Contacts of the strand formed by residues 220 - 236 (chain C) 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 GLY 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216C SER 3.7 0.2 - - - -
217C ASN* 2.9 34.6 + - - +
218C SER 3.7 1.0 - - - -
219C TRP* 1.3 95.5 - - - +
221C SER* 1.3 62.2 + - - -
266C LYS 3.3 12.1 - - - -
267C VAL* 4.3 0.7 - - - -
268C VAL* 4.7 1.6 - - - -
601C C8E 4.1 4.9 - - - -
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Residues in contact with SER 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LEU 3.2 13.0 - - - -
216C SER* 4.0 12.6 - - - -
220C GLY* 1.3 77.2 - - - -
222C ILE* 1.3 62.9 + - - +
264C ASP 4.1 0.5 - - - +
265C GLY* 3.4 1.7 - - - -
266C LYS* 2.9 46.0 + - - +
601C C8E 4.1 7.9 + - - +
38D LEU* 4.6 17.6 - - - +
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Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LEU 3.9 1.0 - - - +
214C PRO* 3.8 0.5 - - - +
215C LEU* 2.9 62.7 + - + +
221C SER* 1.3 75.9 - - - +
223C ASN* 1.3 66.8 + - - +
224C THR* 5.0 5.4 - - - +
263C VAL* 4.3 19.5 - - + -
264C ASP 3.4 13.5 - - - +
265C GLY* 4.2 6.5 - - - -
601C C8E 4.3 25.4 - - - +
607C C8E 4.4 12.1 - - - +
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Residues in contact with ASN 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ASN* 2.8 45.3 + - - +
213C LEU 3.2 15.2 - - - +
214C PRO* 3.5 6.2 - - + +
222C ILE* 1.3 78.3 - - - +
224C THR* 1.3 60.6 + - - +
225C GLU* 4.3 11.8 + - - +
262C LYS* 3.8 3.3 - - - +
263C VAL* 3.5 3.3 - - - +
264C ASP* 2.9 44.5 + - + +
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Residues in contact with THR 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C VAL 4.0 0.5 - - - +
212C ASN* 3.2 4.4 - - - +
213C LEU* 2.8 54.4 + - + +
222C ILE* 5.0 5.9 - - - +
223C ASN* 1.3 74.2 + - - +
225C GLU* 1.3 65.5 + - - +
261C PHE* 3.8 28.5 - - + -
262C LYS 3.7 2.7 - - - +
263C VAL* 4.3 11.6 - - + +
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C THR* 4.0 20.2 - - + +
211C VAL 3.5 3.6 - - - +
212C ASN* 3.7 14.3 - - - +
223C ASN* 4.3 8.9 + - - +
224C THR* 1.3 78.3 - - - +
226C ALA* 1.3 64.5 + - - +
227C LYS* 3.3 33.3 + - + +
260C GLN* 3.7 3.0 + - - +
261C PHE* 3.7 8.5 - - - -
262C LYS* 2.8 77.4 + - + +
318C ASP* 4.4 0.2 - - - +
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Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PRO 4.1 0.2 - - - +
210C THR* 3.4 3.5 - - - +
211C VAL* 2.9 44.6 + - + +
225C GLU* 1.3 74.7 - - - +
227C LYS* 1.3 61.2 + - - +
260C GLN 3.7 4.5 - - - +
261C PHE* 5.1 4.3 - - + +
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C GLU* 3.1 35.3 + - + +
209C PRO 3.4 4.5 - - - +
210C THR* 3.4 19.7 - - - +
225C GLU* 3.3 23.7 + - + +
226C ALA* 1.3 76.1 - - - +
228C LEU* 1.3 67.6 + - - +
229C LEU* 4.1 9.6 - - + -
259C PRO* 3.5 4.2 - - - +
260C GLN* 2.9 58.3 + - + +
262C LYS* 5.5 0.2 - - - +
318C ASP* 3.4 20.7 + - - -
319C ARG* 4.5 3.7 - - - +
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Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ILE 3.6 0.3 - - - +
208C GLU* 3.1 26.9 - - - +
209C PRO* 2.9 34.1 + - + +
227C LYS* 1.3 76.7 - - - +
229C LEU* 1.3 65.3 + - - +
230C ALA* 3.6 7.1 + - + +
257C VAL* 3.8 29.4 - - + -
259C PRO* 4.0 23.6 - - + -
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C HIS* 3.9 13.9 - - + -
207C ILE 4.2 1.6 - - - -
208C GLU* 3.2 36.1 - - + +
227C LYS* 4.2 9.9 - - + -
228C LEU* 1.3 73.8 - - - +
230C ALA* 1.3 59.0 + - - +
231C THR* 4.2 1.3 - - - +
256C ARG* 3.4 5.4 + - - +
257C VAL* 3.3 4.5 - - - -
258C LEU* 2.9 49.5 + - + +
260C GLN* 4.0 22.0 - - + +
292C VAL* 5.5 1.6 - - + -
319C ARG* 4.2 10.3 - - - +
324C LEU* 5.3 2.0 - - + -
327C ILE* 3.7 41.7 - - + -
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C PHE 4.1 0.2 - - - +
206C HIS* 3.2 5.0 + - - -
207C ILE* 2.9 62.1 + - + +
209C PRO* 5.9 0.4 - - + -
228C LEU* 3.6 9.1 + - + +
229C LEU* 1.3 73.9 - - - +
231C THR* 1.3 61.5 + - - +
256C ARG 3.5 3.6 - - - -
257C VAL* 4.2 19.3 - - + -
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Residues in contact with THR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ARG* 4.0 14.1 - - + -
205C PHE 3.4 11.9 - - - +
206C HIS* 2.7 28.9 + - + +
229C LEU* 4.7 1.4 - - - +
230C ALA* 1.3 74.0 + - - +
232C HIS* 1.3 62.9 + - - +
233C TYR* 3.6 21.4 - - + -
254C VAL 3.8 0.7 - - - +
255C ASN* 3.7 3.5 - - - +
256C ARG* 2.9 72.9 + - - +
257C VAL* 5.0 0.9 - - - +
324C LEU* 5.1 0.2 - - + -
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Residues in contact with HIS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C SER 3.8 0.5 - - - +
204C ARG* 3.6 3.5 - - - +
205C PHE* 2.9 61.9 + + + +
231C THR* 1.3 74.6 - - - +
233C TYR* 1.3 75.1 + - - +
234C GLN* 3.8 15.1 + - + +
253C SER* 3.1 27.8 - - - -
254C VAL 3.4 6.3 + - - -
255C ASN* 3.0 24.0 + - - +
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ALA* 4.9 2.7 - - + -
203C SER 3.7 3.6 - - - -
204C ARG* 3.2 31.4 - - + -
231C THR* 3.6 19.7 - - + -
232C HIS* 1.3 85.5 - - - +
234C GLN* 1.3 58.9 + - - +
235C GLN* 3.9 21.3 - - + -
253C SER* 3.4 6.2 - - - -
254C VAL* 2.8 49.5 + - + -
256C ARG* 4.4 6.1 - - + -
300C ILE* 3.5 42.8 - - + -
303C TYR* 4.0 13.0 - + - -
324C LEU 3.1 16.3 + - - -
325C ASP* 2.4 30.7 + - - -
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Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ALA* 3.3 2.6 - - - -
203C SER* 2.9 49.4 + - - +
205C PHE* 5.3 2.9 - - + -
232C HIS* 3.8 19.6 + - + +
233C TYR* 1.3 71.9 - - - +
235C GLN* 1.3 61.3 + - - +
236C ASP* 3.8 14.0 + - - +
252C ASP* 3.5 34.7 + - - +
253C SER* 4.2 8.8 + - - -
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Residues in contact with GLN 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PRO* 5.6 0.9 - - + -
201C GLU 3.5 5.4 - - - +
202C ALA* 4.1 6.5 - - + -
233C TYR* 4.3 15.7 - - + -
234C GLN* 1.3 73.7 - - - +
236C ASP* 1.3 63.1 + - - +
237C ILE* 3.5 13.3 + - + +
250C LEU* 3.9 9.0 - - - +
251C LYS 3.0 25.5 + - - +
252C ASP* 2.8 36.5 + - - +
254C VAL* 4.2 4.4 - - - +
299C ASP 3.1 21.6 + - - -
300C ILE* 3.9 3.8 - - - +
301C TYR* 3.1 24.6 + - - +
303C TYR* 2.8 30.6 + - - +
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Residues in contact with ASP 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS* 3.8 20.8 + - - -
200C PRO* 3.3 4.9 - - - +
201C GLU* 2.9 48.8 + - + +
234C GLN* 3.8 15.2 + - - +
235C GLN* 1.3 72.1 - - - +
237C ILE* 1.3 60.3 + - - +
238C PRO* 3.6 2.6 - - - +
252C ASP* 4.5 7.5 - - - +
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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