Contacts of the strand formed by residues 280 - 292 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ASP* 4.0 28.7 - - + +
271E ARG 3.5 14.5 + - - +
272E SER* 4.9 4.0 - - - -
273E MET* 5.2 1.1 - - - -
279E PHE* 1.3 75.9 + - - +
281E GLN* 1.3 62.6 + - - +
282E THR* 4.4 6.7 - - + -
340E ARG 3.8 0.2 - - - +
341E ILE* 3.4 5.0 - - - -
342E TYR* 2.9 42.4 + - + -
346E ARG* 2.4 39.7 + - - +
10F VAL* 5.7 1.8 - - + -
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Residues in contact with GLN 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ASP* 3.2 0.5 - - - -
271E ARG* 2.9 54.0 + - + +
273E MET* 3.5 27.4 - - + +
280E THR* 1.3 73.4 - - - +
282E THR* 1.3 60.1 + - - +
283E LEU* 6.0 0.4 - - - +
339E SER* 3.5 16.3 + - - +
340E ARG 3.3 10.8 - - - +
341E ILE* 4.0 13.9 - - + +
5F ARG* 2.7 43.8 + - - +
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Residues in contact with THR 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E VAL* 4.6 4.0 - - + -
269E PHE 3.2 11.2 - - - -
270E ASP* 3.9 13.7 - - + -
280E THR* 4.4 5.2 - - + -
281E GLN* 1.3 77.3 - - - +
283E LEU* 1.3 60.3 + - - +
284E GLU* 3.3 24.7 + - - +
339E SER* 3.1 11.3 + - - -
340E ARG* 2.9 37.8 + - - +
342E TYR* 3.7 28.9 - - + -
5F ARG* 3.9 2.0 - - - -
10F VAL* 4.5 12.3 - - + -
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Residues in contact with LEU 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E PHE* 2.9 53.6 + - + -
282E THR* 1.3 72.7 - - - +
284E GLU* 1.3 61.7 + - - +
285E PRO* 3.3 8.8 - - + +
337E LEU* 3.8 35.0 - - + -
338E THR 3.9 0.4 - - - -
339E SER* 4.2 18.8 - - - +
5F ARG* 3.9 33.6 - - + +
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Residues in contact with GLU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E LYS* 3.8 23.7 + - + -
267E VAL 3.3 7.9 - - - +
268E VAL* 4.1 25.6 - - + +
282E THR* 3.3 22.5 + - - +
283E LEU* 1.3 78.2 - - - +
285E PRO* 1.3 64.4 - - - +
286E ARG* 4.8 2.3 - - - +
312E TYR* 5.5 0.2 + - - -
336E GLY 3.8 1.0 - - - +
337E LEU* 3.6 5.6 - - - +
338E THR* 2.9 49.6 + - - +
340E ARG* 3.3 30.8 + - - -
342E TYR* 5.1 1.2 + - - -
137F ARG* 5.8 0.9 - - - -
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Residues in contact with PRO 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E LYS* 3.5 2.9 - - - +
267E VAL* 3.0 46.6 + - + +
269E PHE* 4.0 22.0 - - + -
283E LEU* 3.3 12.6 - - + +
284E GLU* 1.3 87.2 - - - +
286E ARG* 1.3 60.4 + - - +
336E GLY 3.5 7.2 - - - +
337E LEU* 3.7 12.8 - - + -
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Residues in contact with ARG 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E ASP* 3.4 25.1 + - - +
265E GLY 3.3 13.9 - - - +
266E LYS* 4.5 18.1 - - + +
284E GLU 4.8 2.5 - - - +
285E PRO* 1.3 77.2 - - - +
287E ALA* 1.3 64.3 + - - +
312E TYR* 5.1 9.8 - - - +
313E SER* 5.8 1.8 + - - +
316E PHE* 3.5 57.3 - - + +
334E SER 3.9 0.2 - - - +
335E THR* 3.3 4.9 - - - -
336E GLY 2.9 37.5 + - - +
133F GLN* 6.0 2.2 - - - +
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Residues in contact with ALA 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E ASP* 3.1 3.6 - - - +
265E GLY 2.9 33.7 + - - +
286E ARG* 1.3 75.6 - - - +
288E GLN* 1.3 60.9 + - - +
316E PHE* 4.7 0.7 - - - -
333E VAL* 5.2 1.1 - - + -
334E SER 3.4 5.6 - - - +
335E THR* 4.5 12.3 - - + +
602E C8E 3.6 30.8 - - + +
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Residues in contact with GLN 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LYS* 3.6 33.2 + - + +
263E VAL 3.2 11.9 - - - +
264E ASP* 3.0 29.1 - - + +
287E ALA* 1.3 76.4 - - - +
289E TYR* 1.3 63.2 + - - +
290E LEU* 4.1 19.2 + - - +
315E LEU 4.8 0.4 + - - -
316E PHE* 3.3 48.9 + - + +
317E ARG 5.0 1.8 + - - -
332E GLN* 3.7 1.3 - - - +
333E VAL* 3.3 7.5 - - - +
334E SER* 2.9 44.0 + - - +
602E C8E 4.8 1.1 - - - -
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Residues in contact with TYR 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E PHE* 3.9 25.1 - + - -
262E LYS* 3.3 7.3 - - - +
263E VAL* 2.9 39.7 + - + +
288E GLN* 1.3 75.2 - - - +
290E LEU* 1.3 67.2 + - - +
291E TYR* 3.7 29.9 - - + -
331E ASN* 2.5 30.6 + - - -
332E GLN 3.2 18.6 - - - -
333E VAL* 3.8 11.4 - - + +
360E PHE* 4.1 6.7 - + - -
602E C8E 3.2 61.0 + - + +
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Residues in contact with LEU 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E GLN* 3.8 25.4 - - + +
261E PHE 3.6 13.7 - - - +
262E LYS* 3.8 19.3 - - + -
288E GLN* 4.1 14.1 + - - +
289E TYR* 1.3 80.5 - - - +
291E TYR* 1.3 62.1 + - - +
292E VAL* 4.7 1.3 - - + -
317E ARG 4.8 1.1 - - - +
318E ASP* 3.8 33.2 - - + +
330E ALA* 3.8 20.4 - - + -
331E ASN* 3.3 6.2 + - - -
332E GLN* 2.9 55.8 + - + +
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Residues in contact with TYR 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E PRO* 5.4 2.0 - - + -
260E GLN* 3.5 1.6 - - - -
261E PHE* 2.9 52.5 + - + +
289E TYR* 3.7 31.2 - + + -
290E LEU* 1.3 74.2 - - - +
292E VAL* 1.3 67.8 + - - +
293E PRO* 4.0 33.5 - - + +
330E ALA 3.4 14.1 - - - -
331E ASN* 4.2 12.1 - - + -
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Residues in contact with VAL 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E LEU* 5.5 1.1 - - + -
258E LEU* 4.5 8.3 - - + -
259E PRO 4.1 3.6 - - - +
260E GLN* 3.7 32.3 - - + +
290E LEU* 4.7 3.8 - - + -
291E TYR* 1.3 83.0 - - - +
293E PRO* 1.3 83.8 - - + +
318E ASP 5.5 2.7 - - - +
327E ILE* 4.2 19.5 - - + -
328E ALA 3.7 15.3 - - - +
329E SER* 3.4 2.8 - - - -
330E 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