Contacts of the helix formed by residues 244 - 257 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C PRO* 4.0 4.2 - - + +
242C GLU 3.3 1.2 + - - -
243C PRO* 1.3 80.9 - - + +
245C ALA* 1.3 59.6 + - - +
247C GLU* 3.2 34.7 + - + -
248C ALA* 3.0 28.1 + - - +
293C PHE* 4.5 5.4 - + + -
324C ARG* 3.1 57.2 - - + -
325C ILE* 4.3 19.1 - - + -
327C ARG* 3.6 33.4 - - - -
393H ASP* 3.7 30.5 - - + -
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Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLY 5.0 0.9 + - - -
229C PRO* 3.6 23.0 - - + +
230C THR 3.5 22.9 - - - +
231C PHE* 3.9 12.2 - - + -
241C PRO* 3.8 8.5 - - + -
242C GLU 3.1 21.1 + - - +
243C PRO 3.2 0.8 - - - -
244C PHE* 1.3 74.4 - - - +
246C ALA* 1.3 62.2 + - - +
247C GLU* 3.8 0.6 + - - -
248C ALA* 3.2 4.9 + - - +
249C LYS* 2.9 27.9 + - - +
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C PHE* 3.7 21.7 - - + -
241C PRO* 4.8 5.3 - - + +
245C ALA* 1.3 79.2 - - - +
247C GLU* 1.3 63.0 + - - +
249C LYS* 3.3 5.4 + - + +
250C PHE* 3.0 30.1 + - - +
394H TRP* 4.0 18.8 - - + -
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Residues in contact with GLU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C PHE* 3.2 32.2 + - + +
245C ALA 3.8 0.2 + - - -
246C ALA* 1.3 82.1 + - - +
248C ALA* 1.3 61.5 + - - +
250C PHE* 3.4 4.3 + - - +
251C PHE* 3.1 21.0 + - - +
293C PHE* 3.6 15.5 - - + -
393H ASP* 3.4 38.5 - - + +
394H TRP* 3.6 39.1 + - + -
395H ASN 5.5 0.5 + - - -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLY* 3.6 5.0 - - - +
228C CYS* 4.3 17.5 - - + -
229C PRO* 4.6 1.3 - - + -
244C PHE 3.0 20.5 + - - +
245C ALA 3.7 3.6 - - - +
247C GLU* 1.3 73.6 - - - +
249C LYS* 1.3 64.0 + - - +
251C PHE* 3.3 4.8 + - - +
252C THR* 3.3 24.3 + - - -
288C LEU* 4.1 1.4 - - + +
293C PHE* 3.5 41.3 - - + +
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Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 3.2 35.6 + - + +
203C ARG 4.0 12.3 + - - +
204C ASP* 4.2 9.2 - - - -
205C GLY* 3.8 10.5 - - - +
231C PHE* 4.1 16.2 - - + -
245C ALA 2.9 13.9 + - - +
246C ALA* 3.5 10.8 - - + +
248C ALA* 1.3 77.5 - - - +
250C PHE* 1.3 57.3 + - - +
252C THR* 3.4 3.6 + - - -
253C GLU* 2.8 51.7 + - - +
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Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LYS* 5.6 5.8 - - - -
36C ARG* 3.9 14.8 - - - -
39C PRO* 3.5 39.3 - - + -
44C PRO* 3.5 24.5 - - + -
246C ALA 3.0 16.7 + - - +
247C GLU 3.7 4.0 - - - +
249C LYS* 1.3 73.3 - - - +
251C PHE* 1.3 60.3 + - - +
253C GLU* 3.9 16.4 - - + +
254C SER* 2.7 58.0 + - - -
394H TRP* 3.9 23.1 - + + -
395H ASN 3.8 11.9 - - - -
396H ALA* 3.6 22.4 - - + -
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Residues in contact with PHE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C GLU 3.1 14.1 + - - +
248C ALA* 3.5 10.5 - - - +
249C LYS 3.3 0.2 - - - -
250C PHE* 1.3 78.9 - - - +
252C THR* 1.3 59.8 + - - +
254C SER* 3.5 2.4 + - - -
255C ARG* 2.9 72.8 + - - +
284C ILE* 3.9 12.6 - - + -
287C LEU* 3.8 27.4 - - + -
288C LEU* 3.7 25.4 - - + -
291C GLU* 3.6 31.2 - - + -
293C PHE* 3.5 23.1 - + + -
395H ASN* 3.7 20.9 - - + +
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Residues in contact with THR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 4.5 7.0 - - + -
205C GLY* 3.0 29.5 + - - +
208C VAL* 4.5 18.8 - - + -
223C LEU* 6.0 0.7 - - + -
248C ALA 3.3 5.6 + - - -
249C LYS 3.9 4.9 - - - -
250C PHE 3.2 0.2 - - - -
251C PHE* 1.3 74.8 - - - +
253C GLU* 1.3 61.2 + - - +
255C ARG* 3.2 1.9 + - - +
256C LEU* 2.8 54.3 + - + +
277C ILE* 5.7 0.9 - - + -
284C ILE* 4.0 12.9 - - + +
288C LEU* 3.5 18.5 - - - +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LYS* 3.2 36.7 + - - +
26C MSE 5.1 0.9 - - - +
202C VAL* 4.1 22.5 + - + +
249C LYS* 2.8 45.2 + - - +
250C PHE* 3.6 16.9 - - + +
252C THR* 1.3 77.5 - - - +
254C SER* 1.3 58.9 + - - +
255C ARG 3.1 5.1 + - - -
257C LEU* 3.1 49.3 + - + +
259C ARG* 3.7 2.6 + - - -
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 3.9 16.8 + - - +
250C PHE* 2.7 49.6 + - - -
253C GLU* 1.3 72.6 - - - +
255C ARG* 1.3 78.8 + - - +
259C ARG* 3.2 22.0 + - - +
395H ASN 3.9 3.1 + - - -
397H PRO* 3.3 24.3 - - - +
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Residues in contact with ARG 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 2.9 59.0 + - - +
252C THR 3.2 3.5 + - - +
253C GLU 3.1 0.4 - - - -
254C SER* 1.3 85.9 + - - +
256C LEU* 1.3 65.1 + - + +
259C ARG* 3.4 11.3 + - - +
284C ILE* 4.3 6.7 - - + -
287C LEU* 4.8 3.3 - - - +
395H ASN* 2.7 48.3 + - - -
397H PRO* 3.6 28.9 - - + +
401H TRP* 3.2 70.6 - - + +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ILE* 3.2 22.2 - - + +
208C VAL* 5.9 0.2 - - + -
252C THR* 2.8 24.1 + - + +
255C ARG* 1.3 92.4 - - + +
257C LEU* 1.3 65.4 + - - +
258C GLN 3.2 1.0 + - - -
259C ARG* 3.0 20.4 + - - +
261C VAL* 4.0 21.3 - - + -
277C ILE* 3.9 22.0 - - + -
279C HIS* 4.1 11.0 - - + -
284C ILE* 3.7 41.7 - - + -
401H TRP* 4.0 17.9 - - + -
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LYS* 3.7 23.3 - - + +
26C MSE 3.7 32.1 - - + -
91C ILE* 3.7 2.9 - - - +
199C ILE* 3.8 4.9 - - - +
200C GLU 3.5 31.0 - - - +
201C HIS* 4.0 14.1 - - - +
202C VAL* 4.4 6.0 - - + +
252C THR 4.0 1.2 + - - -
253C GLU* 3.1 43.6 + - + +
256C LEU* 1.3 75.3 - - - +
258C GLN* 1.3 77.6 + - + +
259C ARG* 3.0 21.9 + - - +
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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