Contacts of the strand formed by residues 284 - 298 (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 284 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ILE* 4.0 20.0 - - + -
273E ARG 3.4 10.1 - - - +
274E SER* 4.4 5.2 - - - -
277E PHE* 4.0 31.4 - - + +
282E LYS 4.4 6.5 - - - +
283E THR* 1.3 74.5 - - - +
285E ILE* 1.3 72.6 + - - +
286E VAL* 4.0 7.9 + - + +
349E LEU* 4.3 7.4 - - + -
353E PHE* 4.4 4.9 - - + -
452E LEU 3.9 0.3 - - - +
453E LEU* 3.6 4.3 - - - -
454E LEU* 2.9 44.6 + - + +
455E THR* 5.3 1.1 - - - -
456E ARG* 5.2 6.7 - - + +
468E PHE* 3.8 31.6 - - + -
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Residues in contact with ILE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E MET* 4.3 6.3 - - + -
96E TRP* 3.4 35.9 - - + -
260E LEU* 4.5 1.6 - - + -
271E VAL 4.0 0.7 - - - +
272E ILE* 3.4 3.3 - - - -
273E ARG* 2.9 45.7 + - + +
283E THR* 4.5 3.1 - - + +
284E ILE* 1.3 76.2 - - - +
286E VAL* 1.3 70.3 + - - +
287E GLN* 6.1 0.7 - - + -
452E LEU 3.7 4.0 - - - +
453E LEU* 3.9 18.4 - - + -
477E ASP* 3.5 29.8 - - + +
480E ARG* 4.1 10.5 - - + -
481E SER* 3.9 24.5 - - - +
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Residues in contact with VAL 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E LEU* 5.0 0.9 - - - +
270E VAL* 4.5 2.0 - - + -
271E VAL 3.6 7.4 - - - +
272E ILE* 4.3 13.2 - - + -
284E ILE* 4.2 11.2 - - + +
285E ILE* 1.3 83.9 - - - +
287E GLN* 1.3 63.2 + - - +
288E LEU* 4.0 13.0 - - + -
345E ILE* 4.0 29.2 - - + -
451E GLY* 2.9 27.0 - - - -
452E LEU* 2.9 31.6 + - + +
454E LEU* 4.0 23.3 - - + -
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Residues in contact with GLN 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E SER* 3.3 26.9 + - - +
265E LEU 3.6 3.2 + - - -
266E ALA* 3.1 39.4 - - + +
270E VAL* 3.3 6.9 - - - +
271E VAL* 2.9 34.8 + - + +
273E ARG* 3.1 40.3 + - - +
285E ILE* 4.3 1.3 - - + -
286E VAL* 1.3 73.7 - - - +
288E LEU* 1.3 63.9 + - - +
450E THR 3.9 4.9 - - - +
481E SER 4.8 6.1 + - - +
484E TYR* 3.4 26.1 + - - -
485E LYS* 5.8 0.4 - - - +
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU* 3.7 7.8 - - + +
266E ALA* 2.9 28.1 + - - +
270E VAL* 4.4 6.1 - - + -
286E VAL* 4.0 19.3 - - + -
287E GLN* 1.3 80.4 - - - +
289E ASN* 1.3 65.4 + - - +
290E GLU 3.7 18.4 - - - +
292E VAL* 4.8 4.9 - - + +
338E TRP* 6.1 0.2 - - + -
341E THR* 3.7 35.9 - - + +
344E GLN* 6.0 0.2 - - - +
345E ILE* 4.3 5.8 - - + -
449E ILE* 3.3 28.3 - - + +
450E THR 3.4 19.9 + - - +
451E GLY* 4.2 1.8 - - - +
452E LEU* 4.3 12.1 - - + -
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Residues in contact with ASN 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU* 3.9 9.0 - - - +
266E ALA 3.7 9.4 - - - +
268E GLU 3.5 25.9 + - - +
269E LYS* 4.3 9.3 - - - +
270E VAL* 3.5 15.2 - - + +
288E LEU* 1.3 74.7 - - - +
290E GLU* 1.3 66.4 + - + +
344E GLN* 3.1 33.4 + - - +
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Residues in contact with GLU 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU* 3.8 13.2 - - + -
288E LEU* 3.7 17.5 - - - +
289E ASN* 1.3 88.8 - - + +
291E SER* 1.3 67.6 + - - +
292E VAL* 4.7 4.1 - - + +
341E THR* 4.9 2.6 + - - +
344E GLN* 5.0 10.1 + - - +
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Residues in contact with SER 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU* 3.5 24.7 - - - +
290E GLU* 1.3 82.1 - - - +
292E VAL* 1.3 62.6 + - - +
293E LYS* 4.1 2.0 + - - +
337E GLN* 4.6 5.4 - - - +
448E ASN* 3.8 32.7 + - - -
449E ILE 3.8 8.7 - - - -
450E THR* 4.4 1.1 - - - -
518E NAG 3.7 20.6 + - - -
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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
----------------------------------------------------------
288E LEU* 4.8 2.5 - - + -
290E GLU* 4.7 3.6 - - + +
291E SER* 1.3 76.7 - - - +
293E LYS* 1.3 75.5 + - - +
333E ILE* 3.9 20.4 - - + -
334E SER 5.2 0.7 - - - +
337E GLN* 4.0 30.3 - - + +
338E TRP* 4.8 8.5 - - + +
341E THR* 3.1 32.5 - - + +
448E ASN* 4.4 1.6 - - - -
449E ILE* 2.7 54.7 + - + +
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Residues in contact with LYS 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E SER* 4.1 1.9 + - - +
292E VAL* 1.3 85.2 - - - +
294E ILE* 1.3 60.4 + - - +
295E ASN* 4.7 0.2 - - - -
332E ASN 4.0 6.3 - - - +
333E ILE* 4.1 8.1 - - - +
334E SER* 4.5 2.9 + - - -
337E GLN* 4.0 10.6 + - - +
446E SER* 3.4 30.3 + - - +
447E SER 3.9 1.1 - - - -
448E ASN* 2.8 31.6 + - - +
513E NAG 4.3 42.1 - - - +
518E NAG 4.7 11.7 + - - -
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Residues in contact with ILE 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E LEU* 4.8 1.3 - - + -
261E LEU* 4.0 12.6 - - + -
293E LYS* 1.3 73.2 - - - +
295E ASN* 1.3 67.1 + - - +
296E CYS* 4.0 22.4 - - - -
331E CYS* 4.3 7.6 - - + -
332E ASN 3.5 2.5 - - - +
333E ILE* 3.5 31.2 - - + -
374E HIS* 4.2 26.0 - - + +
376E PHE* 5.5 0.2 - - + -
416E LEU* 4.8 1.8 - - + -
445E CYS 3.8 1.4 - - - +
446E SER* 3.4 0.5 - - - -
447E SER* 2.8 58.6 + - - +
449E ILE* 3.9 15.3 - - + -
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Residues in contact with ASN 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E ILE* 1.3 74.8 + - - +
296E CYS* 1.3 61.0 - - - +
297E THR* 5.8 1.3 - - + -
331E CYS* 3.0 2.1 - - - -
332E ASN* 2.5 39.9 + - + +
445E CYS 3.7 4.7 - - - +
446E SER* 2.5 26.0 + - - -
513E NAG 1.4 67.4 + - - +
1G NAG 3.4 24.5 + - + +
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Residues in contact with CYS 296 (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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294E ILE* 4.0 14.8 - - - -
295E ASN* 1.3 75.0 - - - +
297E THR* 1.3 71.0 + - - +
330E HIS 3.1 3.8 - - - +
331E CYS* 2.0 49.1 - - - -
376E PHE* 3.4 29.4 - - + -
378E CYS* 4.4 3.1 - - - -
383E PHE* 4.2 7.9 - - + -
444E ARG* 3.6 0.5 - - - -
445E CYS* 3.0 35.2 + - - +
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Residues in contact with THR 297 (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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295E ASN* 5.1 0.9 - - + -
296E CYS* 1.3 85.0 - - - +
298E ARG* 1.3 60.2 + - - +
299E PRO* 3.5 15.5 - - - +
329E ALA* 3.2 4.2 - - - +
330E HIS* 2.9 49.0 + - - -
383E PHE* 4.0 9.0 - - - -
442E GLN* 6.3 0.2 - - - -
443E ILE 3.2 15.3 - - - +
444E ARG* 3.7 39.5 + - + +
445E CYS 4.7 0.2 - - - +
1G NAG 4.5 12.7 - - - +
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Residues in contact with ARG 298 (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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297E THR* 1.3 73.1 - - - +
299E PRO* 1.3 67.2 - - + +
300E SER* 4.3 15.7 + - - +
302E ASN* 3.4 35.0 + - - +
327E ARG 5.9 0.4 - - - +
329E ALA* 4.0 12.6 - - + +
381E GLU* 2.6 45.9 + - - -
383E PHE* 4.2 2.7 - - + -
420E ILE* 3.6 44.5 + - + +
422E GLN* 5.3 7.7 - - - +
437E PRO* 6.2 0.2 - - - +
438E PRO* 5.3 1.4 - - - +
441E GLY 4.3 1.4 - - - +
442E GLN* 4.0 1.4 - - - -
443E ILE* 3.3 34.4 + - + +
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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
------------------------------------------------------------
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