Contacts of the strand formed by residues 443 - 456 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297E THR* 3.2 25.6 - - - -
298E ARG* 3.3 28.3 + - + +
378E CYS* 3.2 44.9 - - + +
379E GLY* 4.3 10.8 - - - +
381E GLU* 3.4 37.7 - - + +
383E PHE* 4.2 7.9 - - + -
438E PRO* 4.7 7.6 - - + -
439E ILE 5.8 1.8 - - - +
441E GLY 3.7 13.2 - - - +
442E GLN* 1.3 73.9 - - - +
444E ARG* 1.3 62.9 + - - +
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Residues in contact with ARG 444 (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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296E CYS 3.6 4.5 - - - -
297E THR* 3.7 25.0 + - + +
299E PRO* 5.2 1.0 - - - +
378E CYS* 4.3 0.2 - - - -
442E GLN* 3.4 36.0 + - + +
443E ILE* 1.3 81.8 - - - +
445E CYS* 1.3 63.1 + - - +
519E CL 2.5 37.6 - - - +
1G NAG 4.2 15.6 + - - -
2G NAG 4.4 1.8 + - - -
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Residues in contact with CYS 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E ILE 3.8 1.4 - - - +
295E ASN* 3.7 2.4 - - - -
296E CYS* 3.0 38.2 + - - +
297E THR* 4.7 0.4 - - - +
376E PHE* 4.7 8.7 - - - -
377E ASN 5.1 0.9 - - - -
378E CYS* 2.0 47.1 - - - -
379E GLY 5.4 0.7 - - - +
444E ARG* 1.3 75.6 - - - +
446E SER* 1.3 58.8 + - - +
447E SER* 4.0 8.8 + - - -
511E NAG 3.9 27.4 - - - +
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Residues in contact with SER 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E LYS* 3.4 32.1 + - - +
294E ILE 3.4 4.0 - - - -
295E ASN* 2.5 25.1 + - - -
445E CYS* 1.3 73.9 - - - +
447E SER* 1.3 60.3 + - - +
448E ASN 4.4 0.3 + - - -
511E NAG 3.5 25.9 + - - +
513E NAG 3.6 16.1 + - - -
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Residues in contact with SER 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E LEU* 3.7 23.7 - - - +
262E ASN* 3.9 6.5 - - - -
293E LYS* 4.7 2.0 - - - -
294E ILE* 2.8 50.5 + - - +
445E CYS* 4.0 8.1 + - - -
446E SER* 1.3 71.6 + - - +
448E ASN* 1.3 62.8 + - - +
449E ILE 3.5 0.2 + - - -
511E NAG 2.6 40.6 + - - -
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Residues in contact with ASN 448 (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 LEU* 3.3 6.2 - - - +
262E ASN* 3.0 33.2 + - - +
291E SER* 3.8 24.9 + - - -
292E VAL 3.6 3.8 - - - -
293E LYS* 2.8 34.0 - - - +
446E SER 4.4 0.2 + - - -
447E SER* 1.3 72.9 - - - +
449E ILE* 1.3 62.3 + - - +
450E THR* 4.0 10.0 - - + +
518E NAG 1.5 60.3 + - - +
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Residues in contact with ILE 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E LEU* 4.0 33.4 - - + -
260E LEU 3.5 7.2 - - - +
261E LEU* 4.1 8.5 - - + -
288E LEU* 3.3 19.5 - - + +
291E SER* 3.8 1.4 - - - -
292E VAL* 2.7 48.6 + - + +
294E ILE* 3.9 26.0 - - + -
333E ILE* 4.1 14.1 - - + -
338E TRP* 4.6 10.3 - - + -
448E ASN* 1.3 74.0 - - - +
450E THR* 1.3 59.0 + - - +
451E GLY 3.7 20.6 - - - +
452E LEU* 4.5 8.5 - - + -
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Residues in contact with THR 450 (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 LEU* 3.0 10.6 + - - +
262E ASN 4.1 2.5 - - - +
263E GLY* 2.7 55.4 + - - +
264E SER 4.3 2.9 + - - +
265E LEU* 3.9 25.7 - - + +
287E GLN* 3.9 8.1 - - - +
288E LEU* 3.4 25.0 + - - -
291E SER* 4.4 1.8 - - - -
448E ASN* 4.0 20.4 - - + +
449E ILE* 1.3 76.1 - - - +
451E GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 451 (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 LEU 3.9 0.5 - - - -
260E LEU* 2.9 37.5 + - - -
286E VAL 2.9 14.4 - - - -
288E LEU* 4.2 3.2 - - - +
449E ILE* 3.5 8.6 + - - +
450E THR* 1.3 80.9 - - - +
452E LEU* 1.3 73.6 + - - +
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Residues in contact with LEU 452 (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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258E GLN 4.4 4.5 - - - +
259E LEU* 4.3 10.5 - - + -
260E LEU* 4.3 1.4 - - - +
285E ILE* 4.3 0.9 - - - +
286E VAL* 2.9 44.5 + - + +
288E LEU* 4.3 14.6 - - + -
338E TRP* 3.9 22.2 - - + -
341E THR* 5.1 0.4 - - + -
342E LEU* 5.6 2.0 - - + -
345E ILE* 3.9 27.8 - - + -
361E PHE* 6.1 0.4 - - + -
391E PHE* 3.9 29.8 - - + -
449E ILE* 4.5 9.4 - - + -
451E GLY* 1.3 88.3 - - - +
453E LEU* 1.3 70.8 + - - +
454E LEU* 4.0 14.6 - - + -
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Residues in contact with LEU 453 (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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256E SER 5.1 0.4 - - - +
257E THR 4.3 5.2 - - - +
258E GLN 3.6 10.2 + - - +
260E LEU* 3.9 27.6 - - + -
283E THR* 4.4 7.9 - - + -
284E ILE 3.6 2.2 - - - +
285E ILE* 3.9 32.3 - - + -
452E LEU* 1.3 81.3 - - - +
454E LEU* 1.3 58.4 + - - +
470E PRO* 3.3 6.8 - - - +
471E GLY 2.7 45.6 + - - +
472E GLY* 3.6 24.9 - - - -
477E ASP* 4.3 17.3 - - + +
478E ASN* 4.1 15.3 - - - +
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Residues in contact with LEU 454 (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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283E THR* 3.8 1.6 - - - +
284E ILE* 2.9 40.8 + - + +
286E VAL* 4.0 23.3 - - + -
345E ILE* 4.3 11.9 - - + -
349E LEU* 4.6 9.0 - - + -
361E PHE* 4.1 26.2 - - + -
391E PHE* 4.3 11.7 - - + -
452E LEU* 4.1 23.1 - - + -
453E LEU* 1.3 78.8 - - - +
455E THR* 1.3 68.4 + - - +
468E PHE* 4.5 16.4 - - + -
469E ARG 3.1 15.5 - - - +
470E PRO* 4.2 7.4 - - + -
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Residues in contact with THR 455 (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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280E ASN 4.5 3.1 - - - -
281E ALA 6.1 0.7 - - - -
282E LYS 5.0 5.6 - - - -
283E THR* 4.5 17.9 - - + +
284E ILE* 4.9 3.6 - - - +
454E LEU* 1.3 79.7 - - - +
456E ARG* 1.3 61.5 + - - +
457E ASP* 4.2 0.3 + - - -
467E ILE 3.8 0.2 - - - +
468E PHE* 3.3 5.9 - - - -
469E ARG* 2.9 41.9 + - - +
470E PRO 5.2 0.8 + - - +
471E GLY* 4.6 16.4 - - - -
472E GLY 5.6 0.7 - - - +
35F LYS* 3.2 23.2 + - - +
40F GLN* 5.3 6.5 - - - +
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Residues in contact with ARG 456 (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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277E PHE 3.3 14.7 + - - +
278E THR* 3.0 33.3 + - - +
280E ASN* 3.2 19.8 + - - +
282E LYS 5.5 1.0 + - - -
284E ILE* 5.2 5.3 - - + +
353E PHE* 3.1 41.8 - - - -
455E THR* 1.3 75.0 - - - +
457E ASP* 1.3 63.6 + - - +
458E GLY* 3.3 22.4 - - - -
466E GLU* 3.1 30.8 + - - +
467E ILE 3.0 14.1 - - - +
468E PHE* 3.5 20.8 - - + -
35F LYS* 3.2 16.2 + - - -
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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