Contacts of the helix formed by residues 241 - 255 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229D ASP 5.7 2.5 - - - +
230D TYR 5.7 2.9 - - - +
232D LEU 5.5 6.3 - - - +
234D LEU* 3.7 27.1 - - + +
240D MET* 1.3 75.0 - - - +
242D ARG* 1.3 68.6 + - - +
243D MET* 3.8 1.9 + - - +
244D HIS* 2.4 46.0 + - - -
245D GLU* 3.0 9.9 + - - +
285D ILE 4.2 4.9 + - - -
286D CYS* 3.5 34.2 + - - +
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Residues in contact with ARG 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ASP* 4.5 26.6 + - + +
232D LEU* 4.8 11.8 - - + +
234D LEU* 5.2 0.2 - - - +
240D MET 3.9 0.6 + - - -
241D ASN* 1.3 73.8 - - - +
243D MET* 1.3 56.7 + - - +
245D GLU* 3.2 18.9 + - - +
246D SER* 3.0 27.4 + - - -
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Residues in contact with MET 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D VAL* 3.8 24.0 - - - -
226D ALA 3.6 13.9 - - - +
227D LEU* 3.5 30.5 - - + +
229D ASP* 4.1 7.5 + - + +
230D TYR* 3.8 17.9 - - + +
241D ASN* 3.1 1.0 - - - +
242D ARG* 1.3 79.4 - - - +
244D HIS* 1.3 57.7 + - - +
246D SER* 3.0 8.6 + - - -
247D MET* 2.9 29.2 + - + +
286D CYS* 3.4 26.2 - - - -
287D TYR* 3.4 24.2 - - + +
303D ILE* 4.7 11.7 - - + -
307D PHE* 3.9 13.2 - - + -
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Residues in contact with HIS 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D MET* 3.7 25.3 - - + +
241D ASN* 2.4 38.8 + - - +
243D MET* 1.3 73.1 - - - +
245D GLU* 1.3 60.8 + - - +
247D MET* 3.4 23.4 + - + +
248D LYS* 2.9 28.8 + - - +
286D CYS* 3.1 31.8 - - - -
287D TYR* 4.0 26.1 - + - -
288D PRO* 5.7 1.1 - - + -
289D GLU* 5.3 2.0 + - - -
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Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D GLU* 4.2 13.4 - - - +
240D MET* 3.5 34.1 - - + +
241D ASN 3.0 11.5 + - - +
242D ARG* 3.2 19.6 - - - +
243D MET 3.2 0.2 - - - -
244D HIS* 1.3 74.9 - - - +
246D SER* 1.3 65.8 + - - +
248D LYS* 3.1 5.3 + - - +
249D LEU* 2.9 23.6 + - - +
596Z LYS 4.2 6.3 - - - +
597Z CYS* 3.9 38.7 - - + +
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Residues in contact with SER 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA* 4.5 17.4 - - - +
223D PHE* 3.3 29.3 - - - -
224D CYS 4.1 4.9 + - - -
225D VAL* 4.0 12.8 - - - +
226D ALA 5.4 0.3 + - - -
242D ARG 3.0 12.9 + - - -
243D MET* 3.0 12.1 + - - -
245D GLU* 1.3 75.6 - - - +
247D MET* 1.3 57.4 + - - +
249D LEU* 3.4 6.7 + - - -
250D PHE* 2.9 24.8 + - - +
307D PHE* 4.1 12.6 - - - -
597Z CYS* 5.7 0.7 - - - -
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Residues in contact with MET 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D MET 2.9 15.2 + - - +
244D HIS* 3.4 31.0 - - + +
245D GLU 3.2 0.2 - - - -
246D SER* 1.3 76.8 - - - +
248D LYS* 1.3 57.5 + - - +
250D PHE* 3.1 4.2 + - - +
251D ASP* 2.9 24.8 + - - +
287D TYR* 3.3 32.5 - - + -
306D GLN* 4.0 35.0 - - + +
307D PHE* 3.5 28.9 - - + -
310D LEU* 3.4 27.3 - - + +
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Residues in contact with LYS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D MET* 4.6 12.6 - - + -
244D HIS 2.9 17.5 + - - +
245D GLU* 3.1 7.8 + - - +
247D MET* 1.3 71.6 - - - +
249D LEU* 1.3 67.3 + - - +
251D ASP* 3.2 10.2 + - - +
252D SER* 2.9 22.7 + - - -
593Z ILE* 4.8 6.2 - - + +
597Z CYS* 5.6 1.6 - - - -
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Residues in contact with LEU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLY* 4.6 6.1 - - - +
41D ALA* 4.5 15.7 - - - +
223D PHE* 3.6 24.2 - - + -
245D GLU 2.9 12.4 + - - +
246D SER* 3.5 10.3 - - - +
248D LYS* 1.3 75.4 - - - +
250D PHE* 1.3 62.2 + - - +
252D SER* 2.3 32.3 + - - +
253D ILE* 2.9 25.3 + - + +
593Z ILE* 4.0 20.2 - - + +
594Z LEU* 4.0 33.0 - - + +
597Z CYS* 4.1 20.6 - - + -
598Z GLN* 5.2 0.9 - - + +
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Residues in contact with PHE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D PHE* 3.4 49.8 - + + -
246D SER 2.9 14.1 + - - +
247D MET* 3.3 12.6 - - - +
249D LEU* 1.3 78.2 - - - +
251D ASP* 1.3 56.9 + - - +
253D ILE* 3.1 6.8 + - + +
254D CYS* 2.9 47.5 + - + +
264D ILE* 3.8 28.5 - - + -
266D LEU* 4.1 15.5 - - + -
307D PHE* 3.8 34.1 - + + -
310D LEU* 4.4 8.7 - - + -
311D ASN 5.6 0.4 - - - -
319D ILE* 3.9 19.7 - - + -
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Residues in contact with ASP 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D MET 2.9 12.6 + - - +
248D LYS* 3.2 12.8 + - - +
250D PHE* 1.3 75.1 - - - +
252D SER* 1.3 63.8 + - - +
254D CYS* 4.7 2.7 - - - -
255D ASN* 2.3 59.8 + - - +
310D LEU* 4.3 28.1 - - + +
312D ARG* 4.1 8.0 + - - -
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Residues in contact with SER 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D LYS 2.9 10.3 + - - -
249D LEU* 2.3 41.8 + - - +
251D ASP* 1.3 76.4 - - - +
253D ILE* 1.3 61.7 + - - +
255D ASN* 4.3 0.7 - - - -
256D ASN* 3.6 22.7 + - - +
593Z ILE* 3.6 30.5 - - - +
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Residues in contact with ILE 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.5 26.2 - - + -
221D ILE* 4.1 30.7 - - + -
223D PHE* 3.5 39.3 - - + -
249D LEU* 2.9 26.5 + - + +
250D PHE* 3.1 8.9 + - + +
252D SER* 1.3 78.7 - - - +
254D CYS* 1.3 67.1 + - - +
256D ASN* 3.2 19.5 + - - +
259D PHE* 3.6 15.2 - - + +
264D ILE* 4.9 7.4 - - + +
594Z LEU* 5.1 3.1 - - + -
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Residues in contact with CYS 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D PHE* 2.9 50.1 + - + +
251D ASP* 4.0 3.8 - - - +
253D ILE* 1.3 76.7 - - - +
255D ASN* 1.3 69.8 + - - +
256D ASN 3.4 7.6 + - - +
259D PHE* 5.2 2.4 - - - +
264D ILE* 4.2 21.8 - - - -
310D LEU 5.0 0.4 - - - +
311D ASN* 3.8 22.2 - - - +
313D ARG* 4.0 25.4 + - - -
319D ILE* 4.0 12.8 - - - -
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Residues in contact with ASN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ASP* 2.3 40.9 + - - +
252D SER* 4.3 3.1 - - - +
254D CYS* 1.3 83.5 - - - +
256D ASN* 1.3 62.1 + - - +
257D LYS* 3.6 2.4 + - - +
310D LEU 3.6 6.3 + - - +
311D ASN* 4.0 1.0 - - - +
312D ARG* 3.0 70.7 + - - +
313D ARG* 4.8 2.2 - - - +
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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