Contacts of the strand formed by residues 221 - 236 (chain A) in PDB entry 5IXM
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A LEU 3.3 14.4 - - - -
216A SER* 4.0 10.8 - - - -
217A ASN 4.5 0.7 - - - -
220A GLY* 1.3 77.0 - - - -
222A ILE* 1.3 61.4 + - - +
264A ASP 4.2 0.3 - - - +
265A GLY* 3.5 1.2 - - - -
266A LYS* 2.9 40.9 + - - +
38B LEU* 4.4 22.0 - - - +
606C C8E 3.8 9.4 - - - +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU 4.0 0.8 - - - +
214A PRO* 3.9 0.3 - - - +
215A LEU* 2.9 62.8 + - + +
221A SER* 1.3 76.2 - - - +
223A ASN* 1.3 66.4 + - - +
224A THR* 5.2 4.5 - - - +
263A VAL* 4.3 10.1 - - + -
264A ASP 3.5 13.7 - - - +
265A GLY* 4.1 4.9 - - - -
603A C8E 4.3 9.4 - - - +
428C LEU* 4.3 24.7 - - + -
457C VAL* 5.8 7.2 - - + -
606C C8E 3.7 28.9 - - + +
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Residues in contact with ASN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASN* 2.8 45.8 + - - +
213A LEU 3.1 16.5 - - - +
214A PRO* 3.4 6.9 - - + +
222A ILE* 1.3 78.9 - - - +
224A THR* 1.3 60.3 + - - +
225A GLU* 4.3 11.8 + - - +
262A LYS* 4.0 2.2 - - - +
263A VAL* 3.6 2.4 - - - +
264A ASP* 2.9 43.9 + - + +
38B LEU* 6.6 0.2 - - + -
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Residues in contact with THR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL 4.1 0.5 - - - +
212A ASN* 2.9 4.9 - - - +
213A LEU* 2.8 52.0 + - - +
222A ILE* 5.2 5.4 - - - +
223A ASN* 1.3 74.6 + - - +
225A GLU* 1.3 64.8 + - - +
261A PHE* 3.8 28.0 - - + -
262A LYS 3.7 2.9 - - - +
263A VAL* 4.4 11.6 - - + +
601A C8E 4.5 19.0 - - + +
396C LEU* 4.5 12.8 - - + -
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A THR* 3.8 20.9 - - + +
211A VAL 3.6 2.9 - - - +
212A ASN* 3.4 15.4 - - - +
223A ASN* 4.3 9.1 + - - +
224A THR* 1.3 77.7 - - - +
226A ALA* 1.3 62.8 + - - +
227A LYS* 3.2 34.0 + - + +
260A GLN* 3.7 2.4 + - - +
261A PHE* 3.7 6.2 - - - -
262A LYS* 2.8 76.7 + - + +
601A C8E 4.8 1.8 - - - -
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PRO 4.2 0.2 - - - +
210A THR* 3.5 3.1 - - - +
211A VAL* 2.9 35.0 + - + +
225A GLU* 1.3 74.0 - - - +
227A LYS* 1.3 61.5 + - - +
260A GLN 3.6 4.0 - - - -
261A PHE* 5.7 0.2 - - + -
601A C8E 3.7 26.8 - - + +
388C TRP* 3.6 25.6 - - + -
602C C8E 4.2 18.1 - - + +
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLU* 3.4 19.9 + - + +
209A PRO 3.5 4.9 - - - +
210A THR* 3.4 22.0 - - - +
225A GLU* 3.2 25.9 + - + +
226A ALA* 1.3 75.7 - - - +
228A LEU* 1.3 66.5 + - - +
229A LEU* 4.5 4.7 - - + -
259A PRO* 3.5 4.7 - - - +
260A GLN* 2.9 53.6 + - + +
262A LYS* 5.1 0.2 - - - +
318A ASP* 3.1 25.0 + - - -
319A ARG* 3.3 26.9 - - - +
388C TRP* 5.0 0.7 - - - -
602C C8E 4.7 6.3 - - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE 3.6 0.5 - - - +
208A GLU* 3.2 9.9 - - - -
209A PRO* 2.9 47.1 + - + +
227A LYS* 1.3 76.5 - - - +
229A LEU* 1.3 64.4 + - - +
230A ALA* 3.6 6.5 + - + +
257A VAL* 3.8 28.7 - - + -
258A LEU 4.0 6.5 - - - +
259A PRO* 4.1 16.6 - - + -
273C MET* 5.8 7.9 - - + -
602C C8E 4.1 41.5 - - + +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A HIS* 3.7 15.3 - - + -
207A ILE 4.1 1.1 - - - -
208A GLU* 3.2 32.1 - - + +
227A LYS* 4.6 5.2 - - + -
228A LEU* 1.3 73.3 - - - +
230A ALA* 1.3 59.9 + - - +
231A THR* 4.7 1.1 - - - +
256A ARG* 3.3 5.5 + - - +
257A VAL* 3.2 4.5 - - - -
258A LEU* 2.9 48.6 + - + +
260A GLN* 4.2 14.1 - - + +
292A VAL* 5.5 1.6 - - + -
319A ARG* 3.3 30.7 - - - +
324A LEU* 5.2 1.3 - - + -
327A ILE* 3.9 39.5 - - + -
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A HIS* 3.2 5.3 + - - -
207A ILE* 2.9 60.8 + - + +
209A PRO* 5.9 0.2 - - + -
228A LEU* 3.6 9.1 + - + +
229A LEU* 1.3 74.1 - - - +
231A THR* 1.3 62.4 + - - +
256A ARG 3.5 3.6 - - - -
257A VAL* 4.2 13.2 - - + -
275C TRP* 3.6 18.9 - - + -
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Residues in contact with THR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ARG* 3.9 14.8 - - + -
205A PHE 3.4 12.6 - - - +
206A HIS* 2.8 27.2 + - + +
229A LEU* 4.7 1.6 - - - +
230A ALA* 1.3 74.1 + - - +
232A HIS* 1.3 62.6 + - - +
233A TYR* 3.7 27.9 - - + -
254A VAL 3.7 0.9 - - - +
255A ASN* 3.6 3.3 - - - -
256A ARG* 2.9 64.6 + - - +
324A LEU* 4.8 1.1 - - + +
275C TRP* 3.7 6.5 - - - -
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Residues in contact with HIS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER 3.8 1.0 - - - +
204A ARG* 3.6 3.6 - - - +
205A PHE* 2.9 54.0 + + + +
231A THR* 1.3 74.4 - - - +
233A TYR* 1.3 71.0 + - - +
234A GLN* 3.8 22.0 - - + -
253A SER* 3.0 24.3 + - - -
254A VAL 3.3 9.6 - - - -
255A ASN* 3.0 22.4 - - - +
275C TRP* 3.5 34.0 + + + -
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Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA* 5.0 2.5 - - + -
203A SER 3.7 2.7 - - - -
204A ARG* 3.2 31.7 - - + -
231A THR* 3.7 23.6 - - + -
232A HIS* 1.3 81.4 + - - +
234A GLN* 1.3 59.4 + - - +
235A GLN* 3.9 20.6 - - + -
252A ASP 4.2 0.2 - - - -
253A SER* 3.3 6.4 - - - -
254A VAL* 2.8 49.4 + - + -
256A ARG* 4.4 3.4 - - + -
300A ILE* 3.4 43.1 - - + -
303A TYR* 4.1 11.0 - + - -
324A LEU 3.1 19.3 + - - -
325A ASP* 2.4 31.8 + - - -
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Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA* 3.3 2.3 - - - -
203A SER* 2.9 48.9 + - - +
205A PHE* 5.3 3.6 - - + -
232A HIS* 3.8 23.1 + - + -
233A TYR* 1.3 71.4 - - - +
235A GLN* 1.3 60.8 + - - +
236A ASP* 3.8 15.9 + - - +
252A ASP* 3.3 36.5 + - - +
253A SER* 4.3 6.5 - - - -
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PRO* 5.4 0.4 - - + -
201A GLU 3.5 5.4 - - - +
202A ALA* 4.0 6.5 - - + -
233A TYR* 4.3 16.4 - - + -
234A GLN* 1.3 73.0 - - - +
236A ASP* 1.3 63.7 + - - +
237A ILE* 3.5 16.2 - - + +
250A LEU* 3.8 13.6 - - + +
251A LYS 3.0 22.7 + - - +
252A ASP* 2.8 32.8 + - - +
254A VAL* 4.3 4.2 - - - +
299A ASP 3.1 22.6 + - - -
300A ILE* 3.8 4.7 - - - +
301A TYR* 3.0 22.5 + - - +
303A TYR* 2.8 31.3 + - - +
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS* 4.0 19.1 + - - -
200A PRO* 3.3 5.2 - - - +
201A GLU* 2.9 46.3 + - + +
234A GLN* 3.8 16.7 + - - +
235A GLN* 1.3 72.6 - - - +
237A ILE* 1.3 59.4 + - - +
238A PRO* 3.6 3.1 - - - +
252A ASP* 4.2 8.2 - - - +
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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