Contacts of the strand formed by residues 253 - 266 (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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A HIS* 3.0 24.3 + - - -
233A TYR 3.3 3.8 - - - -
234A GLN* 4.3 8.5 + - - -
251A LYS* 3.2 29.1 + - - +
252A ASP* 1.3 83.0 - - - +
254A VAL* 1.3 61.7 + - - +
255A ASN* 5.0 4.7 + - - -
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Residues in contact with VAL 254 (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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231A THR 3.7 1.2 - - - +
232A HIS* 3.3 6.3 - - - -
233A TYR* 2.8 48.6 + - + +
235A GLN* 4.3 5.6 - - - +
251A LYS* 3.8 24.5 - - + +
253A SER* 1.3 79.5 + - - +
255A ASN* 1.3 76.3 + - - +
256A ARG* 5.1 0.9 - - + -
295A ARG* 6.0 0.7 - - - +
299A ASP* 3.6 35.0 - - - +
300A ILE* 3.7 28.7 - - + -
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Residues in contact with ASN 255 (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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231A THR 3.6 2.0 - - - -
232A HIS* 3.0 28.3 - - - +
251A LYS* 6.0 0.4 - - - +
253A SER* 4.3 4.6 + - - -
254A VAL* 1.3 79.9 - - - +
256A ARG* 1.3 61.1 + - - +
257A VAL 4.2 0.2 - - - -
295A ARG* 3.5 23.7 + - - -
275C TRP* 3.3 62.4 + - + +
277C THR* 5.7 0.6 + - - -
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Residues in contact with ARG 256 (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* 5.2 0.8 - - - -
229A LEU* 3.3 7.8 + - - +
231A THR* 2.9 72.3 + - - +
233A TYR* 4.6 5.1 - - + -
254A VAL* 5.1 0.9 - - + -
255A ASN* 1.3 75.6 - - - +
257A VAL* 1.3 62.4 + - - +
258A LEU* 4.2 15.4 - - + +
295A ARG* 4.0 21.5 - - + +
297A GLN* 2.5 50.9 + - + +
300A ILE* 4.1 16.0 - - + +
324A LEU* 2.5 35.8 + - - +
325A ASP 3.4 12.1 + - - -
327A ILE* 3.7 19.6 - - - +
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Residues in contact with VAL 257 (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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228A LEU* 3.8 28.3 - - + -
229A LEU 3.2 4.3 - - - +
230A ALA* 4.2 15.3 - - + -
255A ASN 4.2 0.4 - - - -
256A ARG* 1.3 78.5 - - - +
258A LEU* 1.3 69.9 + - - +
259A PRO* 4.1 5.8 - - + +
295A ARG* 5.6 3.4 - - - +
274C ASP 4.6 2.0 - - - +
275C TRP* 4.0 27.6 - - + -
276C ALA* 4.3 23.8 - - + +
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Residues in contact with LEU 258 (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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228A LEU* 4.2 2.5 - - - -
229A LEU* 2.9 48.8 + - + +
256A ARG* 4.2 18.8 - - + +
257A VAL* 1.3 81.2 - - - +
259A PRO* 1.3 66.9 - - + +
260A GLN 3.9 0.3 + - - -
292A VAL* 4.3 9.9 - - + -
293A PRO* 3.3 37.7 - - + +
294A TYR 4.5 0.9 - - - +
295A ARG* 3.6 26.0 - - + +
297A GLN* 4.4 0.2 - - - +
327A ILE* 3.8 41.3 - - + +
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Residues in contact with PRO 259 (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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227A LYS 3.5 8.1 - - - +
228A LEU* 4.1 8.9 - - + -
229A LEU* 5.9 0.2 - - - -
257A VAL* 4.1 6.1 - - + +
258A LEU* 1.3 86.6 - - - +
260A GLN* 1.3 60.4 + - - +
261A PHE 4.3 0.2 - - - -
291A TYR 4.1 0.5 - - - +
292A VAL* 3.9 3.6 - - - +
293A PRO* 3.1 45.5 - - + +
388C TRP* 4.2 16.4 - - + +
390C ILE 6.0 1.1 - - - +
602C C8E 3.7 52.7 - - - -
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Residues in contact with GLN 260 (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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225A GLU* 3.7 3.0 + - - +
226A ALA* 3.6 4.5 - - - -
227A LYS* 2.9 57.6 + - + +
229A LEU* 4.2 10.3 - - + +
259A PRO* 1.3 75.0 - - - +
261A PHE* 1.3 63.8 + - - +
262A LYS* 3.8 11.3 - - - +
290A LEU* 3.7 18.7 - - + +
291A TYR 3.6 3.4 - - - -
292A VAL* 3.6 21.2 - - + +
318A ASP* 2.9 34.1 + - - +
319A ARG* 2.6 28.6 + - - -
327A ILE* 5.9 0.2 - - - +
388C TRP* 3.8 4.6 - - - -
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Residues in contact with PHE 261 (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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224A THR* 3.8 24.5 - - + -
225A GLU 3.7 4.7 - - - -
260A GLN* 1.3 74.3 - - - +
262A LYS* 1.3 66.7 + - - +
263A VAL* 4.1 16.4 - - + -
289A TYR* 3.9 20.6 - + - -
290A LEU* 3.6 2.9 - - - +
291A TYR* 2.9 36.9 + - + +
388C TRP* 3.7 25.3 - + + -
390C ILE* 3.4 41.1 - - + -
394C LEU* 3.8 19.3 - - + -
396C LEU* 4.1 9.2 - - + -
416C MET* 3.7 28.0 - - + -
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Residues in contact with LYS 262 (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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223A ASN* 4.0 2.7 - - - +
224A THR* 3.7 2.4 - - - +
225A GLU* 2.8 72.9 + - + +
227A LYS* 5.1 0.2 - - - +
260A GLN* 3.8 20.0 - - - +
261A PHE* 1.3 78.9 - - - +
263A VAL* 1.3 65.5 + - - +
264A ASP* 4.6 9.9 - - + +
288A GLN* 3.2 31.8 + - + +
289A TYR 3.3 10.1 - - - +
290A LEU* 3.9 10.1 - - + -
316A PHE 5.1 3.0 + - - -
318A ASP* 3.9 20.8 + - - +
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Residues in contact with VAL 263 (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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222A ILE* 4.3 14.4 - - + -
223A ASN 3.6 7.9 - - - +
224A THR* 4.4 10.8 - - + +
261A PHE* 4.1 23.5 - - + -
262A LYS* 1.3 74.0 - - - +
264A ASP* 1.3 64.5 + - - +
287A ALA 4.0 0.5 - - - +
288A GLN* 3.2 4.0 - - - -
289A TYR* 2.9 55.8 + - + +
603A C8E 3.9 24.7 - - - +
605A C8E 5.5 0.7 - - - +
416C MET* 4.4 11.9 - - + -
428C LEU* 4.4 8.5 - - + -
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Residues in contact with ASP 264 (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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221A SER 4.2 0.3 - - - +
222A ILE* 3.5 4.1 - - - -
223A ASN* 2.9 48.5 + - + +
262A LYS* 4.6 8.1 - - + +
263A VAL* 1.3 76.2 - - - +
265A GLY* 1.3 65.7 + - - +
286A ARG* 3.2 38.0 + - - +
287A ALA 3.0 10.3 - - - +
288A GLN* 3.6 29.8 - - + +
316A PHE 5.1 0.2 - - - +
603A C8E 4.4 0.2 - - - -
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Residues in contact with GLY 265 (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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221A SER 3.5 7.2 - - - -
222A ILE* 4.1 2.0 - - - -
264A ASP* 1.3 75.9 + - - +
266A LYS* 1.3 61.4 + - - +
286A ARG* 3.3 5.0 - - - +
287A ALA 2.9 35.4 + - - +
603A C8E 3.7 17.6 - - - -
606C C8E 3.6 14.9 - - - +
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Residues in contact with LYS 266 (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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220A GLY* 3.0 3.2 - - - -
221A SER* 2.9 42.2 + - - +
264A ASP* 5.7 0.2 - - - +
265A GLY* 1.3 74.8 - - - +
267A VAL* 1.3 73.5 + - - +
268A VAL* 4.3 15.6 - - + +
284A GLU* 3.8 26.9 + - + -
285A PRO 3.4 13.0 - - - +
286A ARG* 4.4 20.4 - - + +
340A ARG* 5.3 5.1 - - - +
133B GLN* 5.4 4.9 + - - -
137B ARG* 5.4 4.9 - - - +
606C C8E 3.6 2.8 - - - +
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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