Contacts of the helix formed by residues 239 - 256 (chain B) in PDB entry 4DAJ
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 PHE 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ALA 2.7 18.7 + - - +
237B ALA 3.2 1.0 - - - -
238B ALA* 1.3 73.8 - - - +
240B TYR* 1.3 92.0 + + - +
241B MET 3.2 2.0 - - - -
242B PRO* 2.9 13.4 - - - +
243B VAL* 3.0 34.0 + - + +
499B PHE* 3.6 20.2 - + - -
500B ILE* 4.6 2.2 - - - -
503B TRP* 3.3 50.5 - + + -
504B THR* 4.1 24.7 - - + -
507B ASN* 3.3 37.7 - - + +
2000B 0HK 3.3 15.9 - - - +
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Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 4.8 7.0 - + - -
235B ALA* 3.2 27.2 + - + -
236B ILE* 3.4 37.7 - - + +
239B PHE* 1.3 89.0 - + - +
241B MET* 1.3 59.6 + - - +
243B VAL* 3.0 8.5 + - - +
244B THR* 2.9 35.6 + - + +
507B ASN* 3.1 41.5 + - + -
508B ILE* 3.7 6.5 + - + -
511B LEU* 3.5 24.2 - - + +
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Residues in contact with MET 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLY* 3.5 39.0 - - - +
234A THR* 4.7 2.0 - - - +
236A ILE* 4.5 22.0 - - + -
237A ALA* 3.7 18.2 - - + +
159B LEU* 5.7 2.9 - - - -
236B ILE* 3.1 12.1 + - + +
237B ALA* 4.1 10.8 - - - +
240B TYR* 1.3 76.1 - - - +
242B PRO* 1.3 83.1 - - + +
243B VAL 3.0 0.2 + - - -
244B THR* 3.2 8.1 + - - +
245B ILE* 2.9 39.2 + - + +
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Residues in contact with PRO 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 4.9 8.7 - - + -
159B LEU* 3.4 35.7 - - + +
237B ALA 3.1 22.2 - - - +
238B ALA* 3.4 20.9 - - - +
239B PHE* 2.9 16.4 - - - +
241B MET* 1.3 92.9 - - + +
243B VAL* 1.3 56.8 + - + +
245B ILE* 4.5 0.4 - - + -
246B MET* 3.0 42.5 + - + +
499B PHE* 6.0 1.1 - - + -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 3.0 51.8 + - + +
240B TYR* 3.0 8.7 + - - +
242B PRO* 1.3 77.4 - - + +
244B THR* 1.3 64.7 + - + +
246B MET* 3.1 11.6 + - - +
247B THR* 2.9 36.8 + - - +
496B LEU* 5.6 1.6 - - + +
499B PHE* 4.0 18.2 - - + -
500B ILE* 4.3 26.5 - - + -
504B THR* 6.0 0.4 - - + -
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Residues in contact with THR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PHE* 4.9 10.6 - - - -
236A ILE* 4.9 6.6 - - - +
240B TYR* 2.9 25.0 + - + +
241B MET* 3.5 11.1 + - - +
243B VAL* 1.3 74.3 - - + +
245B ILE* 1.3 63.1 + - - +
247B THR* 3.5 8.0 - - - -
248B ILE* 2.9 45.3 + - - +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 4.2 13.5 - - - +
230A ILE* 4.7 3.6 - - - -
232A PHE* 5.1 8.1 - - + -
233A GLY* 3.6 35.0 - - - +
159B LEU* 4.2 10.1 - - + -
163B PHE* 3.8 35.0 - - + -
241B MET* 2.9 29.3 + - + +
242B PRO* 3.8 3.4 - - + +
244B THR* 1.3 79.3 + - - +
246B MET* 1.3 59.6 + - - +
248B ILE* 3.3 5.3 + - - +
249B LEU* 2.9 39.1 + - + +
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Residues in contact with MET 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL 4.8 2.2 - - - +
158B LEU* 3.5 32.1 - - + -
159B LEU* 3.2 29.4 - - + -
162B SER* 3.1 24.2 + - - +
242B PRO* 3.0 34.8 + - + +
243B VAL* 3.6 9.4 - - - +
245B ILE* 1.3 77.9 - - + +
247B THR* 1.3 56.7 + - - +
249B LEU* 4.1 3.5 - - - +
250B TYR* 2.9 31.7 + - - +
496B LEU* 3.7 29.8 - - + +
499B PHE* 4.1 19.1 - - + -
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B VAL* 2.9 22.8 + - - +
244B THR* 3.5 12.8 - - - -
245B ILE 3.1 0.2 - - - -
246B MET* 1.3 73.4 - - - +
248B ILE* 1.3 70.1 + - + +
249B LEU 3.1 1.3 - - - -
250B TYR* 3.2 4.9 + - - +
251B TRP* 3.0 50.2 + - + +
496B LEU* 5.1 4.4 - - - +
500B ILE* 5.6 3.5 - - - +
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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
----------------------------------------------------------
229A THR* 5.5 7.9 - - + -
232A PHE* 4.1 28.3 - - + -
514A THR* 4.9 9.6 - - + -
515A PHE* 4.0 37.5 - - + -
244B THR* 2.9 25.0 + - - +
245B ILE* 4.0 4.3 - - - +
247B THR* 1.3 79.6 - - + +
249B LEU* 1.3 62.6 + - + +
251B TRP* 4.1 6.8 + - - +
252B ARG* 3.7 15.8 + - - +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 4.0 26.2 - - + -
162B SER* 4.0 20.2 - - - -
163B PHE* 3.2 47.3 - - + +
166B TYR* 3.9 32.3 - - + -
245B ILE* 2.9 27.6 + - + +
246B MET* 4.1 3.8 - - - +
248B ILE* 1.3 75.6 - - - +
250B TYR* 1.3 66.0 + - - +
251B TRP 3.1 2.0 - - - -
252B ARG* 2.8 16.3 + - + +
253B ILE* 2.9 20.6 + - + +
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Residues in contact with TYR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER* 5.8 0.9 - - - +
246B MET 2.9 22.2 + - - +
247B THR* 3.2 4.7 + - - +
249B LEU* 1.3 76.8 - - - +
251B TRP* 1.3 99.8 + + - +
253B ILE* 3.4 12.7 + - + +
254B TYR* 2.9 39.9 + + + +
489B ALA* 4.8 3.8 - - + -
492B LEU* 3.6 33.7 - - + -
493B SER* 2.4 52.1 + - - -
496B LEU* 3.8 19.1 - - + -
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Residues in contact with TRP 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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247B THR* 3.0 44.0 + - + +
248B ILE* 4.4 7.0 - - - +
250B TYR* 1.3 107.2 - + - +
252B ARG* 1.3 58.5 + - - +
254B TYR* 3.8 31.2 - + + +
255B LYS* 2.9 38.7 + - - +
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Residues in contact with ARG 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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166B TYR* 3.6 28.7 - - + -
169B ILE* 5.8 1.3 - - - +
248B ILE 3.7 11.4 + - - +
249B LEU* 2.8 10.2 + - + +
251B TRP* 1.3 75.9 - - - +
253B ILE* 1.3 65.6 + - - +
255B LYS* 3.8 9.7 - - - +
256B GLU* 3.2 25.6 + - - +
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER* 3.5 33.2 - - - +
165B ARG* 4.3 20.4 - - + -
166B TYR* 3.9 26.9 - - + +
169B ILE* 4.7 14.9 - - + +
249B LEU* 2.9 19.1 + - + +
250B TYR* 3.6 16.2 - - + +
252B ARG* 1.3 78.9 - - - +
254B TYR* 1.3 60.0 + - - +
256B GLU 3.7 8.6 - - - +
257B THR* 3.2 17.7 + - - +
489B ALA* 4.2 20.3 + - - +
492B LEU* 4.5 11.7 - - + -
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Residues in contact with TYR 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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250B TYR* 2.9 32.5 + - + +
251B TRP* 3.8 31.6 - + + +
252B ARG 3.2 0.2 - - - -
253B ILE* 1.3 78.2 - - - +
255B LYS* 1.3 70.4 + - - +
256B GLU 3.4 0.2 + - - -
257B THR* 3.9 8.4 + - - -
489B ALA* 3.6 31.3 - - + +
493B SER* 5.6 0.2 - - - -
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Residues in contact with LYS 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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251B TRP* 2.9 26.7 + - - +
252B ARG* 3.4 8.5 + - - +
254B TYR* 1.3 83.5 - - + +
256B GLU* 1.3 61.2 + - + +
257B THR 4.1 0.7 + - - -
258B GLU* 5.4 1.4 - - - +
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Residues in contact with GLU 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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169B ILE* 3.9 22.6 - - + +
252B ARG 3.2 11.1 + - - +
253B ILE 3.7 8.4 - - - +
255B LYS* 1.3 83.2 - - + +
257B THR* 1.3 59.1 + - - +
258B GLU* 3.3 23.6 - - + +
259B LYS* 4.7 16.4 - - + -
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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
------------------------------------------------------------
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