Contacts of the helix formed by residues 244 - 257 (chain B) in PDB entry 4QMG
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 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B PRO* 4.0 8.9 - - + +
242B GLU 3.3 1.2 + - - -
243B PRO* 1.3 87.7 - - + +
245B ALA* 1.3 59.4 + - - +
246B ALA 3.4 1.3 - - - -
247B GLU* 3.3 35.8 + - + -
248B ALA* 2.9 29.8 + - - +
293B PHE* 4.4 7.2 - + + -
324B ARG* 3.3 55.4 - - + -
325B ILE* 3.9 20.0 - - + -
327B ARG* 3.7 13.5 - - + -
393G ASP* 3.5 23.8 - - + -
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Residues in contact with ALA 245 (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 GLY 4.9 1.4 + - - -
229B PRO* 3.4 29.6 - - + +
230B THR 3.6 20.6 - - - +
231B PHE* 3.9 9.9 - - + -
241B PRO* 3.9 9.2 - - + -
242B GLU 3.1 18.4 + - - +
243B PRO 3.1 3.0 + - - -
244B PHE* 1.3 77.8 - - - +
246B ALA* 1.3 58.2 + - - +
248B ALA* 4.0 1.8 - - - +
249B LYS* 3.0 27.7 + - - +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 3.9 18.8 - - + -
241B PRO* 4.8 7.9 - - + +
245B ALA* 1.3 75.6 - - - +
247B GLU* 1.3 68.3 + - - +
249B LYS* 3.4 5.2 + - - +
250B PHE* 3.0 28.1 + - - +
394G TRP* 3.8 21.8 - - + -
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Residues in contact with GLU 247 (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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244B PHE* 3.3 34.1 + - + +
245B ALA 3.3 0.2 - - - -
246B ALA* 1.3 82.0 + - - +
248B ALA* 1.3 65.0 + - - +
250B PHE* 3.4 4.9 + - - +
251B PHE* 3.1 21.1 + - - +
293B PHE* 3.7 15.4 - - + -
393G ASP* 3.5 33.6 - - + +
394G TRP* 3.7 39.1 + - + +
395G ASN 5.5 0.3 + - - -
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B GLY* 3.6 9.5 - - - -
228B CYS* 4.2 17.9 - - + -
229B PRO* 4.5 1.1 - - + -
244B PHE 2.9 20.0 + - - +
245B ALA 4.0 2.7 - - - +
247B GLU* 1.3 75.1 - - - +
249B LYS* 1.3 65.4 + - - +
251B PHE* 3.2 11.5 + - - +
252B THR* 3.2 11.1 + - - -
288B LEU* 4.2 1.2 - - - +
293B PHE* 3.6 43.0 - - + +
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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
----------------------------------------------------------
202B VAL* 3.2 33.1 + - + +
203B ARG* 3.7 17.6 + - - +
204B ASP* 4.4 1.8 - - - -
205B GLY* 3.8 15.2 - - - +
231B PHE* 3.9 17.1 - - + -
245B ALA 3.0 19.5 + - - +
246B ALA* 3.5 6.7 - - - +
248B ALA* 1.3 77.4 - - - +
250B PHE* 1.3 57.8 + - - +
251B PHE 3.4 0.2 + - - -
252B THR* 3.5 2.4 + - - -
253B GLU* 2.9 50.3 + - - +
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Residues in contact with PHE 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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36B ARG* 4.1 24.9 - - - -
39B PRO* 3.5 33.2 - - + -
44B PRO* 3.5 24.0 - - + -
246B ALA 3.0 16.1 + - - +
247B GLU 3.7 2.7 - - - +
248B ALA 3.3 0.2 - - - -
249B LYS* 1.3 73.4 - - - +
251B PHE* 1.3 55.5 + - - +
253B GLU* 4.0 15.0 - - + -
254B SER* 2.8 55.1 + - - -
394G TRP* 3.6 26.0 - + + -
395G ASN 3.7 31.6 - - - -
396G ALA* 4.0 1.8 - - + -
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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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247B GLU 3.1 13.5 + - - +
248B ALA* 3.3 10.5 - - - +
250B PHE* 1.3 79.4 - - - +
252B THR* 1.3 60.2 + - - +
254B SER* 3.4 3.6 + - - -
255B ARG* 2.8 67.7 + - - +
284B ILE* 4.0 13.9 - - + -
287B LEU* 3.9 35.0 - - + -
288B LEU* 3.5 18.8 - - + -
291B GLU* 3.6 33.0 - - + -
293B PHE* 3.6 23.3 - + + -
395G ASN* 4.1 17.0 - - + +
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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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202B VAL* 4.3 9.6 - - + -
205B GLY* 2.6 35.0 + - - +
208B VAL* 4.3 20.2 - - + -
223B LEU* 6.1 0.4 - - + -
248B ALA 3.2 3.6 + - - -
249B LYS 4.0 5.8 - - - -
251B PHE* 1.3 76.4 - - - +
253B GLU* 1.3 61.4 + - - +
255B ARG* 3.1 2.8 + - - +
256B LEU* 2.8 40.8 + - + +
277B ILE* 5.9 0.7 - - + -
284B ILE* 3.8 21.4 - - + +
288B LEU* 3.7 15.2 - - - +
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Residues in contact with GLU 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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25B LYS* 3.6 29.5 + - + -
46B GLU* 4.9 1.2 - - - +
202B VAL* 3.8 25.3 + - + +
249B LYS* 2.9 46.8 + - - +
250B PHE* 3.7 17.2 - - + +
251B PHE 3.3 0.2 - - - -
252B THR* 1.3 72.8 - - - +
254B SER* 1.3 58.5 + - - +
255B ARG 3.0 10.1 + - - -
257B LEU* 3.1 49.5 + - + +
259B ARG* 3.9 3.1 + - - -
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Residues in contact with SER 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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36B ARG* 4.1 15.1 + - - +
250B PHE* 2.8 42.8 + - - -
251B PHE 3.4 7.6 + - - -
253B GLU* 1.3 74.2 - - - +
255B ARG* 1.3 68.1 + - - +
259B ARG* 3.6 17.9 + - - +
395G ASN 3.7 5.2 + - - -
397G PRO* 3.3 28.8 - - - +
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Residues in contact with ARG 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 PHE* 2.8 63.5 + - - -
252B THR 3.1 6.9 + - - +
253B GLU 3.0 0.6 - - - -
254B SER* 1.3 88.0 + - - +
256B LEU* 1.3 63.4 + - + +
257B LEU 3.8 0.2 - - - -
259B ARG* 3.1 22.7 + - - +
284B ILE* 4.3 5.6 - - + -
287B LEU* 4.8 3.5 - - - +
395G ASN* 3.3 25.7 + - - +
396G ALA 4.1 2.4 + - - -
397G PRO* 3.8 29.3 - - + +
401G TRP* 3.2 65.1 - - + +
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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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199B ILE* 3.1 23.4 - - + +
252B THR* 2.8 21.7 + - + +
255B ARG* 1.3 88.8 - - + +
257B LEU* 1.3 68.1 + - - +
259B ARG* 3.0 19.9 + - + +
261B VAL* 4.0 19.7 - - + -
277B ILE* 3.9 24.7 - - + -
279B HIS* 4.3 11.9 - - + -
284B ILE* 3.7 39.5 - - + -
401G TRP* 3.8 21.1 - - + -
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Residues in contact with LEU 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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25B LYS* 3.7 40.9 - - + +
26B MSE 4.1 15.9 - - + -
91B ILE* 4.0 3.6 - - - +
199B ILE* 3.8 8.9 - - - +
200B GLU 3.4 27.8 - - - +
201B HIS* 4.1 11.9 - - - -
202B VAL* 4.6 4.2 - - + +
252B THR 4.1 0.6 + - - -
253B GLU* 3.1 46.0 + - + +
255B ARG 3.8 0.2 - - - -
256B LEU* 1.3 74.6 - - - +
258B GLN* 1.3 81.8 + - + +
259B ARG* 3.2 18.8 + - - +
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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