.6 - - + +
250A THR* 4.9 7.6 - - + +
242B VAL 5.6 0.4 - - - -
243B GLU* 3.5 32.0 + - + +
244B PRO* 3.6 25.8 - - + +
245B VAL 3.6 0.2 - - - -
246B THR* 1.4 75.2 - - - +
248B PHE* 1.4 77.8 + + - +
250B THR* 3.2 18.8 + - + +
251B TYR* 3.0 25.6 + - - +
247C TYR* 5.9 1.0 - - + +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 5.8 0.9 - - + -
246A THR* 2.9 40.4 - - + -
220B ALA* 4.1 23.7 - - + +
221B ALA* 4.6 16.2 + - + +
224B VAL* 3.7 41.3 - - + -
244B PRO* 3.5 22.2 + - + +
245B VAL 4.0 3.6 - - - +
246B THR 3.4 0.4 - - - -
247B TYR* 1.4 92.4 - + - +
249B ALA* 1.4 61.6 + - - +
251B TYR* 3.1 28.0 + + + +
252B SER* 3.4 6.2 + - - -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA* 4.9 9.5 - - + +
245B VAL* 3.1 19.3 + - + +
246B THR* 3.2 12.5 + - + +
248B PHE* 1.4 74.4 - - - +
250B THR* 1.4 61.7 + - - +
252B SER* 2.5 30.4 + - - -
253B THR* 3.3 6.1 + - - +
248C PHE* 6.3 1.3 - - + -
251C TYR* 3.8 18.9 - - + +
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Residues in contact with THR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 4.8 12.6 - - + -
246B THR* 2.9 13.9 + - - -
247B TYR* 3.2 20.8 + - + +
249B ALA* 1.4 74.1 - - - +
251B TYR* 1.4 64.0 + - - +
253B THR* 2.4 30.8 + - - +
254B VAL* 3.3 7.7 + - + +
250C THR* 4.8 5.1 + - - +
251C TYR* 3.8 31.4 + - - +
254C VAL* 4.4 3.5 - - - +
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A THR* 5.1 6.3 - - + -
249A ALA* 3.9 25.7 + - + +
250A THR* 4.3 21.1 - - + -
253A THR* 3.2 32.2 - - + +
216B TRP* 4.2 31.5 - + - -
217B ALA* 5.3 3.1 - - + -
220B ALA* 4.7 19.5 - - + -
247B TYR 3.0 11.9 + - - +
248B PHE* 3.1 25.5 + + + +
250B THR* 1.4 74.8 - - - +
252B SER* 1.4 60.3 + - - +
254B VAL* 3.0 27.1 - - - +
255B ALA* 3.4 6.9 + - + +
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B VAL* 4.7 3.2 - - - +
217B ALA* 4.3 22.4 - - - +
218B GLY* 6.1 0.7 - - - -
220B ALA* 6.5 0.2 - - - -
221B ALA* 5.5 6.5 - - - -
248B PHE 3.4 4.8 + - - -
249B ALA* 2.5 24.9 + - - +
251B TYR* 1.4 80.0 - - - +
253B THR* 1.4 59.4 + - - +
255B ALA* 3.0 30.4 + - - +
256B ALA* 3.2 5.4 + - - +
251C TYR* 5.0 3.1 + - - -
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA 3.7 2.9 - - - +
250B THR* 2.4 24.0 + - - +
252B SER* 1.4 78.1 + - - +
254B VAL* 1.4 55.0 + - - +
256B ALA* 2.7 36.9 + - - +
257B THR* 3.2 5.4 + - - -
216C TRP* 5.9 2.9 - - + -
251C TYR* 3.3 46.4 - - + +
254C VAL* 3.4 37.0 - - + +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 5.7 2.9 - - + -
253A THR* 3.4 53.2 - - + +
254A VAL* 4.7 4.0 - - - +
256A ALA* 5.9 0.9 - - + -
257A THR* 5.5 3.8 - - - +
250B THR 4.0 4.0 - - - +
251B TYR* 3.0 29.6 - - + +
253B THR* 1.4 78.5 + - - +
255B ALA* 1.4 54.1 + - - +
257B THR* 2.8 43.1 + - + +
258B PHE* 3.2 6.2 + - - +
254C VAL* 4.4 4.4 - - + +
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Residues in contact with ALA 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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214B VAL* 4.0 14.3 - - + +
216B TRP* 3.7 31.1 + - + +
217B ALA* 3.7 19.1 - - + -
251B TYR* 3.4 8.0 + - + +
252B SER* 3.0 17.6 + - - +
254B VAL* 1.4 76.5 - - - +
256B ALA* 1.4 58.5 + - - +
258B PHE* 3.2 18.7 + - - +
259B GLY* 3.3 8.3 + - - -
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Residues in contact with ALA 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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214B VAL* 3.9 16.0 - - + +
252B SER 3.2 6.3 + - - +
253B THR* 2.7 27.6 + - - +
255B ALA* 1.4 69.3 - - - +
257B THR* 1.4 59.5 + - - +
259B GLY* 3.1 17.2 + - - +
260B TYR* 4.1 0.9 + - - +
254C VAL* 6.0 0.4 - - + -
258C PHE* 4.0 34.3 - - + -
260C TYR* 4.8 0.3 + - - -
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A THR* 3.5 24.5 - - - +
253B THR 3.2 4.9 + - - -
254B VAL* 2.8 36.8 + - + +
256B ALA* 1.4 70.6 - - - +
258B PHE* 1.4 54.1 + - - -
259B GLY 3.3 0.2 + - - -
260B TYR* 2.9 48.6 + - + -
254C VAL* 4.3 3.6 - - - +
257C THR* 3.7 21.5 - - + +
260C TYR* 3.6 15.9 - - + +
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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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256A ALA* 3.6 40.4 - - + -
257A THR* 5.1 0.9 - - - -
259A GLY* 5.5 4.3 - - - -
260A TYR 6.0 0.4 - - - -
263A TYR* 4.4 26.5 - + - -
216B TRP* 6.0 3.6 - - - +
254B VAL 3.2 6.7 + - - +
255B ALA* 3.2 14.3 + - - +
257B THR* 1.4 69.4 - - - +
259B GLY* 1.3 53.8 + - - +
260B TYR* 2.7 31.5 + + - -
261B TYR* 2.9 29.9 + + + +
262B LEU* 3.7 31.4 - - + +
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Residues in contact with GLY 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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214B VAL* 5.9 3.4 - - - -
255B ALA 3.3 6.0 + - - -
256B ALA* 3.1 15.7 + - - -
258B PHE* 1.3 76.5 - - - +
260B TYR* 1.4 56.0 + - - +
261B TYR 3.3 0.7 - - - -
262B LEU* 3.5 16.6 - - - +
263B TYR* 3.0 28.4 + - - +
258C PHE* 5.9 3.6 - - - -
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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
------------------------------------------------------------
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