Contacts of the helix formed by residues 248 - 262 (chain B) in PDB entry 1D8D
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 HIS 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A TYR* 4.1 8.1 - + + -
239B ILE 3.0 6.9 + - - +
246B GLU 3.5 0.4 + - - +
247B ALA* 1.3 74.5 - - - +
249B GLY* 1.3 54.3 + - - +
250B GLY* 3.1 21.6 + - - -
251B TYR* 3.2 18.8 + - + -
252B THR* 2.7 41.3 + - - -
276B TRP* 3.7 2.0 - - - -
290B GLY 3.4 5.7 + - - -
291B ARG* 3.4 33.8 - - + +
300B TYR* 3.2 34.4 + + - -
1000B FII 2.8 57.5 + - + +
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B HIS* 1.3 75.9 + - - +
250B GLY* 1.3 61.4 + - - +
252B THR* 4.3 1.1 - - - -
253B PHE* 2.9 26.5 + - - +
276B TRP* 4.0 1.6 - - - -
290B GLY 2.9 15.0 + - - -
300B TYR* 5.0 1.6 - - - -
303B TRP* 3.7 11.6 - - - +
304B GLN* 3.4 35.7 - - - +
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Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B HIS* 3.1 11.1 + - - -
249B GLY* 1.3 75.9 - - - +
251B TYR* 1.3 63.2 + - - +
253B PHE* 3.6 2.6 + - - +
254B CYS* 3.2 27.6 + - - -
300B TYR* 4.6 0.6 - - - -
303B TRP* 4.2 8.0 - - - +
1000B FII 3.5 40.8 - - - +
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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
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166A TYR* 2.7 35.5 + - - -
200A TYR* 3.4 35.3 - + - -
201A HIS* 5.0 1.4 - - - -
204A GLN* 4.7 4.0 + - - -
200B ASP* 3.6 25.2 + - - +
201B VAL* 3.4 30.7 - - + +
202B ARG* 3.8 17.9 - - + -
239B ILE* 3.6 17.7 - - - +
240B GLY 3.8 3.6 - - - -
241B GLY* 3.4 21.5 - - - -
248B HIS* 3.2 11.5 + - + +
250B GLY* 1.3 75.6 - - - +
252B THR* 1.3 60.2 + - - +
254B CYS* 3.3 0.8 + - - -
255B GLY* 2.8 26.0 + - - -
1000B FII 3.9 19.8 - - + +
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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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239B ILE* 2.8 36.6 + - + +
248B HIS 2.7 26.8 + - - -
249B GLY 4.0 2.9 - - - -
251B TYR* 1.3 68.9 - - - +
253B PHE* 1.3 68.0 + - - +
255B GLY 3.2 0.3 + - - -
256B LEU* 2.9 25.1 + - - +
273B LEU* 3.4 33.4 - - + -
276B TRP* 3.5 16.9 - - + -
307B LEU* 3.7 19.1 - - + -
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Residues in contact with PHE 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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154B TYR* 5.4 0.4 - - - -
205B TYR* 3.7 28.9 - + - -
249B GLY 2.9 19.1 + - - +
250B GLY 3.8 2.9 - - - +
252B THR* 1.3 76.6 - - - +
254B CYS* 1.3 62.7 + - - +
257B ALA* 2.8 44.3 + - + +
302B PHE* 3.6 33.0 - + - -
303B TRP* 3.5 44.4 - + + +
306B GLY 4.6 7.4 - - - -
307B LEU* 3.7 12.2 - - + +
310B LEU* 4.1 14.4 - - + -
399B PRO 3.2 29.2 - - - -
400B VAL 3.6 10.8 - - - -
402B ASN* 5.6 0.2 - - + -
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Residues in contact with CYS 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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201B VAL* 3.9 16.6 - - + +
202B ARG* 3.8 20.2 - - - -
205B TYR* 3.4 24.9 - - + +
250B GLY 3.2 16.6 + - - +
251B TYR 3.5 8.3 - - - +
253B PHE* 1.3 81.3 - - - +
255B GLY* 1.3 57.8 + - - +
258B ALA* 3.0 32.4 + - - +
1000B FII 3.4 35.7 - - - -
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.8 9.3 - - - +
229B ILE* 3.7 23.9 - - - +
239B ILE* 4.0 8.3 - - - -
251B TYR 2.8 19.2 + - - -
252B THR 3.2 0.9 + - - -
254B CYS* 1.3 74.8 - - - +
256B LEU* 1.3 62.1 + - - +
258B ALA* 3.7 1.5 - - - +
259B LEU* 3.0 27.8 + - - +
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Residues in contact with LEU 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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239B ILE* 4.0 2.6 - - + +
252B THR 2.9 20.3 + - - +
255B GLY* 1.3 70.5 - - - -
257B ALA* 1.3 57.4 - - - +
259B LEU* 3.0 6.0 + - + +
260B VAL* 2.8 41.2 + - + +
265B GLU* 4.4 15.3 - - + -
268B LEU* 3.8 23.3 - - + -
270B LEU* 4.4 6.1 - - + -
273B LEU* 4.0 21.1 - - + -
307B LEU* 3.6 24.9 - - + +
310B LEU* 3.7 26.9 - - + +
311B LEU* 4.0 20.0 - - + +
314B ALA* 5.7 1.1 - - + -
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Residues in contact with ALA 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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205B TYR* 3.5 28.0 - - + -
253B PHE* 2.8 40.7 + - + +
256B LEU* 1.3 73.4 - - - +
258B ALA* 1.3 61.8 + - - +
260B VAL* 3.2 6.7 + - - +
261B ILE* 3.0 26.5 + - - +
310B LEU* 3.9 14.0 - - + +
400B VAL* 4.1 8.5 - - + +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA* 4.1 6.3 - - + +
205B TYR* 3.8 27.5 - - - +
208B ALA* 4.4 3.3 - - + +
229B ILE* 3.8 19.1 - - + -
254B CYS 3.0 20.7 + - - +
255B GLY 3.7 3.4 - - - +
257B ALA* 1.3 76.0 - - - +
259B LEU* 1.3 58.8 + - - +
261B ILE* 3.1 10.0 + - - +
262B LEU* 3.0 35.8 + - + +
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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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226B ALA* 3.7 42.2 - - + +
229B ILE* 3.8 20.2 - - + -
230B ALA 5.1 0.2 - - - +
255B GLY 3.0 13.8 + - - +
256B LEU* 3.5 8.1 - - + +
258B ALA* 1.3 74.3 - - - +
260B VAL* 1.3 54.3 + - - +
262B LEU* 3.1 3.8 + - + +
263B LYS 2.7 30.3 + - - -
264B LYS* 2.8 27.9 + - + +
265B GLU* 4.0 13.7 - - + -
267B SER* 4.9 4.0 - - - +
268B LEU* 3.3 45.3 - - + -
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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 LEU* 2.8 32.1 + - + +
257B ALA 3.5 7.9 - - - +
259B LEU* 1.3 71.8 - - - +
261B ILE* 1.3 64.1 + - - +
263B LYS* 3.0 16.1 + - - +
265B GLU* 3.6 27.1 - - + +
310B LEU* 4.2 23.8 - - + +
313B ARG* 3.8 43.0 + - - +
314B ALA* 5.7 0.2 - - + -
400B VAL* 3.8 16.4 - - + -
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Residues in contact with ILE 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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205B TYR* 4.5 4.9 - - + -
208B ALA* 3.8 18.4 - - + +
209B SER* 3.8 32.5 - - - +
212B SER* 3.6 27.1 - - - +
217B ILE* 4.9 4.5 - - + -
257B ALA 3.0 19.2 + - - +
258B ALA* 3.1 9.2 + - - +
260B VAL* 1.3 76.9 - - - +
262B LEU* 1.3 63.8 + - + +
263B LYS* 3.2 15.0 + - - +
400B VAL* 3.5 28.5 - - + -
401B TYR* 4.1 10.3 - - + +
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Residues in contact with LEU 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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208B ALA* 4.7 8.7 - - + -
217B ILE* 5.2 4.9 - - + -
222B PHE* 3.5 50.5 - - + +
225B THR* 4.3 20.4 - - + -
226B ALA* 4.3 16.8 - - + +
229B ILE* 4.7 3.8 - - + -
258B ALA* 3.0 22.7 + - + +
259B LEU* 3.1 5.8 + - + +
261B ILE* 1.3 78.8 - - + +
263B LYS* 1.3 70.8 + - - +
264B LYS* 3.2 24.2 + - + +
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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