Contacts of the strand formed by residues 443 - 456 (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 443 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297O THR* 3.1 22.1 + - - -
298O ARG* 3.5 14.8 + - - +
378O CYS* 3.7 17.0 - - - +
379O GLY* 4.9 17.0 - - - +
381O GLU* 2.4 34.1 - - + +
383O PHE* 3.5 27.8 - - + -
438O PRO* 5.5 4.9 - - + -
439O ILE 5.1 9.0 - - - +
440O LYS 5.7 0.4 - - - +
441O GLY* 4.4 7.2 - - - +
442O GLN* 1.3 78.5 - - - +
444O ARG* 1.3 62.0 + - - +
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Residues in contact with ARG 444 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296O CYS 3.2 8.1 - - - +
297O THR* 3.9 21.8 + - - +
378O CYS* 4.0 0.2 - - - -
442O GLN* 3.4 44.8 + - - +
443O ILE* 1.3 74.7 - - - +
445O CYS* 1.3 68.0 + - - +
446O SER 4.1 1.6 + - - +
511O NAG 5.2 1.7 + - - -
518O CL 4.0 11.3 - - - +
1R NAG 5.3 5.7 + - - -
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Residues in contact with CYS 445 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294O ILE 3.4 4.5 - - - +
295O ASN* 5.2 0.2 - - - -
296O CYS* 2.8 37.1 + - + +
376O PHE* 5.4 2.7 - - + -
377O ASN 4.8 0.7 - - - -
378O CYS* 2.0 56.3 - - + -
379O GLY* 3.9 4.5 - - - -
444O ARG* 1.3 76.3 - - - +
446O SER* 1.3 63.6 + - - +
447O SER* 3.6 8.2 + - - +
511O NAG 3.3 30.1 - - + +
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Residues in contact with SER 446 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O LYS* 5.0 6.2 + - - +
294O ILE 3.3 3.8 - - - -
295O ASN* 3.2 26.7 + - - +
444O ARG* 4.1 1.6 + - - +
445O CYS* 1.3 72.1 - - - +
447O SER* 1.3 60.2 + - - +
511O NAG 3.4 27.3 + - - +
513O NAG 3.6 20.2 + - - -
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Residues in contact with SER 447 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261O LEU* 4.2 15.3 - - - +
262O ASN* 3.9 6.5 - - - -
293O LYS* 3.4 5.5 - - - +
294O ILE* 2.7 52.0 + - - +
296O CYS* 5.9 0.7 - - - -
376O PHE* 6.0 1.9 - - - -
445O CYS* 3.7 11.4 + - - +
446O SER* 1.3 79.1 + - - +
448O ASN* 1.3 65.1 + - - +
449O ILE 3.9 0.2 - - - -
511O NAG 3.4 29.3 + - - +
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Residues in contact with ASN 448 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261O LEU* 3.3 5.3 - - - -
262O ASN* 2.8 38.9 + - - +
291O SER* 4.3 13.5 + - - -
292O VAL 4.0 3.6 - - - -
293O LYS* 4.1 20.8 + - - +
447O SER* 1.3 77.8 - - - +
449O ILE* 1.3 63.2 + - - +
450O THR* 3.2 13.5 - - + +
517O NAG 1.4 64.8 + - - +
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Residues in contact with ILE 449 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259O LEU* 4.0 26.0 - - + -
260O LEU 3.7 5.8 - - - +
261O LEU* 4.4 4.3 - - + -
288O LEU* 4.2 8.8 - - + +
291O SER* 3.3 7.3 - - - -
292O VAL* 2.7 63.9 + - + +
294O ILE* 4.0 19.1 - - + -
333O ILE* 4.0 27.1 - - + -
338O TRP* 4.2 18.4 - - + -
448O ASN* 1.3 71.3 - - - +
450O THR* 1.3 64.3 + - - +
451O GLY 3.9 17.9 - - - +
452O LEU* 4.7 1.6 - - + -
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Residues in contact with THR 450 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260O LEU* 3.0 13.5 + - - +
263O GLY* 2.7 49.9 + - - +
264O SER 4.2 6.2 + - - +
265O LEU* 4.4 10.7 - - + +
287O GLN* 3.9 6.8 - - - +
288O LEU* 3.1 32.6 + - - +
291O SER* 4.4 6.3 - - - -
448O ASN* 3.2 24.5 - - + +
449O ILE* 1.3 81.7 - - - +
451O GLY* 1.3 61.9 + - - +
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Residues in contact with GLY 451 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259O LEU* 3.8 3.1 - - - -
260O LEU* 3.0 32.6 + - - +
286O VAL 2.9 15.9 - - - -
288O LEU* 3.9 8.0 - - - +
449O ILE* 3.7 5.5 - - - +
450O THR* 1.3 82.7 + - - +
452O LEU* 1.3 71.1 + - - +
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Residues in contact with LEU 452 (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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258O GLN 3.7 9.6 - - - +
259O LEU* 4.6 4.3 - - + -
260O LEU* 4.4 3.5 - - - +
285O ILE* 3.8 1.7 - - - +
286O VAL* 2.9 40.2 + - + +
288O LEU* 4.2 17.9 - - + -
338O TRP* 4.1 22.9 - - + -
341O THR* 4.9 0.2 - - + -
342O LEU* 5.4 1.8 - - + -
345O ILE* 3.9 28.7 - - + -
361O PHE* 6.5 0.2 - - + -
391O PHE* 3.6 33.9 - - + -
449O ILE* 4.7 2.9 - - + -
451O GLY* 1.3 83.7 - - - +
453O LEU* 1.3 72.2 + - - +
454O LEU* 4.2 13.9 - - + -
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Residues in contact with LEU 453 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256O SER 5.2 1.6 - - - +
258O GLN 3.0 17.7 + - - +
260O LEU* 3.7 27.4 - - + -
283O THR* 4.1 13.0 - - + -
284O ILE 3.7 0.4 - - - -
285O ILE* 3.9 30.1 - - + -
452O LEU* 1.3 82.0 - - - +
454O LEU* 1.3 65.8 + - - +
470O PRO* 3.5 1.9 - - - +
471O GLY* 2.7 42.2 + - - +
472O GLY* 3.6 22.4 - - - +
473O GLY 4.9 0.2 - - - +
474O ASP 5.5 0.2 - - - +
477O ASP* 4.3 14.8 - - + +
478O ASN* 4.1 15.5 - - - +
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Residues in contact with LEU 454 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283O THR* 3.3 7.8 - - - +
284O ILE* 2.9 44.2 + - + +
286O VAL* 4.2 19.1 - - + -
345O ILE* 4.5 14.6 - - + -
349O LEU* 4.9 8.5 - - + -
361O PHE* 4.9 7.4 - - + -
391O PHE* 4.1 21.1 - - + -
452O LEU* 4.3 17.7 - - + -
453O LEU* 1.3 84.1 - - - +
455O THR* 1.3 64.4 + - - +
468O PHE* 4.7 21.8 - - + -
469O ARG* 3.4 18.4 - - - +
470O PRO* 3.8 8.7 - - + -
471O GLY 4.1 0.2 - - - +
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Residues in contact with THR 455 (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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35B LYS* 3.6 20.6 + - - -
40B GLN* 6.0 4.5 - - - +
280O ASN 4.5 4.9 - - - -
281O ALA 6.5 0.4 - - - -
282O LYS 5.0 2.7 - - - -
283O THR* 4.5 14.4 - - + +
284O ILE* 4.9 4.3 - - - +
454O LEU* 1.3 79.5 - - - +
456O ARG* 1.3 61.0 + - - +
457O ASP* 4.6 0.7 + - - +
468O PHE* 3.3 5.6 - - - -
469O ARG* 2.9 41.4 + - - +
470O PRO 4.9 1.5 + - - +
471O GLY* 4.1 20.4 - - - -
472O GLY 5.3 0.2 - - - +
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Residues in contact with ARG 456 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 2.8 26.4 + - - +
277O PHE 3.1 24.5 + - - +
278O THR* 3.3 20.2 + - - +
279O ASP 4.1 6.0 + - - +
280O ASN* 3.2 19.7 + - - +
282O LYS 5.4 1.3 + - - +
284O ILE* 4.5 8.0 - - + +
353O PHE* 3.3 36.5 - - - -
455O THR* 1.3 74.3 - - - +
457O ASP* 1.3 63.0 + - - +
458O GLY* 3.4 27.2 - - - -
459O GLY 4.9 0.2 - - - +
466O GLU* 2.9 29.5 + - - +
467O ILE 3.0 13.5 - - - +
468O PHE* 3.5 23.1 - - + -
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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