Contacts of the helix formed by residues 223 - 241 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546J ARG* 4.2 17.9 - - - +
550J ARG* 5.4 3.4 - - - -
218L THR* 6.4 2.0 - - - -
222L LEU* 1.3 78.7 - - - +
224L PHE* 1.3 78.8 + - - +
225L LEU 3.7 1.8 - - - -
226L ASP* 4.0 7.3 - - - +
227L LEU* 3.0 21.6 + - - +
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Residues in contact with PHE 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L VAL* 4.6 12.6 - - + -
211L VAL* 5.4 0.9 - - + -
214L ALA 4.4 2.5 - - - -
215L LYS* 4.1 10.1 - - + -
218L THR* 3.7 32.7 - - + +
223L SER* 1.3 81.9 + - - +
225L LEU* 1.3 73.2 + - + +
227L LEU* 3.0 7.2 + - - +
228L ILE* 2.9 45.9 + - + +
32R G 3.4 60.1 - - - -
33R G 3.9 17.3 - - - -
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Residues in contact with LEU 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550J ARG* 4.9 5.2 - - - +
569J ASN* 3.3 33.9 - - - +
572J ARG* 4.4 3.6 - - - +
573J MET* 3.6 25.6 - - + -
576J GLU* 4.8 2.5 - - - +
95L PRO* 3.7 23.6 - - + +
96L VAL* 3.5 43.1 - - + +
99L TYR* 4.8 9.9 - - + -
223L SER* 4.9 0.8 + - - -
224L PHE* 1.3 80.5 - - + +
226L ASP* 1.3 56.9 + - - +
228L ILE* 4.4 10.8 - - + -
229L GLN* 2.9 36.8 + - - +
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Residues in contact with ASP 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546J ARG* 3.2 21.5 + - - +
550J ARG* 3.0 41.0 + - - +
553J ARG* 2.4 49.2 + - - -
573J MET* 3.6 5.5 - - - +
222L LEU* 3.5 31.4 - - + +
223L SER 3.7 11.4 - - - +
224L PHE 3.2 0.2 - - - -
225L LEU* 1.3 78.6 - - - +
227L LEU* 1.3 61.5 + - - +
230L GLU* 3.7 13.7 + - - +
269L GLN* 5.2 1.3 - - - +
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Residues in contact with LEU 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L ALA* 3.5 29.8 - - + +
217L TYR* 3.3 33.2 - - + +
218L THR* 4.7 2.2 - - + -
220L ARG* 4.0 20.2 - - + -
222L LEU* 3.6 36.1 - - + +
223L SER 3.0 14.4 + - - +
224L PHE* 3.0 4.5 + - - +
226L ASP* 1.3 74.9 - - - +
228L ILE* 1.3 65.5 + - - +
230L GLU* 3.2 6.8 + - - +
231L GLY* 3.0 19.2 + - - -
262L ILE* 3.8 22.2 - - + +
265L ALA* 5.7 4.2 - - + +
266L ILE* 4.7 3.8 - - + -
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Residues in contact with ILE 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L TYR* 3.9 15.9 - - + -
210L VAL* 3.7 3.2 - - - +
211L VAL* 3.8 50.9 - - + +
214L ALA* 3.6 24.2 - - + -
224L PHE* 2.9 42.9 + - + +
225L LEU* 3.9 10.5 - - + +
227L LEU* 1.3 74.1 - - - +
229L GLN* 1.3 54.6 + - + +
231L GLY* 3.1 3.6 + - - -
232L ASN* 2.4 48.6 + - - +
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Residues in contact with GLN 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J ARG* 3.3 19.2 - - - +
557J LEU* 4.9 2.9 - - + +
566J ILE* 3.2 40.9 + - - +
569J ASN* 3.0 28.0 - - - +
570J GLU* 2.8 34.6 - - - +
573J MET* 3.5 17.0 - - - -
99L TYR* 3.8 12.2 + - + -
225L LEU* 2.9 18.2 + - - +
228L ILE* 1.3 77.3 - - + +
230L GLU* 1.3 58.5 + - - +
231L GLY 3.0 0.2 - - - -
232L ASN* 2.9 24.5 + - - +
233L GLN* 2.9 13.6 + - - +
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Residues in contact with GLU 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J ARG* 3.3 43.1 - - - +
222L LEU* 5.5 3.1 - - + -
226L ASP 3.7 8.3 + - - +
227L LEU 3.2 7.9 + - - +
229L GLN* 1.3 78.3 - - - +
231L GLY* 1.3 59.8 + - - +
233L GLN* 3.6 23.2 + - - +
261L ALA* 3.4 25.8 - - - +
262L ILE* 5.0 0.2 - - - -
264L ARG* 5.8 1.7 - - - +
265L ALA* 3.6 34.3 + - + +
269L GLN* 6.0 2.5 - - - +
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Residues in contact with GLY 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L VAL* 3.6 8.1 - - - -
227L LEU 3.0 13.5 + - - -
228L ILE 3.4 4.9 - - - -
229L GLN 3.0 0.4 - - - -
230L GLU* 1.3 76.9 - - - +
232L ASN* 1.3 58.9 + - - +
233L GLN 3.1 0.2 - - - -
234L GLY* 2.8 17.5 + - - -
235L LEU 3.0 8.8 + - - -
258L ILE* 3.2 27.5 - - - +
261L ALA* 4.3 2.5 - - - -
262L ILE* 4.0 11.0 - - - +
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Residues in contact with ASN 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566J ILE* 3.6 22.9 - - + +
99L TYR* 3.6 17.1 + - - -
203L ILE* 5.2 0.2 - - - +
207L LEU* 3.2 25.9 - - - +
210L VAL* 3.3 16.7 - - - +
228L ILE* 2.4 49.1 + - - +
229L GLN* 2.9 10.9 + - - +
231L GLY* 1.3 71.9 - - - +
233L GLN* 1.3 60.6 + - - +
235L LEU* 2.8 26.5 + - + +
236L ILE* 3.0 19.9 + - - +
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Residues in contact with GLN 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J ARG* 4.6 4.8 - - - +
556J LYS* 4.5 12.5 - - - +
557J LEU* 3.4 41.0 - - + +
560J GLN* 3.9 15.0 + - - +
566J ILE* 6.0 0.4 - - - +
229L GLN 2.9 11.1 + - - +
230L GLU* 3.6 28.2 + - - +
232L ASN* 1.3 76.5 - - - +
234L GLY* 1.3 60.6 + - - +
236L ILE* 3.5 30.0 + - - +
237L ARG* 3.7 13.2 + - - +
261L ALA* 6.1 0.4 - - + -
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Residues in contact with GLY 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230L GLU 3.7 3.0 + - - -
231L GLY 2.8 12.0 + - - -
233L GLN* 1.3 78.1 - - - +
235L LEU* 1.3 59.4 + - - +
237L ARG* 3.5 6.2 + - - +
238L ALA* 2.9 27.5 + - - +
257L TRP* 3.5 13.4 - - - +
258L ILE* 3.8 5.2 - - - -
260L GLN* 4.9 3.4 - - - -
261L ALA* 3.6 19.4 - - - +
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Residues in contact with LEU 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203L ILE* 3.3 41.5 - - + +
206L ASN* 4.1 12.1 - - + +
207L LEU* 4.1 3.4 - - - +
209L LEU* 6.3 0.4 - - + -
210L VAL* 3.6 25.4 - - + -
231L GLY 3.0 4.6 + - - -
232L ASN* 2.8 18.4 + - - +
234L GLY* 1.3 78.9 - - - +
236L ILE* 1.3 54.1 + - - +
238L ALA* 3.2 3.9 + - - +
239L VAL* 2.9 29.2 + - + +
250L PHE* 3.7 15.3 - - + -
254L ALA* 3.7 29.8 - - + -
258L ILE* 3.3 13.6 - - + +
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Residues in contact with ILE 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557J LEU* 5.0 2.9 - - + -
560J GLN* 3.3 33.0 - - - +
562J ALA* 3.9 19.5 - - + -
563J PRO* 4.8 1.8 - - + -
566J ILE* 5.2 6.5 - - + -
199L ARG* 4.0 17.7 - - - +
203L ILE* 3.8 33.4 - - + -
232L ASN 3.0 13.9 + - - +
233L GLN* 3.5 23.6 - - - +
234L GLY 3.3 0.4 - - - -
235L LEU* 1.3 76.1 - - - +
237L ARG* 1.3 58.4 + - + +
239L VAL* 3.0 18.2 + - - +
240L GLU* 3.0 23.1 + - - +
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Residues in contact with ARG 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J GLN* 6.0 4.3 - - - +
233L GLN 3.7 8.1 + - - +
234L GLY* 3.5 7.7 + - - +
235L LEU 3.4 0.4 - - - -
236L ILE* 1.3 77.4 - - + +
238L ALA* 1.3 63.0 + - - +
240L GLU* 4.5 25.1 + - - +
241L LYS* 3.3 56.8 + - - +
257L TRP* 4.1 24.3 - - + -
24R C 2.8 32.6 + - - -
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Residues in contact with ALA 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L GLY 2.9 15.7 + - - +
235L LEU* 3.2 14.1 + - - +
237L ARG* 1.3 77.7 - - - +
239L VAL* 1.3 60.2 + - - +
242L PHE* 3.3 11.1 - - - +
250L PHE* 3.2 15.2 - - + -
253L TYR* 3.3 9.4 - - - +
254L ALA* 3.6 26.7 - - + -
257L TRP* 3.5 29.3 - - + +
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Residues in contact with VAL 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L VAL* 5.5 8.1 - - + +
199L ARG* 4.1 28.0 - - + +
202L LEU* 3.8 27.8 - - + +
203L ILE* 3.6 25.6 - - + -
235L LEU* 2.9 19.1 + - + +
236L ILE 3.0 8.0 + - - +
238L ALA* 1.3 74.3 - - - +
240L GLU* 1.3 70.3 + - - +
241L LYS 3.1 1.8 - - - -
242L PHE* 2.9 21.0 + - - +
250L PHE* 3.5 22.7 - - + -
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Residues in contact with GLU 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J GLN* 4.9 5.4 + - - +
121L VAL* 6.2 2.5 - - - -
125L MET* 4.8 23.7 - - + +
143L ARG* 4.3 16.6 + - - +
147L ARG* 4.2 5.0 + - - -
199L ARG* 3.2 42.3 + - - +
236L ILE* 3.0 23.6 + - - +
237L ARG* 3.6 27.3 + - - +
239L VAL* 1.3 77.1 - - - +
241L LYS* 1.3 58.8 + - - +
242L PHE 3.4 2.5 + - - +
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Residues in contact with LYS 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237L ARG* 3.3 40.6 + - - +
239L VAL 3.1 0.8 - - - -
240L GLU* 1.3 76.3 - - - +
242L PHE* 1.3 63.9 + - - +
243L GLU* 3.8 7.4 + - - +
253L TYR* 3.2 32.3 + - + +
257L TRP* 3.8 12.1 - - + -
24R C 3.3 33.3 + - - -
25R T 3.8 15.8 + - - -
26R A 4.0 11.5 + - - +
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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