Contacts of the helix formed by residues 223 - 241 (chain F) in PDB entry 4XLN
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 SER 223 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D ARG* 4.2 18.4 - - - +
550D ARG* 5.4 3.6 - - - -
218F THR* 6.4 2.0 - - - -
222F LEU* 1.3 79.2 - - - +
224F PHE* 1.3 77.8 + - - +
225F LEU 3.7 1.3 - - - -
226F ASP* 3.6 7.5 + - - +
227F LEU* 3.0 21.8 + - - +
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Residues in contact with PHE 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F VAL* 4.6 12.3 - - + -
211F VAL 5.4 1.1 - - - -
214F ALA 4.4 2.7 - - - -
215F LYS* 4.1 9.4 - - + -
218F THR* 3.7 31.8 - - + +
223F SER* 1.3 82.4 + - - +
225F LEU* 1.3 71.9 + - + +
227F LEU* 3.0 6.4 + - - +
228F ILE* 2.9 46.7 + - + +
32O G 3.3 60.1 - - - -
33O G 3.9 17.5 - - - -
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Residues in contact with LEU 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D ARG* 4.9 4.5 - - - +
569D ASN* 3.3 34.1 - - - +
572D ARG* 4.4 3.6 - - - +
573D MET* 3.6 26.2 - - + -
576D GLU* 4.8 3.1 - - - +
95F PRO* 3.7 23.6 - - + +
96F VAL* 3.5 42.4 - - + +
99F TYR* 4.8 9.6 - - + -
223F SER* 5.1 0.4 - - - -
224F PHE* 1.3 79.3 - - + +
226F ASP* 1.3 58.0 + - - +
228F ILE* 4.4 10.5 - - + -
229F GLN* 2.9 37.0 + - - +
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Residues in contact with ASP 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D ARG* 3.2 21.8 + - - +
549D ASN* 6.0 0.2 - - - +
550D ARG* 3.0 42.1 + - - +
553D ARG* 2.4 48.3 + - - -
573D MET* 3.6 5.9 - - - +
222F LEU* 3.5 30.8 - - + +
223F SER* 3.7 11.2 - - - +
224F PHE 3.2 0.2 - - - -
225F LEU* 1.3 78.8 - - - +
227F LEU* 1.3 61.8 + - - +
230F GLU* 3.7 14.0 + - - +
269F GLN* 5.1 1.5 - - - +
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Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F ALA* 3.5 28.7 - - + +
217F TYR* 3.3 33.4 - - + +
218F THR* 4.3 2.5 - - + +
220F ARG* 4.0 20.0 - - + -
222F LEU* 3.5 35.9 - - + +
223F SER 3.0 14.7 + - - +
224F PHE* 3.4 4.3 - - - +
226F ASP* 1.3 75.9 - - - +
228F ILE* 1.3 66.2 + - - +
230F GLU* 3.2 6.9 + - - +
231F GLY* 3.0 19.4 + - - -
262F ILE* 3.8 23.2 - - + +
265F ALA* 6.1 3.4 - - + -
266F ILE* 4.7 4.5 - - + -
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Residues in contact with ILE 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F TYR* 3.9 15.7 - - + -
210F VAL* 3.7 2.5 - - - +
211F VAL* 3.8 52.5 - - + +
214F ALA* 3.6 22.4 - - + -
224F PHE* 2.9 43.3 + - + +
225F LEU* 3.9 10.8 - - + +
227F LEU* 1.3 74.9 - - - +
229F GLN* 1.3 53.4 + - + +
231F GLY* 3.1 3.8 + - - -
232F ASN* 2.4 47.5 + - - +
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Residues in contact with GLN 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ARG* 3.3 20.5 - - - +
557D LEU* 4.5 2.8 - - - +
566D ILE* 3.2 40.6 + - - +
569D ASN* 3.0 27.8 - - - +
570D GLU* 2.8 33.6 - - - +
573D MET* 3.5 17.7 - - - -
99F TYR* 3.8 12.0 + - + -
225F LEU* 2.9 18.0 + - - +
228F ILE* 1.3 77.6 - - + +
230F GLU* 1.3 56.9 + - - +
232F ASN* 2.9 24.5 + - - +
233F GLN* 2.9 13.3 + - - +
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Residues in contact with GLU 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ARG* 3.3 43.9 - - - +
222F LEU* 5.5 3.1 - - + -
226F ASP 3.7 7.7 + - - +
227F LEU* 3.2 8.8 + - - +
229F GLN* 1.3 77.5 - - - +
231F GLY* 1.3 59.9 + - - +
233F GLN* 3.6 25.2 + - - +
261F ALA* 3.4 26.0 - - - +
262F ILE* 5.0 0.4 - - - -
264F ARG* 5.8 1.7 - - - +
265F ALA* 3.6 33.9 - - + +
269F GLN* 6.0 2.0 - - - +
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Residues in contact with GLY 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F VAL* 3.6 7.4 - - - -
227F LEU 3.0 13.3 + - - -
228F ILE 3.4 4.9 - - - -
229F GLN 3.0 0.4 - - - -
230F GLU* 1.3 76.2 - - - +
232F ASN* 1.3 59.1 + - - +
233F GLN 3.1 0.2 - - - -
234F GLY* 2.8 17.3 + - - -
235F LEU 3.0 8.8 + - - -
258F ILE* 3.2 27.7 - - - +
261F ALA* 4.3 2.7 - - - -
262F ILE* 4.0 11.2 - - - +
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Residues in contact with ASN 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D ILE* 3.6 23.5 - - + +
99F TYR* 3.6 16.3 + - - -
207F LEU* 3.2 25.5 - - - +
210F VAL* 3.3 16.3 - - - +
228F ILE* 2.4 49.3 + - - +
229F GLN* 2.9 11.1 + - - +
231F GLY* 1.3 73.4 - - - +
233F GLN* 1.3 60.7 + - - +
235F LEU* 2.8 29.0 + - + +
236F ILE* 3.0 19.3 + - - +
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Residues in contact with GLN 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ARG* 4.6 4.8 - - - +
556D LYS* 4.5 12.9 - - - +
557D LEU* 3.4 40.8 - - + +
560D GLN* 3.9 14.9 + - - +
566D ILE* 6.0 0.4 - - - +
229F GLN 2.9 11.7 + - - +
230F GLU* 3.6 27.7 + - - +
232F ASN* 1.3 75.6 - - - +
234F GLY* 1.3 60.2 + - - +
236F ILE* 3.5 30.0 + - - +
237F ARG* 3.7 13.9 + - - +
261F ALA* 5.6 0.2 - - + -
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Residues in contact with GLY 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F GLU 3.7 3.0 + - - -
231F GLY 2.8 11.2 + - - -
233F GLN* 1.3 79.5 - - - +
235F LEU* 1.3 58.1 + - - +
237F ARG* 3.5 6.2 + - - +
238F ALA* 2.9 27.9 + - - +
257F TRP* 3.5 12.8 - - - +
258F ILE* 3.8 4.9 - - - -
260F GLN* 4.9 3.1 - - - -
261F ALA* 3.6 20.4 - - - +
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Residues in contact with LEU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F ILE* 3.3 42.0 - - + +
206F ASN* 4.1 12.3 - - + +
207F LEU* 4.1 3.1 - - - +
209F LEU* 6.3 0.2 - - + -
210F VAL* 3.6 25.8 - - + -
231F GLY 3.0 4.9 + - - -
232F ASN* 2.8 18.6 + - - +
234F GLY* 1.3 78.1 - - - +
236F ILE* 1.3 54.7 + - - +
238F ALA* 3.2 3.4 + - + +
239F VAL* 2.9 29.8 + - + +
250F PHE* 3.7 15.5 - - + -
254F ALA* 3.7 29.8 - - + -
258F ILE* 3.3 13.1 - - + +
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Residues in contact with ILE 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D LEU* 5.0 2.5 - - + -
560D GLN* 3.3 33.7 - - - +
562D ALA* 3.9 18.8 - - + -
563D PRO* 4.8 1.8 - - + -
566D ILE* 5.2 6.5 - - + -
199F ARG* 4.0 18.2 - - - +
203F ILE* 3.8 32.8 - - + -
232F ASN 3.0 13.6 + - - +
233F GLN* 3.5 23.3 - - - +
234F GLY 3.2 0.4 - - - -
235F LEU* 1.3 75.7 - - - +
237F ARG* 1.3 58.4 + - + +
239F VAL* 3.0 18.2 + - - +
240F GLU* 3.0 22.9 + - - +
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Residues in contact with ARG 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D GLN* 6.0 3.8 - - - +
233F GLN 3.7 8.3 + - - +
234F GLY* 3.5 8.2 + - - +
235F LEU 3.4 0.2 - - - -
236F ILE* 1.3 76.0 - - + +
238F ALA* 1.3 63.7 + - - +
240F GLU* 4.5 24.9 + - - +
241F LYS* 3.3 56.2 + - - +
257F TRP* 4.1 24.7 - - + -
24O C 2.9 30.8 + - - -
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F GLY 2.9 15.9 + - - +
235F LEU* 3.2 14.5 + - - +
237F ARG* 1.3 77.1 - - - +
239F VAL* 1.3 60.2 + - - +
242F PHE* 3.3 11.1 - - - +
250F PHE* 3.2 14.8 - - + -
253F TYR* 3.3 9.5 - - - +
254F ALA* 3.6 26.5 - - + -
257F TRP* 3.5 29.3 - - + +
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Residues in contact with VAL 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F VAL* 5.5 7.7 - - + +
199F ARG* 4.1 28.7 - - + +
202F LEU* 3.8 27.3 - - + +
203F ILE* 3.6 25.4 - - + -
235F LEU* 2.9 19.1 + - + +
236F ILE 3.0 8.0 + - - +
238F ALA* 1.3 73.8 - - - +
240F GLU* 1.3 69.7 + - - +
241F LYS 3.1 1.8 - - - -
242F PHE* 2.9 20.6 + - - +
250F PHE* 3.5 23.3 - - + -
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Residues in contact with GLU 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D GLN* 4.9 5.5 + - - +
121F VAL* 6.2 2.2 - - - -
125F MET* 4.8 22.6 - - + +
143F ARG* 4.3 16.3 + - - +
147F ARG* 4.2 5.6 + - - -
199F ARG* 3.2 40.6 + - - +
236F ILE* 3.0 24.8 + - - +
237F ARG* 3.6 27.0 + - - +
239F VAL* 1.3 75.9 - - - +
241F LYS* 1.3 57.9 + - - +
242F PHE 3.8 2.3 + - - +
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Residues in contact with LYS 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F ARG* 3.3 41.7 + - - +
239F VAL 3.1 0.8 - - - -
240F GLU* 1.3 75.9 - - - +
242F PHE* 1.3 63.1 + - - +
243F GLU* 3.8 6.6 + - - +
253F TYR* 3.2 31.7 + - + +
257F TRP* 3.8 11.4 - - + -
24O C 3.5 32.4 + - - -
25O T 3.5 18.4 + - - -
26O A 3.9 11.9 + - - +
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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
------------------------------------------------------------
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