Contacts of the helix formed by residues 398 - 421 (chain E) in PDB entry 2M6I
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 398 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E TRP* 3.4 37.2 - - + -
242E PHE* 4.8 7.6 - - + -
243E TRP* 3.4 41.1 - - + -
246E LEU* 6.0 1.8 - - + -
300E GLU* 3.3 37.7 - - + +
396E ASP* 4.5 4.0 - - - -
397E LYS* 1.3 81.4 - - + +
399E SER* 1.3 61.4 + - - +
400E ARG 3.1 8.5 + - - -
401E ILE* 3.3 22.8 - - + +
402E GLY* 3.4 4.3 + - - -
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Residues in contact with SER 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E TRP* 6.1 0.4 - - - -
240E ILE* 5.9 1.6 - - - -
243E TRP* 5.5 5.6 - - - -
396E ASP* 3.3 19.7 + - - +
397E LYS 3.3 0.2 - - - -
398E ILE* 1.3 82.0 - - - +
400E ARG* 1.3 62.1 + - - +
401E ILE 3.3 0.4 - - - -
402E GLY* 4.0 4.3 - - - +
403E PHE* 3.2 53.5 - - - +
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Residues in contact with ARG 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E ASP 4.5 3.7 + - - +
397E LYS* 3.5 28.4 - - + +
398E ILE 3.1 0.4 - - - -
399E SER* 1.3 82.0 - - - +
401E ILE* 1.3 63.7 + - + +
404E PRO* 3.0 19.9 - - - +
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Residues in contact with ILE 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E TRP* 3.2 34.5 - - + -
296E SER* 5.4 5.6 - - - +
397E LYS 5.1 2.9 - - - +
398E ILE* 3.3 21.3 - - + +
400E ARG* 1.3 86.3 - - + +
402E GLY* 1.3 73.6 + - - +
403E PHE 3.4 0.7 - - - -
404E PRO* 3.3 6.4 - - - +
405E LEU* 2.9 36.3 + - + +
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Residues in contact with GLY 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E TRP* 4.1 19.7 - - - -
240E ILE* 6.0 2.2 - - - -
398E ILE 3.4 5.9 + - - -
399E SER* 4.8 1.6 - - - -
401E ILE* 1.3 89.9 - - - +
403E PHE* 1.3 67.6 + - - +
405E LEU* 2.9 22.2 + - - +
406E ALA* 2.9 15.9 + - - +
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Residues in contact with PHE 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 5.9 8.3 - + - -
240E ILE* 3.4 33.2 - - + -
399E SER* 3.2 35.3 + - - +
402E GLY* 1.3 78.2 - - - +
404E PRO* 1.3 69.0 - - + +
406E ALA* 3.3 12.3 + - - +
407E PHE* 3.4 12.5 + - - +
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Residues in contact with PRO 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400E ARG* 3.0 29.6 - - - +
401E ILE* 3.3 12.6 - - - +
403E PHE* 1.3 96.8 - - + +
405E LEU* 1.3 58.0 + - - -
406E ALA 3.4 0.2 - - - -
407E PHE* 4.1 8.7 - - + +
408E LEU* 3.3 27.7 + - - +
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Residues in contact with LEU 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E ILE* 6.4 0.9 - - - -
239E TRP* 5.1 22.9 - - + +
296E SER* 5.4 10.1 - - - +
401E ILE* 2.9 31.3 + - + +
402E GLY* 2.9 13.4 + - - +
404E PRO* 1.3 78.1 - - - +
406E ALA* 1.3 70.0 + - + +
408E LEU* 3.8 6.2 + - - +
409E ILE* 3.4 37.1 + - + +
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Residues in contact with ALA 406 (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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236E ILE* 3.2 52.5 - - + +
402E GLY 2.9 13.5 + - - +
403E PHE* 3.3 5.8 + - - +
405E LEU* 1.3 83.7 - - + +
407E PHE* 1.3 58.8 + - - +
409E ILE* 3.4 5.2 + - - +
410E PHE* 3.0 30.1 + - - +
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Residues in contact with PHE 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403E PHE 3.4 12.6 + - - +
404E PRO* 4.4 7.4 - - + +
406E ALA* 1.3 76.6 - - - +
408E LEU* 1.3 62.0 + - + +
410E PHE* 4.4 16.2 - + - -
411E ASN* 3.0 42.5 + - + +
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Residues in contact with LEU 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404E PRO 3.3 19.2 + - - +
405E LEU* 4.0 6.5 - - - +
406E ALA 3.3 0.4 - - - -
407E PHE* 1.3 82.9 - - + +
409E ILE* 1.3 57.9 + - + +
411E ASN* 3.8 3.2 - - - +
412E LEU* 2.9 51.8 + - + +
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Residues in contact with ILE 409 (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 LEU* 3.2 34.3 - - + -
235E VAL* 6.2 3.8 - - + -
236E ILE* 6.3 2.0 - - + -
289E VAL* 6.4 2.9 - - + -
405E LEU* 3.4 33.4 + - + +
406E ALA* 3.9 5.4 - - - +
407E PHE 3.3 0.2 - - - -
408E LEU* 1.3 78.7 - - + +
410E PHE* 1.3 60.9 + - - +
412E LEU* 3.5 12.0 - - + +
413E PHE* 2.9 39.3 + - + +
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Residues in contact with PHE 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E ILE* 3.7 30.5 - - + -
232E LEU* 5.1 17.7 - - + -
233E LEU* 5.6 15.7 - - + -
236E ILE* 4.7 12.6 - - + -
406E ALA 3.0 19.0 + - - +
407E PHE* 4.0 17.9 - + - +
409E ILE* 1.3 79.3 - - - +
411E ASN* 1.3 57.1 + - - +
413E PHE* 4.1 2.7 - - - +
414E TYR* 3.1 41.3 + + + +
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Residues in contact with ASN 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407E PHE* 3.0 37.3 + - + +
408E LEU* 4.1 4.0 - - - +
410E PHE* 1.3 76.1 - - - +
412E LEU* 1.3 60.3 + - - +
414E TYR* 3.9 8.7 - - - +
415E TRP* 3.2 71.9 + - - +
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Residues in contact with LEU 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E LEU* 2.9 45.0 + - + +
409E ILE* 3.0 13.2 + - + +
411E ASN* 1.3 80.0 - - - +
413E PHE* 1.3 60.8 + - + +
415E TRP* 5.2 0.4 - - - -
416E ILE* 2.9 40.0 + - + +
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Residues in contact with PHE 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E TYR* 3.6 35.7 - + - -
232E LEU* 4.0 33.9 - - + -
285E ILE* 5.0 17.7 - - + -
289E VAL* 5.9 7.0 - - + -
409E ILE* 2.9 25.9 + - + +
410E PHE 4.4 1.6 - - - +
412E LEU* 1.3 79.3 - - + +
414E TYR* 1.3 59.9 + - - +
415E TRP 3.5 0.2 - - - -
416E ILE* 4.0 10.8 - - + -
417E ILE* 2.9 48.0 + - + +
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Residues in contact with TYR 414 (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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225E ILE* 6.3 1.6 - - + -
229E ILE* 5.5 7.9 - - + -
410E PHE* 3.1 41.1 + + + +
411E ASN* 4.3 7.6 - - - +
412E LEU 3.4 0.2 - - - -
413E PHE* 1.3 78.2 - - - +
415E TRP* 1.3 78.1 + + - +
417E ILE* 3.7 5.0 + - + +
418E TYR* 3.4 62.2 + + - +
430E HIS* 5.1 6.0 + + - -
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Residues in contact with TRP 415 (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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411E ASN* 3.2 47.6 + - - +
412E LEU* 5.0 0.9 - - - +
414E TYR* 1.3 87.0 - + - +
416E ILE* 1.3 61.5 + - + +
418E TYR* 3.7 1.4 + - - +
419E LYS* 2.9 60.3 + - - +
430E HIS* 3.3 44.3 + + + -
431E HIS* 3.3 43.1 - + - -
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Residues in contact with ILE 416 (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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412E LEU* 2.9 33.9 + - + +
413E PHE* 4.4 11.9 - - + +
414E TYR 3.4 0.2 - - - -
415E TRP* 1.3 77.7 - - + +
417E ILE* 1.3 61.3 + - + +
419E LYS* 3.7 14.8 - - + +
420E ILE* 2.9 35.0 + - + +
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Residues in contact with ILE 417 (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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225E ILE* 3.5 65.1 - - + +
228E TYR* 5.2 7.4 - - + -
413E PHE* 2.9 40.2 + - + +
414E TYR* 3.9 7.0 - - + +
415E TRP 3.3 0.4 - - - -
416E ILE* 1.3 82.0 - - + +
418E TYR* 1.3 72.8 + - + +
419E LYS 3.1 0.4 - - - -
420E ILE* 3.0 22.9 - - + +
421E VAL* 3.2 13.9 - - + +
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Residues in contact with TYR 418 (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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225E ILE* 5.7 3.8 - - + -
414E TYR* 3.4 57.6 + + - +
415E TRP 3.9 1.3 - - - +
416E ILE 3.4 0.2 - - - -
417E ILE* 1.3 90.1 - - + +
419E LYS* 1.3 59.4 + - - +
421E VAL* 4.4 7.0 + - - +
422E ARG* 2.9 43.7 + - - +
428E GLU* 4.8 0.7 - - - +
430E HIS* 4.0 24.0 - - + +
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Residues in contact with LYS 419 (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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415E TRP* 2.9 58.8 + - - +
416E ILE* 3.7 17.5 - - + +
417E ILE 3.1 0.2 - - - -
418E TYR* 1.3 78.0 - - - +
420E ILE* 1.3 55.9 + - - +
421E VAL 3.1 1.8 - - - -
422E ARG* 2.7 28.2 + - - +
423E ARG* 2.8 12.3 + - - -
425E ASP* 4.7 9.8 - - - +
428E GLU* 2.8 40.2 + - + +
430E HIS* 5.0 2.9 - - + +
431E HIS* 5.5 5.1 - - - +
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Residues in contact with ILE 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ILE* 6.2 1.3 - - + -
281E LYS* 6.2 4.0 - - + -
416E ILE* 2.9 21.4 + - + +
417E ILE* 3.0 22.9 - - + +
419E LYS* 1.3 75.9 - - - +
421E VAL* 1.3 76.0 + - + +
422E ARG 3.0 1.9 + - - -
423E ARG* 3.3 17.4 + - - +
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Residues in contact with VAL 421 (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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222E TYR* 5.3 16.8 - - + +
225E ILE* 5.5 7.0 - - + -
417E ILE* 3.2 22.4 - - + +
418E TYR* 4.5 9.2 - - - +
419E LYS 3.1 0.6 - - - -
420E ILE* 1.3 80.0 - - + +
422E ARG* 1.3 68.6 + - + +
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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
------------------------------------------------------------
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