Contacts of the helix formed by residues 241 - 255 (chain C) in PDB entry 4G5S
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 ASN 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C ASP 5.8 2.2 - - - +
230C TYR 5.6 3.4 - - - +
232C LEU 5.6 5.6 - - - +
234C LEU* 4.0 26.7 - - + +
240C MET* 1.3 76.0 - - - +
242C ARG* 1.3 65.7 + - - +
243C MET* 3.9 1.5 + - - +
244C HIS* 2.4 39.8 + - - -
245C GLU* 3.2 8.3 + - - +
285C ILE* 4.0 6.8 + - + +
286C CYS* 3.4 42.0 + - - +
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Residues in contact with ARG 242 (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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229C ASP* 4.6 23.6 + - + +
232C LEU* 4.9 12.1 - - + +
234C LEU* 5.3 1.2 - - - +
241C ASN* 1.3 73.9 - - - +
243C MET* 1.3 56.7 + - - +
245C GLU* 3.2 18.7 + - - +
246C SER* 3.0 26.2 + - - -
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Residues in contact with MET 243 (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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225C VAL* 4.0 10.1 - - - -
226C ALA 3.6 21.8 - - - +
227C LEU* 3.7 21.5 - - + +
229C ASP* 4.3 7.9 + - + +
230C TYR* 4.0 17.7 - - + +
241C ASN* 3.0 1.4 + - - +
242C ARG* 1.3 79.1 - - - +
244C HIS* 1.3 57.8 + - - +
246C SER* 3.0 8.6 + - - -
247C MET* 2.9 29.3 + - - +
286C CYS* 3.4 26.2 - - - -
287C TYR* 3.4 24.5 - - + +
303C ILE* 4.8 11.7 - - + -
307C PHE* 3.9 27.4 - - + -
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Residues in contact with HIS 244 (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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240C MET* 3.9 25.5 - - + +
241C ASN* 2.4 35.6 + - - +
243C MET* 1.3 75.5 - - - +
245C GLU* 1.3 61.1 + - - +
247C MET* 3.5 22.7 - - + +
248C LYS* 2.9 27.7 + - - +
286C CYS* 3.1 31.3 - - - -
287C TYR* 4.3 22.5 - + - -
288C PRO* 5.5 1.3 - - + -
289C GLU* 5.5 1.6 + - - -
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Residues in contact with GLU 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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238C GLU* 4.6 9.4 - - - +
240C MET* 3.6 38.6 - - + +
241C ASN 3.2 7.2 + - - +
242C ARG* 3.2 19.8 - - - +
244C HIS* 1.3 76.1 - - - +
246C SER* 1.3 64.1 + - - +
248C LYS* 3.0 7.6 + - + +
249C LEU* 3.0 22.2 + - - +
596G LYS 4.5 3.7 - - - +
597G CYS* 3.9 38.7 - - + +
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Residues in contact with SER 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA* 4.7 16.4 + - - +
223C PHE* 3.4 27.1 - - - -
224C CYS 4.4 4.0 + - - -
225C VAL* 3.9 14.5 - - - +
226C ALA 5.5 0.3 + - - -
242C ARG 3.0 12.9 + - - -
243C MET* 3.0 11.9 + - - -
245C GLU* 1.3 76.5 - - - +
247C MET* 1.3 56.4 + - - +
249C LEU* 3.3 7.3 + - - +
250C PHE* 2.9 25.3 + - - +
307C PHE* 4.1 12.8 - - - -
597G CYS* 5.5 0.9 - - - +
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Residues in contact with MET 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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243C MET 2.9 14.9 + - - +
244C HIS* 3.5 29.8 - - + +
246C SER* 1.3 75.5 - - - +
248C LYS* 1.3 58.3 + - - +
250C PHE* 3.2 1.1 + - - +
251C ASP* 2.9 26.4 + - - +
287C TYR* 3.2 32.8 - - + +
306C GLN* 3.9 27.8 - - + +
307C PHE* 3.5 30.5 - - + -
310C LEU* 3.3 36.9 - - + +
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Residues in contact with LYS 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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239C GLU* 5.2 9.7 + - - -
240C MET* 4.4 26.1 - - + +
244C HIS 2.9 14.1 + - - +
245C GLU* 3.0 9.8 + - + +
247C MET* 1.3 76.0 - - - +
249C LEU* 1.3 64.2 + - - +
251C ASP* 3.3 9.6 + - + +
252C SER* 3.0 21.8 + - - -
593G ILE* 4.7 25.8 - - + -
597G CYS* 5.0 7.6 - - - -
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 5.9 0.4 - - + -
40C GLY* 4.6 7.4 - - - +
41C ALA* 4.6 5.6 - - + +
223C PHE* 3.5 23.3 - - + -
245C GLU 3.0 12.0 + - - +
246C SER* 3.5 10.8 - - - +
248C LYS* 1.3 75.1 - - - +
250C PHE* 1.3 62.0 + - - +
252C SER* 2.3 32.5 + - - +
253C ILE* 3.0 20.2 + - + +
590G PHE* 4.7 0.2 - - + -
593G ILE* 4.5 6.0 - - + +
594G LEU* 3.9 41.1 - - + +
597G CYS* 4.3 22.0 - - + -
598G GLN* 4.1 20.0 - - - +
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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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223C PHE* 3.8 39.6 - + + -
246C SER 2.9 14.9 + - - +
247C MET 3.3 9.9 - - - +
249C LEU* 1.3 76.1 - - - +
251C ASP* 1.3 56.2 + - - +
253C ILE* 3.0 8.1 + - + -
254C CYS* 2.8 58.0 + - + +
264C ILE* 3.8 20.4 - - + -
266C LEU* 4.1 11.9 - - + -
307C PHE* 3.4 55.4 - + + -
310C LEU* 4.2 5.2 - - + -
319C ILE* 4.1 17.0 - - + -
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Residues in contact with ASP 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 MET 2.9 13.0 + - - +
248C LYS* 3.3 12.8 - - + +
250C PHE* 1.3 76.7 - - - +
252C SER* 1.3 63.8 + - - +
253C ILE 3.3 0.3 + - - -
254C CYS* 4.7 1.8 - - - -
255C ASN* 2.5 54.5 + - - +
310C LEU* 4.2 30.9 - - + +
312C ARG* 4.5 7.6 + - - -
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Residues in contact with SER 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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248C LYS 3.0 11.2 + - - -
249C LEU* 2.3 42.5 + - - +
251C ASP* 1.3 77.1 - - - +
253C ILE* 1.3 58.9 + - - +
255C ASN 4.3 0.5 - - - -
256C ASN* 3.4 21.1 + - - +
590G PHE* 3.8 23.8 - - - +
593G ILE* 4.1 22.6 - - - +
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Residues in contact with ILE 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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39C LEU* 3.7 22.9 - - + -
221C ILE* 4.1 31.4 - - + -
223C PHE* 3.5 38.8 - - + -
249C LEU* 3.0 18.9 + - + +
250C PHE* 3.0 10.7 + - + +
252C SER* 1.3 75.3 - - - +
254C CYS* 1.3 68.6 + - - +
256C ASN* 3.3 17.7 + - - +
259C PHE* 3.5 14.7 - - + +
264C ILE* 4.5 7.3 - - + +
590G PHE* 3.9 21.5 - - + -
594G LEU* 5.0 0.7 - - + -
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Residues in contact with CYS 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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250C PHE* 2.8 53.7 + - + +
251C ASP* 4.1 3.4 - - - +
253C ILE* 1.3 76.4 - - - +
255C ASN* 1.3 70.2 + - - +
256C ASN 3.4 6.4 + - - +
259C PHE* 5.4 4.5 - - - +
260C THR* 6.2 0.2 - - - -
264C ILE* 4.0 22.2 - - - +
310C LEU 5.0 1.1 - - - +
311C ASN* 4.6 16.2 - - - +
313C ARG* 6.1 0.5 - - - +
319C ILE* 3.8 20.9 - - - -
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Residues in contact with ASN 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 ASP* 2.5 38.7 + - - +
252C SER 4.3 1.6 - - - -
253C ILE 3.3 0.4 - - - -
254C CYS* 1.3 84.6 - - - +
256C ASN* 1.3 63.3 + - - +
257C LYS* 3.5 2.9 + - - +
310C LEU 3.0 17.1 + - - +
311C ASN* 3.6 4.9 - - - +
312C ARG* 3.1 56.9 + - + +
313C ARG* 4.5 4.8 + - + +
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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