Contacts of the strand formed by residues 280 - 292 (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 THR 280 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270G ASP* 4.2 9.9 - - + +
271G ARG 3.3 14.4 + - - +
272G SER* 4.6 3.8 - - - -
273G MET* 4.4 3.8 - - - -
279G PHE* 1.3 74.2 + - - +
281G GLN* 1.3 70.2 + - - +
282G THR* 4.3 7.4 - - + -
340G ARG 3.6 0.5 - - - +
341G ILE* 3.3 4.8 - - - -
342G TYR* 2.9 40.0 + - + -
346G ARG* 2.7 40.7 + - - +
9H GLN* 3.2 23.4 + - + +
10H VAL* 5.7 2.7 - - + -
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Residues in contact with GLN 281 (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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270G ASP* 3.3 0.5 - - - +
271G ARG* 2.8 63.6 + - + +
273G MET* 4.0 25.0 - - + +
280G THR* 1.3 73.7 - - - +
282G THR* 1.3 63.9 + - - +
283G LEU* 5.8 0.2 - - - +
339G SER* 3.2 21.8 + - - +
340G ARG 3.2 11.2 - - - +
341G ILE* 4.2 12.4 - - + +
5H ARG* 3.2 26.1 + - - +
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Residues in contact with THR 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G VAL* 4.3 2.9 - - + -
269G PHE 3.4 11.7 - - - -
270G ASP* 4.0 12.3 - - + -
280G THR* 4.3 4.9 - - + -
281G GLN* 1.3 77.7 - - - +
283G LEU* 1.3 60.3 + - - +
284G GLU* 2.9 26.2 + - - +
339G SER* 3.0 11.4 + - - -
340G ARG* 2.9 35.4 + - - +
342G TYR* 3.7 31.4 - - + -
5H ARG* 3.9 2.0 - - - -
10H VAL* 4.4 11.0 - - + -
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Residues in contact with LEU 283 (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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269G PHE* 2.9 48.0 + - + -
282G THR* 1.3 72.5 - - - +
284G GLU* 1.3 60.7 + - - +
285G PRO* 3.3 8.7 - - + +
337G LEU* 3.8 37.9 - - + -
338G THR 3.8 0.7 - - - -
339G SER* 4.1 20.4 - - - +
5H ARG* 3.8 37.1 - - + +
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Residues in contact with GLU 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G LYS* 3.6 23.8 + - - -
267G VAL 3.2 7.4 - - - +
268G VAL* 3.8 28.1 - - + +
282G THR* 2.9 25.2 + - - +
283G LEU* 1.3 78.5 - - - +
285G PRO* 1.3 64.8 - - - +
286G ARG* 3.9 2.8 + - - +
312G TYR* 5.4 0.2 + - - -
336G GLY 3.8 0.9 - - - +
337G LEU* 3.6 3.3 - - - +
338G THR* 2.9 43.2 + - - +
340G ARG* 3.1 37.8 + - - -
342G TYR* 5.0 2.3 + - - -
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Residues in contact with PRO 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G LYS* 3.5 2.1 - - - +
267G VAL* 3.1 43.5 + - + +
269G PHE* 4.0 23.6 - - + -
283G LEU* 3.3 12.1 - - + +
284G GLU* 1.3 86.7 - - - +
286G ARG* 1.3 60.9 + - - +
336G GLY 3.4 7.6 - - - +
337G LEU* 3.8 14.6 - - + -
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Residues in contact with ARG 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ASP* 2.9 29.6 + - - +
265G GLY 3.4 13.7 - - - +
266G LYS* 4.4 19.3 - - + +
284G GLU 4.8 2.2 - - - +
285G PRO* 1.3 77.0 - - - +
287G ALA* 1.3 64.3 + - - +
288G GLN* 4.5 0.4 + - - -
312G TYR* 5.1 8.5 - - - +
313G SER* 5.7 1.2 + - - +
316G PHE* 3.4 57.7 + - + +
334G SER 3.8 0.6 - - - +
335G THR* 3.2 5.7 - - - -
336G GLY 2.9 36.2 + - - +
133H GLN* 6.0 1.6 - - - +
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Residues in contact with ALA 287 (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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263G VAL 4.0 0.7 - - - +
264G ASP* 3.1 3.5 - - - +
265G GLY* 2.9 34.2 + - - +
286G ARG* 1.3 75.6 - - - +
288G GLN* 1.3 61.2 + - - +
333G VAL* 5.1 4.5 - - + -
334G SER 3.4 5.6 - - - +
335G THR* 4.4 12.3 - - + -
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Residues in contact with GLN 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G LYS* 3.7 27.3 + - + +
263G VAL 3.2 11.2 - - - +
264G ASP* 2.8 31.5 - - + +
287G ALA* 1.3 77.3 - - - +
289G TYR* 1.3 63.2 + - - +
290G LEU* 4.1 18.2 + - - +
315G LEU 4.7 0.6 + - - -
316G PHE* 3.3 45.4 + - + +
317G ARG 5.0 2.0 + - - -
318G ASP 5.4 0.2 - - - +
332G GLN* 3.7 1.5 - - - +
333G VAL* 3.3 7.2 - - - +
334G SER* 2.9 47.9 + - - +
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Residues in contact with TYR 289 (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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391E ASN* 4.5 5.5 + - - -
394E LEU* 3.8 19.1 - - + +
261G PHE* 3.8 19.7 - + - -
262G LYS* 3.4 6.1 - - - +
263G VAL* 2.9 43.9 + - + +
288G GLN* 1.3 74.4 - - - +
290G LEU* 1.3 60.3 + - - +
291G TYR* 3.6 34.2 - - + +
331G ASN* 2.7 25.9 + - - -
332G GLN 3.2 26.7 - - - -
333G VAL* 3.7 17.3 - - + +
360G PHE* 4.1 2.2 - + - -
603G C8E 3.5 47.1 + - - +
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Residues in contact with LEU 290 (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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260G GLN* 3.8 25.1 - - + +
261G PHE 3.5 14.8 - - - +
262G LYS* 3.8 19.1 - - + -
288G GLN* 4.1 13.7 + - - +
289G TYR* 1.3 78.1 - - - +
291G TYR* 1.3 62.3 + - - +
292G VAL* 4.7 2.2 - - + -
317G ARG 4.7 2.0 - - - +
318G ASP* 3.9 32.1 - - + +
330G ALA* 3.7 21.3 - - + -
331G ASN* 3.3 6.6 + - - -
332G GLN* 2.9 53.9 + - + +
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Residues in contact with TYR 291 (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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390E ILE* 3.7 35.1 + - + -
391E ASN* 3.9 26.1 - - + +
604E C8E 4.7 10.8 - - - +
259G PRO* 4.1 1.6 - - + +
260G GLN* 3.6 1.4 - - - -
261G PHE* 2.9 44.8 + - + +
289G TYR* 3.6 30.9 - - + +
290G LEU* 1.3 74.6 - - - +
292G VAL* 1.3 68.8 + - - +
293G PRO* 4.0 33.9 - - + +
330G ALA 3.3 15.5 - - - -
331G ASN* 4.0 15.7 - - + -
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Residues in contact with VAL 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G LEU* 5.7 1.1 - - + -
258G LEU* 4.4 15.9 - - + -
259G PRO 3.9 4.7 - - - +
260G GLN* 3.6 33.9 - - + +
290G LEU* 4.7 3.6 - - + -
291G TYR* 1.3 84.2 - - - +
293G PRO* 1.3 82.7 - - + +
318G ASP 5.8 2.0 - - - +
327G ILE* 4.4 12.8 - - + -
328G ALA 3.9 14.6 - - - +
329G SER* 3.4 3.5 - - - -
330G ALA* 2.9 48.3 + - + +
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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