Contacts of the helix formed by residues 335 - 353 (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 ARG 335 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E ILE 3.5 3.0 + - - -
334E SER* 1.3 71.9 - - - +
336E ALA* 1.3 58.6 + - - +
338E TRP* 3.8 1.3 - - - +
339E ASN* 2.9 37.6 + - - +
389E GLN* 4.0 28.3 + - - +
403E GLY 5.2 1.8 + - - -
404E THR* 3.4 18.1 + - - +
405E GLU 4.1 3.2 + - - -
410E GLY* 3.2 29.4 - - - +
411E ASN* 2.3 43.7 + - - +
412E ASP* 2.9 25.3 + - - +
414E ILE* 3.8 36.9 - - + +
514E NAG 3.6 18.6 - - - +
517E NAG 5.4 4.2 - - - +
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Residues in contact with ALA 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E SER* 3.2 8.8 + - - +
335E ARG* 1.3 78.6 - - - +
337E GLN* 1.3 58.9 + - + +
339E ASN* 3.1 3.5 + - - +
340E ASN* 2.6 41.0 + - - +
412E ASP* 4.2 1.4 + - - +
514E NAG 4.2 22.7 + - - -
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Residues in contact with GLN 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E SER 4.6 3.2 - - - +
292E VAL* 4.1 19.5 - - + +
293E LYS* 4.0 22.7 + - - +
334E SER* 3.6 23.4 + - - +
335E ARG 3.5 0.4 - - - -
336E ALA* 1.3 74.6 - - + +
338E TRP* 1.3 62.9 + - - +
340E ASN* 3.8 9.4 - - - +
341E THR* 2.9 33.6 + - - -
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Residues in contact with TRP 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E LEU* 5.0 2.9 - - + -
292E VAL* 4.7 10.4 - - + +
333E ILE* 4.3 13.0 - - + -
334E SER 3.0 20.2 + - - +
335E ARG* 3.8 2.9 - - - +
337E GLN* 1.3 76.8 - - - +
339E ASN* 1.3 62.7 + - - +
341E THR* 3.3 16.3 + - + -
342E LEU* 2.9 53.3 + - + +
389E GLN 5.2 1.1 - - - -
390E LEU* 2.7 61.2 + - + +
391E PHE* 3.9 12.8 - + - -
414E ILE* 4.0 22.7 - - + -
449E ILE* 4.6 18.4 - - + -
452E LEU* 3.9 33.7 - - + -
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Residues in contact with ASN 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E ARG* 2.9 16.5 + - - +
336E ALA 3.1 3.8 + - - +
338E TRP* 1.3 81.7 - - - +
340E ASN* 1.3 58.2 + - - +
342E LEU* 3.3 14.3 + - - +
343E LYS* 3.0 26.5 + - - +
395E TRP* 3.7 5.8 - - - -
404E THR* 3.3 30.4 + - - +
514E NAG 1.4 77.6 + - - +
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Residues in contact with ASN 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E ALA* 2.6 29.0 + - - +
337E GLN* 3.8 8.1 - - - +
338E TRP 3.3 0.2 - - - -
339E ASN* 1.3 76.6 - - - +
341E THR* 1.3 66.0 + - - +
343E LYS* 3.2 11.7 + - - +
344E GLN* 3.2 33.9 + - - +
514E NAG 5.2 2.4 + - - +
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Residues in contact with THR 341 (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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288E LEU* 3.7 39.0 - - + +
290E GLU* 4.9 2.9 + - - +
292E VAL* 3.1 20.7 - - + +
337E GLN 2.9 19.2 + - - -
338E TRP* 3.6 17.7 - - + -
340E ASN* 1.3 72.9 - - - +
342E LEU* 1.3 61.3 + - + +
344E GLN* 3.2 13.3 + - + +
345E ILE* 3.0 41.4 + - + +
452E LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 342 (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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338E TRP* 2.9 59.7 + - + +
339E ASN* 3.5 9.4 - - - +
340E ASN 3.3 0.2 - - - -
341E THR* 1.3 76.3 - - - +
343E LYS* 1.3 56.7 + - - +
345E ILE* 3.3 12.4 + - + +
346E VAL* 2.9 35.8 + - - +
361E PHE* 3.8 31.4 - - + -
390E LEU 4.1 7.2 - - - +
391E PHE* 5.3 2.7 - - + -
393E SER* 4.3 14.8 - - - +
395E TRP* 3.5 24.9 - - + -
404E THR* 5.2 1.6 - - + -
452E LEU* 5.6 0.9 - - + -
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Residues in contact with LYS 343 (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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339E ASN 3.0 13.9 + - - +
340E ASN* 3.4 15.0 - - - +
342E LEU* 1.3 78.5 - - - +
344E GLN* 1.3 64.5 + - - +
346E VAL* 3.5 2.8 + - - +
347E GLU* 3.2 29.6 + - - +
395E TRP* 3.9 15.9 - - + -
398E THR* 3.4 34.1 + - - +
399E GLU* 3.8 23.8 - - + -
514E NAG 5.4 5.2 - - - +
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Residues in contact with GLN 344 (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 VAL* 3.1 32.2 - - + +
288E LEU* 5.8 0.3 - - - +
289E ASN* 3.1 28.3 + - - +
290E GLU* 5.0 10.6 + - - +
340E ASN* 3.2 23.9 + - - +
341E THR* 3.2 12.6 + - + +
343E LYS* 1.3 78.9 - - + +
345E ILE* 1.3 66.7 + - - +
346E VAL 3.1 1.6 - - - -
347E GLU* 3.1 17.2 + - - +
348E LYS* 3.0 28.8 + - - +
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Residues in contact with ILE 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E VAL* 4.9 5.6 - - + -
272E ILE* 5.3 3.3 - - + +
286E VAL* 4.0 27.1 - - + -
288E LEU* 4.3 4.0 - - + -
338E TRP* 5.8 0.2 - - + -
341E THR* 3.0 30.3 + - + +
342E LEU* 3.7 13.9 - - + +
344E GLN* 1.3 75.0 - - + +
346E VAL* 1.3 57.9 + - - +
348E LYS* 3.5 5.0 + - - +
349E LEU* 2.9 39.7 + - + +
361E PHE* 3.9 20.0 - - + -
452E LEU* 3.9 33.9 - - + -
454E LEU* 4.3 11.0 - - + -
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Residues in contact with VAL 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E LEU 2.9 21.6 + - - +
343E LYS 3.8 5.4 - - - +
344E GLN 3.1 0.2 - - - -
345E ILE* 1.3 74.8 - - - +
347E GLU* 1.3 60.9 + - - +
350E ARG* 2.9 45.3 + - + +
359E ILE* 3.5 24.6 - - + +
361E PHE* 3.6 19.7 - - + -
395E TRP* 3.5 42.4 - - + -
397E ASP 4.2 9.9 - - - +
398E THR* 4.7 1.6 - - - -
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Residues in contact with GLU 347 (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 LYS* 3.1 33.1 + - - +
270E VAL* 5.8 1.0 + - - +
343E LYS* 3.2 17.6 + - - +
344E GLN* 3.1 22.9 + - - +
346E VAL* 1.3 78.4 - - - +
348E LYS* 1.3 70.8 + - + +
350E ARG* 4.1 3.9 - - - +
351E GLU* 3.3 24.7 + - - +
398E THR* 3.7 26.0 - - + +
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Residues in contact with LYS 348 (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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232E THR* 6.2 2.2 - - - +
269E LYS* 4.1 21.6 - - - +
270E VAL* 3.2 42.7 + - + +
271E VAL* 5.1 1.8 - - - +
272E ILE* 3.5 34.1 - - + +
344E GLN 3.0 16.5 + - - +
345E ILE 4.0 2.9 - - - +
347E GLU* 1.3 92.9 - - + +
349E LEU* 1.3 66.5 + - - +
351E GLU* 3.6 30.1 + - - +
352E GLN* 3.6 12.3 + - - +
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Residues in contact with LEU 349 (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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272E ILE* 3.6 23.6 - - + -
284E ILE* 4.3 8.5 - - + -
345E ILE* 2.9 34.2 + - + +
348E LYS* 1.3 75.0 - - - +
350E ARG* 1.3 61.4 + - - +
352E GLN* 3.1 2.9 + - - -
353E PHE* 2.9 49.1 + - + +
359E ILE* 3.5 21.5 - - + -
361E PHE* 4.4 6.7 - - + -
454E LEU* 4.6 4.9 - - + -
468E PHE* 3.5 52.7 - - + -
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Residues in contact with ARG 350 (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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346E VAL* 2.9 34.1 + - + +
347E GLU* 4.1 3.8 - - - +
349E LEU* 1.3 73.8 - - - +
351E GLU* 1.3 68.8 + - - +
353E PHE* 4.4 3.8 - - - +
354E ASN 3.1 3.1 + - - -
356E ASN* 2.9 73.2 + - - +
357E LYS 3.9 20.2 - - - +
359E ILE* 4.1 7.4 - - + -
395E TRP 5.2 0.2 - - - -
396E ASN 3.6 25.3 + - - -
397E ASP* 4.1 19.6 + - - +
398E THR* 4.1 23.4 - - - +
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Residues in contact with GLU 351 (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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347E GLU* 3.3 12.1 + - - +
348E LYS* 3.6 39.2 + - - +
350E ARG* 1.3 83.1 - - - +
352E GLN* 1.3 61.7 + - + +
353E PHE 3.2 0.2 + - - -
354E ASN* 3.6 7.4 + - - +
356E ASN* 4.9 2.9 - - - -
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Residues in contact with GLN 352 (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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272E ILE* 4.3 9.1 - - + +
277E PHE* 3.1 61.8 - - + +
348E LYS 3.6 8.8 + - - +
349E LEU 3.1 8.3 + - - +
351E GLU* 1.3 80.5 - - + +
353E PHE* 1.3 69.2 + - + +
354E ASN* 3.6 4.9 - - - +
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Residues in contact with PHE 353 (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* 3.9 35.0 - + + -
284E ILE* 4.4 2.5 - - + -
349E LEU* 2.9 38.3 + - + +
350E ARG* 4.6 2.2 - - - +
351E GLU 3.2 0.4 - - - -
352E GLN* 1.3 86.8 - - + +
354E ASN* 1.3 72.0 + - - +
356E ASN 3.3 2.9 - - - -
357E LYS* 3.3 25.0 + - + +
359E ILE* 5.2 5.8 - - + -
456E ARG* 3.1 45.3 - - - -
466E GLU* 4.4 20.6 - - + -
468E PHE* 3.5 27.1 - + - -
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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
------------------------------------------------------------
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