Contacts of the strand formed by residues 280 - 292 (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 THR 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270C ASP* 4.2 19.7 - - + +
271C ARG 3.4 13.9 + - - +
272C SER* 5.0 2.9 - - - -
273C MET* 4.5 2.7 - - - -
278C GLY 4.1 3.5 + - - -
279C PHE* 1.3 77.3 + - - +
281C GLN* 1.3 68.4 + - - +
282C THR* 4.5 6.1 - - + -
340C ARG 3.8 0.2 - - - +
341C ILE* 3.4 4.6 - - - +
342C TYR* 2.9 50.6 + - + +
343C ASP 5.5 0.5 + - - -
346C ARG* 4.9 14.3 + - - -
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Residues in contact with GLN 281 (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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270C ASP* 3.2 1.0 - - - +
271C ARG* 2.5 65.9 + - + +
273C MET* 3.4 32.7 - - + +
280C THR* 1.3 73.7 - - - +
282C THR* 1.3 64.0 + - - +
283C LEU* 6.0 0.2 - - - +
339C SER* 3.5 19.2 + - - +
340C ARG 3.3 11.2 - - - +
341C ILE* 4.3 11.0 - - + +
5D ARG* 3.0 29.3 + - - +
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Residues in contact with THR 282 (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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268C VAL* 4.6 2.5 - - - -
269C PHE 3.3 9.9 - - - -
270C ASP* 4.0 13.2 - - + -
280C THR* 4.5 3.8 - - + -
281C GLN* 1.3 77.9 - - - +
283C LEU* 1.3 59.9 + - - +
284C GLU* 3.0 25.5 + - - +
339C SER* 3.1 12.8 + - - -
340C ARG* 2.9 37.4 + - - +
342C TYR* 3.7 31.0 - - + -
5D ARG* 4.0 2.0 - - - -
9D GLN* 4.5 11.7 - - - +
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Residues in contact with LEU 283 (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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269C PHE* 2.9 52.5 + - + -
282C THR* 1.3 72.3 - - - +
284C GLU* 1.3 62.5 + - - +
285C PRO* 3.3 9.2 - - + +
337C LEU* 3.8 34.3 - - + -
338C THR 3.9 0.4 - - - -
339C SER* 4.6 14.1 - - - +
605C C8E 3.9 37.9 - - + -
5D ARG* 3.9 31.3 - - - +
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Residues in contact with GLU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LYS* 3.8 23.9 + - - +
267C VAL 3.3 7.0 - - - +
268C VAL* 3.9 26.8 - - + +
282C THR* 3.0 24.7 + - - +
283C LEU* 1.3 79.7 - - - +
285C PRO* 1.3 64.5 - - - +
286C ARG* 4.8 2.1 - - - +
312C TYR* 5.3 0.2 + - - -
336C GLY 3.9 1.0 - - - +
337C LEU* 3.6 5.6 - - - +
338C THR* 2.9 48.8 + - - +
340C ARG* 3.2 31.3 + - - -
342C TYR* 5.1 0.7 + - - -
9D GLN* 5.5 1.7 + - - -
137D ARG* 6.0 0.5 - - - -
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Residues in contact with PRO 285 (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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266C LYS* 3.5 2.8 - - - +
267C VAL* 3.0 43.7 + - + +
269C PHE* 3.8 23.8 - - + -
283C LEU* 3.3 12.8 - - + +
284C GLU* 1.3 86.3 - - - +
286C ARG* 1.3 61.4 + - - +
336C GLY 3.5 6.7 - - - +
337C LEU* 3.7 13.4 - - + -
601C C8E 3.6 31.9 - - + +
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Residues in contact with ARG 286 (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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264C ASP* 3.0 29.8 + - - +
265C GLY 3.4 12.8 - - - +
266C LYS* 4.3 21.5 - - + +
284C GLU 4.8 2.5 - - - +
285C PRO* 1.3 77.5 - - - +
287C ALA* 1.3 63.9 + - - +
288C GLN* 4.6 0.2 - - - +
312C TYR* 5.1 7.4 - - - +
313C SER* 5.6 2.2 + - - +
316C PHE* 3.4 57.9 + - + +
334C SER 3.9 0.2 - - - +
335C THR* 3.3 5.4 - - - -
336C GLY 2.9 36.6 + - - +
601C C8E 3.9 4.8 - - - +
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Residues in contact with ALA 287 (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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264C ASP* 3.1 3.4 - - - +
265C GLY 2.9 33.8 + - - -
286C ARG* 1.3 75.5 - - - +
288C GLN* 1.3 61.0 + - - +
333C VAL* 5.2 0.9 - - + -
334C SER 3.4 7.0 - - - +
335C THR* 4.4 10.1 - - + -
601C C8E 3.8 29.6 - - + +
607C C8E 3.8 25.0 - - - +
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Residues in contact with GLN 288 (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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262C LYS* 3.6 34.2 - - + +
263C VAL 3.2 11.2 - - - +
264C ASP* 2.9 31.7 + - - +
286C ARG* 4.6 0.2 - - - +
287C ALA* 1.3 76.2 - - - +
289C TYR* 1.3 63.4 + - - +
290C LEU* 4.1 15.8 + - - +
315C LEU 4.7 1.7 - - - +
316C PHE* 3.3 49.5 + - + +
317C ARG 5.0 1.2 - - - +
332C GLN 3.7 0.7 - - - +
333C VAL* 3.3 7.6 - - - +
334C SER* 2.9 40.1 + - - +
607C C8E 4.4 1.3 - - - -
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Residues in contact with TYR 289 (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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261C PHE* 4.0 23.3 - + - -
262C LYS* 3.4 7.4 - - - +
263C VAL* 2.9 38.7 + - + +
288C GLN* 1.3 74.1 - - - +
290C LEU* 1.3 65.4 + - - +
291C TYR* 3.8 28.3 - + + -
331C ASN* 2.8 27.7 + - - -
332C GLN 3.2 22.0 - - - -
333C VAL* 3.8 16.4 - - + +
360C PHE* 4.1 2.5 - + - -
603C C8E 3.7 56.8 + - - +
607C C8E 4.0 6.7 + - - +
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Residues in contact with LEU 290 (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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260C GLN* 3.7 32.8 - - + +
261C PHE 3.6 10.1 - - - +
262C LYS* 4.0 10.3 - - + -
288C GLN* 4.4 13.0 - - + +
289C TYR* 1.3 78.7 - - - +
291C TYR* 1.3 66.5 + - - +
292C VAL* 4.6 2.2 - - + -
317C ARG 4.7 2.2 - - - +
318C ASP* 3.9 32.1 - - + +
330C ALA* 3.6 21.1 - - + -
331C ASN* 3.3 6.1 + - - -
332C GLN* 2.9 55.9 + - + +
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Residues in contact with TYR 291 (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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259C PRO* 5.4 2.5 - - + -
260C GLN* 3.5 1.7 - - - -
261C PHE* 2.9 52.8 + + + +
289C TYR* 3.8 29.4 - + + +
290C LEU* 1.3 77.0 - - - +
292C VAL* 1.3 69.1 + - - +
293C PRO* 3.9 35.9 - - + +
330C ALA 3.3 14.6 - - - -
331C ASN* 4.1 13.9 - - + -
603C C8E 5.1 14.4 - - + +
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LEU* 5.5 0.9 - - + -
258C LEU* 4.5 8.7 - - + -
259C PRO 4.3 3.4 - - - +
260C GLN* 3.7 26.2 - - + -
290C LEU* 4.6 2.0 - - + -
291C TYR* 1.3 83.3 - - - +
293C PRO* 1.3 83.5 - - + +
319C ARG* 3.9 15.3 - - - +
327C ILE* 4.3 14.4 - - + -
328C ALA 3.6 16.4 - - - +
329C SER* 3.3 4.0 - - - -
330C ALA* 2.8 48.3 + - + +
603C C8E 5.3 1.6 - - - +
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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
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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