Contacts of the strand formed by residues 284 - 298 (chain O) in PDB entry 4R2G
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 ILE 284 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272O ILE* 4.0 20.2 - - + -
273O ARG 3.2 9.4 - - - +
274O SER* 4.2 15.0 - - - +
277O PHE* 4.0 22.2 - - + +
282O LYS 3.7 4.5 + - - +
283O THR* 1.3 75.0 - - - +
285O ILE* 1.3 71.3 + - - +
286O VAL* 3.8 8.4 + - + +
349O LEU* 4.5 5.6 - - + -
353O PHE* 4.5 7.9 - - + -
453O LEU* 3.7 3.1 - - - -
454O LEU* 2.9 48.8 + - + +
455O THR* 5.3 1.3 - - - -
456O ARG* 4.5 9.4 - - + +
468O PHE* 3.9 30.3 - - + -
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Residues in contact with ILE 285 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O MET* 4.2 5.4 - - + -
96O TRP* 3.8 28.9 - - + -
260O LEU* 4.6 1.8 - - + -
271O VAL 3.8 0.3 - - - +
272O ILE* 3.3 4.5 - - - -
273O ARG* 2.8 50.2 + - + +
283O THR* 4.8 2.7 - - + +
284O ILE* 1.3 74.7 - - - +
286O VAL* 1.3 70.9 + - - +
287O GLN* 5.0 1.6 - - + +
452O LEU 3.8 8.5 - - - +
453O LEU* 3.9 15.3 - - + -
477O ASP* 3.4 30.7 - - + +
480O ARG* 4.1 8.3 - - + -
481O SER* 3.8 31.0 - - - +
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Residues in contact with VAL 286 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260O LEU* 5.1 1.2 - - - +
270O VAL* 5.7 2.7 - - + -
271O VAL 3.5 8.1 - - - +
272O ILE* 3.8 19.5 - - + -
284O ILE* 4.3 9.2 - - + +
285O ILE* 1.3 82.6 - - - +
287O GLN* 1.3 62.1 + - - +
288O LEU* 4.0 13.9 - - + -
345O ILE* 3.7 31.0 - - + -
349O LEU* 6.3 0.4 - - + -
451O GLY* 2.9 26.2 - - - -
452O LEU* 2.9 25.2 + - + +
454O LEU* 4.2 25.6 - - + -
481O SER* 6.0 0.2 - - - -
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Residues in contact with GLN 287 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264O SER* 3.5 22.6 + - - +
265O LEU 3.5 3.0 + - - -
266O ALA* 3.3 41.6 - - + +
270O VAL* 3.5 4.5 - - - +
271O VAL* 2.9 37.4 + - + +
273O ARG* 3.4 29.3 + - - +
285O ILE* 4.1 1.7 + - + -
286O VAL* 1.3 74.3 - - - +
288O LEU* 1.3 65.8 + - - +
450O THR 3.9 4.3 - - - +
481O SER* 4.8 8.6 + - - +
484O TYR* 3.3 30.8 + - - -
485O LYS* 5.5 1.2 - - - +
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Residues in contact with LEU 288 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265O LEU* 3.1 12.2 - - + +
266O ALA* 2.8 28.9 + - - -
270O VAL* 4.1 7.2 - - + -
286O VAL* 4.0 22.2 - - + -
287O GLN* 1.3 73.4 - - - +
289O ASN* 1.3 59.2 + - - +
290O GLU 3.4 22.2 - - - +
292O VAL* 4.4 8.1 - - + -
341O THR* 3.6 35.0 - - + -
345O ILE* 4.1 8.7 - - + -
449O ILE* 4.2 23.1 - - + +
450O THR 3.1 24.9 + - - +
451O GLY* 3.9 4.3 - - - +
452O LEU* 4.2 5.2 - - + -
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Residues in contact with ASN 289 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265O LEU* 3.5 12.0 - - - +
266O ALA* 3.6 12.8 - - - +
268O GLU* 2.6 32.1 + - - +
269O LYS* 3.7 12.7 - - - +
270O VAL* 3.1 26.9 - - + +
288O LEU* 1.3 75.7 - - - +
290O GLU* 1.3 62.6 + - + +
344O GLN* 3.6 13.4 + - - +
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Residues in contact with GLU 290 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265O LEU* 3.6 7.2 - - + -
288O LEU* 3.4 20.6 - - - +
289O ASN* 1.3 81.1 - - + +
291O SER* 1.3 73.7 + - - +
292O VAL* 4.4 3.5 - - - +
337O GLN* 4.6 12.8 + - - +
341O THR* 5.1 1.2 + - - +
344O GLN* 5.1 7.2 + - - +
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Residues in contact with SER 291 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265O LEU* 3.6 23.1 - - - +
290O GLU* 1.3 88.0 - - - +
292O VAL* 1.3 64.3 + - - +
293O LYS* 4.1 4.2 + - - +
337O GLN* 4.1 9.9 + - - +
448O ASN* 4.3 18.9 + - - -
449O ILE 3.3 16.6 - - - -
450O THR* 4.4 1.6 - - - -
517O NAG 4.0 21.0 + - - -
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Residues in contact with VAL 292 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288O LEU* 4.4 7.0 - - + -
290O GLU 4.4 6.5 - - - +
291O SER* 1.3 77.9 - - - +
293O LYS* 1.3 65.5 + - - +
333O ILE* 4.3 17.5 - - + -
334O SER* 5.2 0.7 - - - +
337O GLN* 3.5 35.4 - - + +
338O TRP* 4.5 6.5 - - + +
341O THR* 3.2 29.4 - - + +
448O ASN* 4.7 0.7 - - - -
449O ILE* 2.7 61.7 + - + +
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Residues in contact with LYS 293 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291O SER* 4.1 4.6 + - - +
292O VAL* 1.3 84.1 - - - +
294O ILE* 1.3 59.8 + - - +
295O ASN* 4.0 9.6 - - - +
332O ASN 4.0 6.4 - - - +
333O ILE* 4.2 8.8 - - - +
334O SER* 4.5 0.5 + - - -
337O GLN* 4.3 15.1 + - - +
446O SER* 5.0 4.2 + - - +
447O SER 3.4 7.2 - - - +
448O ASN* 4.1 19.3 + - - +
513O NAG 3.9 47.9 - - + +
517O NAG 4.7 16.9 + - - -
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Residues in contact with ILE 294 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259O LEU* 4.6 4.3 - - + -
261O LEU* 4.0 15.3 - - + -
292O VAL 3.6 0.2 + - - -
293O LYS* 1.3 74.5 - - - +
295O ASN* 1.3 66.5 + - - +
296O CYS* 4.5 8.5 - - - -
331O CYS* 4.3 19.3 - - + -
332O ASN 3.6 2.5 - - - +
333O ILE* 3.5 31.2 - - + -
374O HIS* 4.1 27.6 - - + +
376O PHE* 5.5 0.2 - - + -
416O LEU* 4.8 2.5 - - + -
445O CYS 3.4 1.6 - - - +
446O SER* 3.3 0.9 - - - -
447O SER* 2.7 64.5 + - - +
449O ILE* 4.0 13.9 - - + -
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Residues in contact with ASN 295 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293O LYS* 4.0 1.0 - - - +
294O ILE* 1.3 88.0 + - - +
296O CYS* 1.3 59.7 + - - +
330O HIS 3.6 0.7 - - - +
331O CYS* 3.0 4.9 - - - -
332O ASN* 2.6 39.2 + - + +
445O CYS 3.7 3.6 - - - -
446O SER* 3.2 14.2 + - - +
513O NAG 1.5 61.8 + - - +
1R NAG 3.7 27.1 + - + +
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Residues in contact with CYS 296 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294O ILE* 4.5 12.8 - - - -
295O ASN* 1.3 76.0 - - - +
297O THR* 1.3 65.8 + - - +
330O HIS 3.2 4.0 - - - +
331O CYS* 2.2 45.5 - - - -
376O PHE* 3.2 28.0 - - + -
378O CYS* 5.1 0.2 - - - -
383O PHE* 4.0 8.3 - - + -
444O ARG* 3.2 4.2 - - - +
445O CYS* 2.8 42.7 + - + +
447O SER* 5.9 0.9 - - - -
1R NAG 5.3 0.2 - - - -
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Residues in contact with THR 297 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296O CYS* 1.3 78.8 - - - +
298O ARG* 1.3 61.5 + - - +
299O PRO* 3.7 20.7 - - + +
327O ARG* 6.1 0.4 - - - +
329O ALA* 3.1 5.2 - - - +
330O HIS* 3.0 59.8 + - + +
383O PHE* 3.7 8.6 - - - -
443O ILE 3.1 16.5 + - - -
444O ARG* 3.9 22.8 + - - +
1R NAG 4.6 11.2 - - + +
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Residues in contact with ARG 298 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297O THR* 1.3 71.8 + - - +
299O PRO* 1.3 67.2 - - + +
300O SER* 3.8 20.0 + - - +
302O ASN* 3.7 40.0 - - - +
327O ARG 6.0 0.2 - - - +
329O ALA* 4.0 7.4 - - + +
381O GLU* 3.1 38.7 + - - +
383O PHE* 3.5 3.0 - - + -
420O ILE* 3.4 26.5 - - + -
438O PRO* 4.6 14.8 - - - +
440O LYS* 5.7 0.8 - - - +
441O GLY 2.6 33.5 + - - +
442O GLN* 3.7 2.4 - - - -
443O ILE* 3.5 23.6 + - - +
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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