Contacts of the strand formed by residues 221 - 236 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU 3.3 15.0 - - - -
216E SER* 4.0 10.3 - - - +
217E ASN* 4.5 0.9 - - - -
220E GLY* 1.3 76.0 - - - -
222E ILE* 1.3 62.0 + - - +
264E ASP 4.2 0.6 - - - +
265E GLY* 3.5 0.9 - - - -
266E LYS* 2.9 43.9 + - - +
38F LEU* 4.4 22.2 - - - +
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Residues in contact with ILE 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E LEU 4.0 0.6 - - - +
214E PRO* 3.9 0.3 - - - +
215E LEU* 2.9 63.0 + - + +
221E SER* 1.3 76.5 - - - +
223E ASN* 1.3 66.4 + - - +
224E THR* 5.3 4.3 - - - +
263E VAL* 4.4 18.2 - - + -
264E ASP 3.5 11.7 - - - +
265E GLY* 4.1 7.2 - - - -
602E C8E 4.4 15.0 - - + -
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Residues in contact with ASN 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E ASN* 2.8 42.1 + - - +
213E LEU 3.1 16.7 - - - +
214E PRO* 3.5 6.9 - - + +
222E ILE* 1.3 80.0 - - - +
224E THR* 1.3 62.1 + - - +
225E GLU* 4.3 11.9 + - - +
262E LYS* 3.9 2.8 - - - +
263E VAL* 3.5 3.3 - - - +
264E ASP* 2.9 47.0 + - + +
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Residues in contact with THR 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E VAL 4.1 0.2 - - - +
212E ASN* 3.0 5.1 - - - +
213E LEU* 2.8 54.1 + - + +
222E ILE* 5.3 5.0 - - - +
223E ASN* 1.3 75.6 + - - +
225E GLU* 1.3 65.3 + - - +
261E PHE* 3.8 28.5 - - + -
262E LYS 3.7 2.7 - - - +
263E VAL* 4.3 11.2 - - + +
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Residues in contact with GLU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E THR* 3.8 21.8 - - + +
211E VAL 3.6 2.7 - - - +
212E ASN* 3.5 16.2 - - - +
223E ASN* 4.3 9.3 + - - +
224E THR* 1.3 81.3 - - - +
226E ALA* 1.3 63.2 + - - +
227E LYS* 3.2 33.1 + - + -
260E GLN* 3.7 3.4 + - - +
261E PHE* 3.7 6.9 - - - -
262E LYS* 2.9 75.2 + - + +
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Residues in contact with ALA 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E PRO 4.1 0.2 - - - +
210E THR* 3.4 3.1 - - - +
211E VAL* 2.9 45.5 + - + +
224E THR 4.4 0.2 - - - -
225E GLU* 1.3 73.0 - - - +
227E LYS* 1.3 61.2 + - - +
260E GLN 3.6 4.5 - - - +
261E PHE* 5.1 4.9 - - + +
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Residues in contact with LYS 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E GLU* 3.3 33.1 + - + +
209E PRO 3.4 4.9 - - - +
210E THR* 3.3 22.7 - - - +
225E GLU* 3.2 24.6 + - + +
226E ALA* 1.3 76.2 - - - +
228E LEU* 1.3 65.6 + - - +
229E LEU* 4.2 9.0 - - + -
259E PRO* 3.5 4.9 - - - +
260E GLN* 2.9 58.7 + - + +
318E ASP* 3.3 21.2 + - - -
319E ARG* 4.2 6.0 - - - +
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Residues in contact with LEU 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E ILE 3.5 1.4 - - - +
208E GLU* 3.1 10.6 - - - +
209E PRO* 2.9 51.6 + - + +
227E LYS* 1.3 75.3 - - - +
229E LEU* 1.3 64.5 + - - +
230E ALA* 5.0 7.0 - - + +
257E VAL* 4.0 24.9 - - + -
258E LEU 4.0 9.2 - - - +
259E PRO* 4.0 17.9 - - + -
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Residues in contact with LEU 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E HIS* 3.9 12.3 - - + +
207E ILE 4.1 1.3 - - - -
208E GLU* 3.3 35.9 - - + +
227E LYS* 4.3 7.0 - - + -
228E LEU* 1.3 72.3 - - - +
230E ALA* 1.3 60.1 + - - +
231E THR* 4.6 1.8 - - - +
256E ARG* 3.6 4.3 + - - +
257E VAL* 3.4 3.5 - - - +
258E LEU* 2.9 52.4 + - + +
260E GLN* 4.2 20.9 - - + +
292E VAL* 5.5 1.8 - - + -
319E ARG* 3.7 22.9 - - - +
327E ILE* 3.8 38.8 - - + -
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205E PHE 4.1 0.2 - - - +
206E HIS* 3.1 6.7 + - - -
207E ILE* 2.9 62.5 + - + +
209E PRO* 5.9 0.2 - - + -
228E LEU* 3.6 9.8 + - + +
229E LEU* 1.3 73.0 - - - +
231E THR* 1.3 62.0 + - - +
256E ARG 3.6 3.1 - - - -
257E VAL* 4.4 17.0 - - + -
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Residues in contact with THR 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E ARG* 4.2 12.6 - - + -
205E PHE 3.5 9.6 - - - +
206E HIS* 2.8 25.5 + - + +
229E LEU* 4.6 1.4 - - - +
230E ALA* 1.3 75.1 + - - +
232E HIS* 1.3 62.3 + - - +
233E TYR* 3.5 30.5 - - + -
254E VAL 3.8 0.9 - - - +
255E ASN* 3.7 3.8 - - - +
256E ARG* 2.9 69.5 + - - +
257E VAL* 5.0 1.7 - - - +
324E LEU* 5.1 0.7 - - + -
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Residues in contact with HIS 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E SER 3.9 0.2 - - - +
204E ARG* 3.6 4.7 - - - +
205E PHE* 2.9 66.3 + + + +
231E THR* 1.3 74.7 - - - +
233E TYR* 1.3 73.2 + - - +
234E GLN* 4.2 13.8 + - - +
253E SER* 3.5 23.8 - - - -
254E VAL 3.6 2.8 + - - -
255E ASN* 3.4 20.2 + - - +
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Residues in contact with TYR 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E ALA* 4.9 3.4 - - + -
203E SER 3.8 1.8 - - - -
204E ARG* 3.2 31.9 - - + -
231E THR* 3.5 26.0 - - + -
232E HIS* 1.3 77.8 - - - +
234E GLN* 1.3 61.1 + - - +
235E GLN* 3.9 18.8 - - + -
253E SER* 3.3 10.6 + - - -
254E VAL* 2.9 49.3 + - + +
256E ARG* 4.4 2.9 - - + -
300E ILE* 3.7 42.6 - - + -
303E TYR* 4.3 12.1 - + - -
324E LEU 3.1 18.7 + - - -
325E ASP* 2.3 33.2 + - - -
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Residues in contact with GLN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E ALA* 3.2 2.4 - - - -
203E SER* 2.9 47.6 + - - +
205E PHE* 5.6 2.5 - - + -
232E HIS* 4.2 13.8 + - + +
233E TYR* 1.3 71.9 - - - +
235E GLN* 1.3 61.0 + - - +
236E ASP* 3.8 5.7 + - + +
252E ASP* 3.6 31.5 + - - -
253E SER* 3.9 18.1 + - - -
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Residues in contact with GLN 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E PRO* 5.3 0.9 - - + -
201E GLU 3.4 7.0 - - - +
202E ALA* 3.8 9.2 - - + -
233E TYR* 3.9 12.3 - - + -
234E GLN* 1.3 73.7 - - - +
236E ASP* 1.3 56.6 + - - +
237E ILE* 3.5 13.6 - - + +
250E LEU* 4.1 11.0 - - - +
251E LYS 3.1 22.8 + - - +
252E ASP* 2.7 37.1 + - - +
254E VAL* 4.3 4.4 - - - +
299E ASP 3.1 20.2 + - - -
300E ILE* 3.9 7.8 - - - +
301E TYR* 3.0 23.7 + - - +
303E TYR* 2.6 33.0 + - - +
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Residues in contact with ASP 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E LYS* 4.1 8.2 + - - -
200E PRO* 3.5 3.1 - - - +
201E GLU* 2.7 71.9 + - - +
202E ALA* 3.8 1.2 + - - -
234E GLN* 3.8 8.1 + - + +
235E GLN* 1.3 69.4 - - - +
237E ILE* 1.3 59.9 + - - +
238E PRO* 3.6 3.0 - - - +
252E ASP* 4.1 5.4 - - - +
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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