Contacts of the strand formed by residues 253 - 266 (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 SER 253 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G HIS* 3.0 25.6 + - - -
233G TYR 3.3 3.8 - - - -
234G GLN* 3.5 17.0 + - - -
251G LYS* 4.0 12.5 - - - +
252G ASP* 1.3 80.9 - - - +
254G VAL* 1.3 65.6 + - - +
255G ASN* 4.4 3.9 + - - -
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Residues in contact with VAL 254 (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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231G THR 3.8 0.5 - - - +
232G HIS* 3.4 5.9 - - - -
233G TYR* 2.9 47.5 + - + -
235G GLN* 4.6 1.1 - - - +
251G LYS* 3.7 23.1 - - + +
253G SER* 1.3 80.5 + - - +
255G ASN* 1.3 75.6 + - - +
256G ARG* 5.2 1.3 - - + -
299G ASP* 3.4 37.9 - - - +
300G ILE* 3.9 25.8 - - + -
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Residues in contact with ASN 255 (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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274E ASP 4.9 1.6 + - - -
275E TRP* 3.4 61.3 + - + +
231G THR 3.7 2.0 - - - -
232G HIS* 3.0 29.4 - - - +
253G SER* 4.4 3.6 + - - -
254G VAL* 1.3 79.1 - - - +
256G ARG* 1.3 60.6 + - - +
257G VAL 4.3 0.4 - - - -
295G ARG* 3.7 21.7 + - - -
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Residues in contact with ARG 256 (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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206G HIS* 5.2 0.4 - - - -
229G LEU* 3.4 6.4 + - - +
230G ALA* 3.6 0.3 - - - -
231G THR* 2.9 74.5 + - - +
233G TYR* 4.2 5.1 - - + -
254G VAL* 5.2 1.1 - - + -
255G ASN* 1.3 75.6 - - - +
257G VAL* 1.3 63.1 + - - +
258G LEU* 4.0 16.7 - - + +
295G ARG* 4.1 21.3 - - + +
297G GLN* 2.5 49.6 + - + -
300G ILE* 4.1 16.0 - - + +
324G LEU* 2.5 34.2 + - - +
325G ASP 3.5 11.9 + - - -
327G ILE* 3.6 20.2 - - - +
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Residues in contact with VAL 257 (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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273E MET* 6.5 0.2 - - + -
275E TRP* 3.8 41.2 + - + -
276E ALA* 4.5 21.3 - - + +
228G LEU* 3.8 28.7 - - + -
229G LEU 3.4 4.0 - - - +
230G ALA* 4.3 6.7 - - + -
255G ASN 4.3 0.4 - - - -
256G ARG* 1.3 77.6 - - - +
258G LEU* 1.3 72.2 + - - +
259G PRO* 4.1 5.6 - - + +
295G ARG* 5.5 3.9 - - - +
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Residues in contact with LEU 258 (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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604E C8E 6.3 0.4 - - + -
228G LEU* 4.0 3.1 - - - -
229G LEU* 2.9 49.6 + - + +
256G ARG* 4.0 23.1 - - + -
257G VAL* 1.3 81.6 - - - +
259G PRO* 1.3 65.2 - - + +
260G GLN 3.9 0.2 + - - -
292G VAL* 4.4 10.3 - - + -
293G PRO* 3.5 34.5 - - + +
294G TYR 4.7 1.3 - - - +
295G ARG* 3.6 25.6 - - + -
297G GLN* 4.3 0.4 - - - +
327G ILE* 3.8 39.5 - - + +
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Residues in contact with PRO 259 (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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388E TRP* 4.4 16.2 - - + -
604E C8E 3.6 47.1 - - - +
227G LYS 3.6 6.7 - - - +
228G LEU* 3.9 11.2 - - + -
257G VAL* 4.1 7.0 - - + +
258G LEU* 1.3 86.7 - - - +
260G GLN* 1.3 61.1 + - - +
291G TYR* 4.1 0.9 - - + +
292G VAL* 3.9 3.8 - - - +
293G PRO* 3.2 46.7 - - + +
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Residues in contact with GLN 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E TRP* 3.9 5.6 - - - -
225G GLU* 3.7 3.0 + - - +
226G ALA* 3.6 4.5 - - - -
227G LYS* 2.9 60.2 + - + +
229G LEU* 4.1 11.3 - - + +
258G LEU 5.0 0.2 - - - +
259G PRO* 1.3 76.3 - - - +
261G PHE* 1.3 63.9 + - - +
262G LYS* 3.7 16.4 - - - +
290G LEU* 3.8 13.4 - - + +
291G TYR 3.6 2.5 - - - -
292G VAL* 3.6 20.9 - - + +
318G ASP* 3.1 33.3 + - - +
319G ARG* 2.8 25.7 + - - -
327G ILE* 5.9 0.3 - - - +
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Residues in contact with PHE 261 (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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388E TRP* 3.8 23.8 - + + -
390E ILE* 3.5 36.6 - - + -
394E LEU* 3.6 23.6 - - + -
396E LEU* 4.3 8.1 - - + -
416E MET* 3.7 25.8 - - + -
224G THR* 3.9 25.1 - - + -
225G GLU 3.7 5.6 - - - -
259G PRO 4.3 0.4 - - - -
260G GLN* 1.3 73.4 - - - +
262G LYS* 1.3 67.7 + - - +
263G VAL* 3.8 17.5 - - + -
289G TYR* 3.8 23.1 - + - -
290G LEU* 3.5 4.1 - - - +
291G TYR* 2.9 37.8 + - + +
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Residues in contact with LYS 262 (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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223G ASN* 4.0 2.1 - - - +
224G THR* 3.7 2.1 - - - +
225G GLU* 2.8 71.5 + - + +
260G GLN* 3.7 19.9 - - - +
261G PHE* 1.3 80.1 - - - +
263G VAL* 1.3 63.2 + - - +
264G ASP* 4.7 7.6 - - + +
288G GLN* 3.7 31.4 + - + +
289G TYR 3.4 9.6 - - - +
290G LEU* 3.8 9.9 - - + -
316G PHE 5.2 2.4 + - - -
318G ASP* 3.7 26.3 + - - +
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Residues in contact with VAL 263 (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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416E MET* 4.3 13.5 - - + -
428E LEU* 4.3 22.4 - - + -
222G ILE* 4.4 11.2 - - + -
223G ASN 3.5 9.0 - - - +
224G THR* 4.2 13.5 - - + +
261G PHE* 3.8 24.9 - - + -
262G LYS* 1.3 75.6 - - - +
264G ASP* 1.3 64.1 + - - +
287G ALA 4.0 0.5 - - - +
288G GLN* 3.2 3.6 - - - +
289G TYR* 2.9 51.5 + - + -
603G C8E 5.6 0.7 - - - +
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Residues in contact with ASP 264 (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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221G SER 4.3 0.5 - - - +
222G ILE* 3.5 3.5 - - - -
223G ASN* 2.9 46.3 + - + +
262G LYS* 4.3 8.4 - - + +
263G VAL* 1.3 76.7 - - - +
265G GLY* 1.3 70.5 + - - +
266G LYS* 5.7 0.2 - - - +
286G ARG* 2.9 38.3 + - - -
287G ALA 3.1 9.9 - - - +
288G GLN* 2.8 32.6 - - + +
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Residues in contact with GLY 265 (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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221G SER 3.6 7.2 - - - -
222G ILE* 4.0 13.6 - - - +
263G VAL* 4.3 0.6 - - - +
264G ASP* 1.3 76.7 + - - +
266G LYS* 1.3 60.6 + - - -
267G VAL* 5.8 0.2 - - - -
286G ARG* 3.4 6.1 - - - +
287G ALA* 2.9 37.5 + - - +
602G C8E 5.7 1.1 - - - -
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Residues in contact with LYS 266 (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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220G GLY* 3.0 3.1 - - - -
221G SER* 2.9 42.2 + - - +
265G GLY* 1.3 74.5 - - - +
267G VAL* 1.3 75.6 + - - +
268G VAL* 4.0 14.7 - - + +
284G GLU* 3.6 28.4 + - + -
285G PRO 3.5 12.8 - - - +
286G ARG* 4.4 18.4 - - + +
340G ARG* 5.1 6.1 - - - +
602G C8E 4.3 1.8 + - - -
133H GLN* 5.5 4.2 + - - -
137H ARG* 6.0 3.2 - - - +
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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