Contacts of the strand formed by residues 201 - 216 (chain G) 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 GLU 201 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G LYS* 5.9 0.7 - - - +
192G PHE 3.5 7.6 - - - +
193G THR* 3.6 35.9 - - + +
194G SER 4.6 10.9 - - - +
199G ASN 3.7 5.6 + - - +
200G PRO* 1.3 78.5 - - - +
202G ALA* 1.3 64.8 + - - +
235G GLN* 3.3 4.0 - - - +
236G ASP* 2.8 54.0 + - - +
238G PRO* 5.0 0.2 - - - +
303G TYR* 4.1 0.4 + - - -
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Residues in contact with ALA 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G ALA 3.8 0.5 - - - +
191G LYS* 3.4 6.3 - - - +
192G PHE* 2.9 42.3 + - + +
193G THR* 5.3 0.2 - - - +
201G GLU* 1.3 78.6 - - - +
203G SER* 1.3 65.2 + - - +
204G ARG* 4.1 0.4 - - + -
233G TYR* 5.1 4.5 - - + -
234G GLN 3.2 10.1 - - - +
235G GLN* 3.9 6.5 - - + -
236G ASP* 3.7 1.8 + - - -
303G TYR* 3.2 37.5 - - + +
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Residues in contact with SER 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G ALA 3.5 6.7 - - - -
191G LYS* 3.6 24.1 - - - +
202G ALA* 1.3 72.6 - - - +
204G ARG* 1.3 59.9 + - - +
205G PHE* 4.0 23.8 - - - -
232G HIS 3.9 1.4 - - - +
233G TYR* 3.8 1.1 - - - -
234G GLN* 2.9 42.4 + - - +
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Residues in contact with ARG 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G GLN* 2.6 30.9 + - - +
189G ALA* 3.3 5.5 - - - -
190G ALA* 2.9 38.0 + - - +
192G PHE* 3.4 28.0 - - + -
202G ALA* 4.1 0.8 - - + -
203G SER* 1.3 74.1 - - - +
205G PHE* 1.3 69.1 + - - +
206G HIS* 5.2 1.5 - - + +
231G THR* 4.0 15.9 - - + -
232G HIS 3.6 3.6 - - - +
233G TYR* 3.3 37.5 - - + +
304G ASP* 3.0 35.0 + - - -
324G LEU* 3.5 28.8 - - - +
325G ASP* 2.9 22.6 + - - -
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Residues in contact with PHE 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E TRP* 5.0 6.8 - - + -
188G GLN 3.5 2.9 - - - +
189G ALA* 4.1 22.9 - - + -
190G ALA 6.1 0.2 - - - -
203G SER* 4.0 30.7 - - - -
204G ARG* 1.3 75.9 - - - +
206G HIS* 1.3 60.5 + - - +
230G ALA 4.1 0.2 - - - +
231G THR* 3.4 5.7 - - - +
232G HIS* 2.9 61.1 + + + +
234G GLN* 5.5 2.5 - - + -
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Residues in contact with HIS 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E TRP* 6.1 0.2 - - - -
186G TYR* 4.1 16.6 - + - -
187G GLY* 3.2 5.4 - - - -
188G GLN* 2.9 40.1 + - + +
204G ARG* 5.2 2.7 - - + +
205G PHE* 1.3 75.4 - - - +
207G ILE* 1.3 70.7 + - - +
208G GLU* 3.1 30.7 + - + +
229G LEU* 3.7 20.9 - - + -
230G ALA 3.2 11.0 + - - -
231G THR* 2.7 31.8 + - + +
256G ARG* 5.2 0.7 - - - -
324G LEU* 3.6 40.4 - - + +
327G ILE* 6.1 0.4 - - + -
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Residues in contact with ILE 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E TRP* 4.8 8.9 - - + -
185G VAL* 3.8 20.0 - - + -
186G TYR 3.7 12.3 - - - +
187G GLY* 4.2 9.9 - - - -
206G HIS* 1.3 76.3 - - - +
208G GLU* 1.3 64.8 + - - +
209G PRO* 4.0 9.4 - - + -
228G LEU 3.5 0.5 - - - +
230G ALA* 2.9 53.8 + - + +
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Residues in contact with GLU 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G HIS* 3.7 5.0 - - + +
185G VAL* 3.5 3.2 - - - -
186G TYR* 2.9 55.2 + - + +
206G HIS* 3.1 23.1 + - + +
207G ILE* 1.3 79.5 - - - +
209G PRO* 1.3 61.9 - - - +
210G THR* 4.2 3.6 + - - +
227G LYS* 3.3 32.6 + - + +
228G LEU 3.2 6.1 - - - +
229G LEU* 3.3 23.5 - - + +
319G ARG* 3.3 9.4 + - - -
324G LEU* 5.0 2.8 - - - +
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Residues in contact with PRO 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604E C8E 4.9 8.7 + - - +
184G HIS 3.8 3.4 - - - +
185G VAL* 4.1 18.1 - - + -
207G ILE* 4.0 13.2 - - + +
208G GLU* 1.3 86.3 - - - +
210G THR* 1.3 65.4 + - - +
211G VAL* 5.7 2.7 - - + -
226G ALA 4.1 0.2 - - - +
227G LYS* 3.4 1.2 - - - +
228G LEU* 2.9 60.8 + - + +
230G ALA* 6.0 0.2 - - + -
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Residues in contact with THR 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G ASP 3.9 0.5 - - - +
183G MET* 3.4 5.9 - - - +
184G HIS* 2.9 57.4 + - + +
185G VAL* 4.9 0.4 - - - +
208G GLU* 4.2 6.2 + - - +
209G PRO* 1.3 77.4 + - - +
211G VAL* 1.3 69.5 + - - +
212G ASN* 5.1 4.5 - - + -
225G GLU* 3.9 30.5 - - + +
226G ALA 3.4 10.5 - - - +
227G LYS* 3.3 23.0 - - - +
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Residues in contact with VAL 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603E C8E 4.6 24.8 - - - +
604E C8E 4.9 11.4 - - - +
181G PHE* 3.7 39.9 - - + -
182G ASP 3.7 2.5 - - - +
183G MET* 4.3 23.6 - - + +
209G PRO* 5.7 1.8 - - + -
210G THR* 1.3 78.2 - - - +
212G ASN* 1.3 62.7 - - - +
224G THR 4.0 0.5 - - - +
225G GLU* 3.5 3.8 - - - +
226G ALA* 2.9 39.2 + - + +
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Residues in contact with ASN 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G PHE* 3.2 8.6 - - - -
182G ASP* 2.9 51.5 + - + +
210G THR* 5.1 6.5 - - + -
211G VAL* 1.3 77.4 - - - +
213G LEU* 1.3 59.2 + - - +
214G PRO* 3.2 15.5 - - - +
223G ASN* 2.8 45.8 + - - +
224G THR 3.1 7.8 - - - +
225G GLU* 3.5 14.0 - - - +
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Residues in contact with LEU 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E ALA* 4.3 9.2 - - + -
603E C8E 3.5 78.2 - - + +
180G PRO* 3.6 24.2 - - + +
181G PHE* 4.1 4.9 - - + -
212G ASN* 1.3 73.7 - - - +
214G PRO* 1.3 60.8 - - + +
215G LEU* 3.9 22.3 + - + +
222G ILE 4.0 0.5 - - - +
223G ASN* 3.0 5.5 - - - +
224G THR* 2.8 43.8 + - - +
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Residues in contact with PRO 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G PRO 3.9 14.2 - - - +
182G ASP* 3.7 22.7 - - - +
212G ASN* 3.2 20.4 - - - +
213G LEU* 1.3 86.2 - - + +
215G LEU* 1.3 69.5 + - - +
216G SER* 4.1 2.6 + - - -
222G ILE 3.9 2.5 - - - +
223G ASN* 3.4 13.7 - - + +
602G C8E 4.6 13.5 - - + +
37H ARG* 4.2 9.6 - - - +
38H LEU* 5.2 12.6 - - + -
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Residues in contact with LEU 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E ALA* 6.5 0.4 - - + -
430E TYR* 3.5 43.5 - - + -
457E VAL* 5.9 0.2 - - + -
603E C8E 3.7 31.9 - - + -
213G LEU* 3.9 22.9 + - + +
214G PRO* 1.3 81.6 - - - +
216G SER* 1.3 60.6 + - - +
221G SER* 3.4 5.0 - - - -
222G ILE* 2.9 60.9 + - + +
602G C8E 3.6 23.4 - - - +
38H LEU* 5.7 1.3 - - - +
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Residues in contact with SER 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G PRO* 4.1 2.3 + - - -
215G LEU* 1.3 75.0 - - - +
217G ASN* 1.3 67.9 + - - +
221G SER* 4.0 9.0 - - - -
602G C8E 3.1 35.3 - - - +
37H ARG 4.9 1.1 - - - -
38H LEU* 2.4 37.6 + - - -
39H ASN* 4.0 0.2 - - - -
40H ASN* 3.1 31.6 + - - -
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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
------------------------------------------------------------
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