Contacts of the helix formed by residues 398 - 421 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B TRP* 3.4 35.6 - - + -
242B PHE* 4.9 3.8 - - + -
243B TRP* 3.4 42.3 + - + -
246B LEU* 6.4 0.7 - - + -
300B GLU* 3.3 38.4 - - + +
394B LYS* 6.3 2.2 - - + -
396B ASP* 4.0 10.5 - - - +
397B LYS* 1.3 79.5 - - + +
399B SER* 1.3 58.9 + - - +
400B ARG 3.1 8.4 + - - -
401B ILE* 3.3 23.1 - - + +
402B GLY 3.4 4.3 + - - -
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B TRP* 3.2 43.1 - - - -
396B ASP* 3.3 18.5 + - - +
397B LYS 3.3 0.4 - - - -
398B ILE* 1.3 79.5 - - - +
400B ARG* 1.3 61.9 + - - +
401B ILE 3.3 0.7 - - - -
402B GLY 4.0 3.1 - - - +
403B PHE* 3.2 39.0 - - - +
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ASP 4.5 3.5 + - - +
397B LYS* 3.5 29.2 - - + +
398B ILE 3.1 0.8 - - - -
399B SER* 1.3 82.6 - - - +
401B ILE* 1.3 63.2 + - + +
404B PRO* 3.0 19.8 - - - +
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Residues in contact with ILE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.2 34.5 - - + -
296B SER* 5.3 5.8 - - - +
397B LYS 5.1 3.1 - - - +
398B ILE* 3.3 20.6 - - + +
400B ARG* 1.3 85.8 - - + +
402B GLY* 1.3 73.0 + - - +
403B PHE 3.4 0.4 - - - -
404B PRO* 3.3 6.8 - - - +
405B LEU* 2.9 36.7 + - + +
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 4.1 19.5 - - - -
240B ILE* 6.1 1.8 - - - -
243B TRP* 5.8 1.8 - - - -
398B ILE 3.4 5.7 + - - -
399B SER* 4.8 1.6 - - - -
401B ILE* 1.3 90.3 - - - +
403B PHE* 1.3 66.8 + - - +
405B LEU* 2.9 22.1 + - - +
406B ALA* 2.9 15.6 + - - +
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 3.4 32.1 - - + -
243B TRP* 3.8 14.4 - + - -
399B SER* 3.2 26.7 + - - +
400B ARG* 5.3 0.2 - - - -
402B GLY* 1.3 78.1 - - - +
404B PRO* 1.3 69.6 - - + +
405B LEU 3.2 0.2 + - - -
406B ALA* 3.3 11.8 + - - +
407B PHE* 3.4 12.1 + - - +
306C PHE* 6.0 5.4 - + - -
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Residues in contact with PRO 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG* 3.0 28.7 - - - +
401B ILE* 3.3 12.8 - - - +
403B PHE* 1.3 98.3 - - + +
405B LEU* 1.3 56.9 + - - -
406B ALA 3.4 0.4 - - - -
407B PHE* 4.1 8.8 - - + +
408B LEU* 3.3 27.7 + - - +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 6.4 0.7 - - - -
239B TRP* 5.2 22.9 - - + -
296B SER* 5.4 9.9 - - - +
401B ILE* 2.9 32.6 + - + +
402B GLY* 2.9 14.3 + - - +
404B PRO* 1.3 78.9 - - - +
406B ALA* 1.3 69.1 + - + +
408B LEU* 4.0 5.2 - - - +
409B ILE* 3.4 37.3 + - + +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ILE* 3.2 51.5 - - + +
402B GLY 2.9 13.1 + - - +
403B PHE* 3.3 5.6 + - - +
405B LEU* 1.3 83.4 - - + +
407B PHE* 1.3 60.1 + - - +
409B ILE* 3.4 5.2 + - - +
410B PHE* 3.0 30.1 + - - +
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Residues in contact with PHE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B PHE 3.4 12.2 + - - +
404B PRO* 4.0 7.2 + - + +
406B ALA* 1.3 75.8 - - - +
408B LEU* 1.3 63.1 + - + +
410B PHE* 4.4 16.8 - + - -
411B ASN* 3.0 41.3 + - + +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B PRO 3.3 18.3 + - - +
405B LEU* 4.0 7.0 - - - +
406B ALA 3.3 0.6 - - - -
407B PHE* 1.3 83.8 - - + +
409B ILE* 1.3 56.6 + - + +
411B ASN* 3.8 3.2 - - - +
412B LEU* 2.9 51.8 + - + +
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 3.2 33.2 - - + -
235B VAL* 6.2 4.7 - - + -
236B ILE* 6.3 1.8 - - + -
289B VAL* 6.4 2.2 - - + -
405B LEU* 3.4 34.5 + - + +
406B ALA* 3.4 5.1 + - - +
407B PHE 3.3 0.4 - - - -
408B LEU* 1.3 79.6 - - + +
410B PHE* 1.3 60.7 + - - +
412B LEU* 3.5 10.4 - - + +
413B PHE* 2.9 39.3 + - + +
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Residues in contact with PHE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 3.7 32.5 - - + -
232B LEU* 5.1 16.6 - - + -
233B LEU* 5.6 12.8 - - + -
236B ILE* 4.7 11.2 - - + -
406B ALA 3.0 19.0 + - - +
407B PHE* 4.0 17.3 - + - +
409B ILE* 1.3 79.9 - - - +
411B ASN* 1.3 58.4 - - - +
413B PHE* 3.8 3.1 + - + +
414B TYR* 3.1 39.6 + + + +
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Residues in contact with ASN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B PHE* 3.0 38.2 + - + +
408B LEU* 4.1 3.6 - - - +
410B PHE* 1.3 76.5 - - - +
412B LEU* 1.3 59.9 + - - +
413B PHE 3.4 0.2 - - - -
414B TYR* 3.9 8.3 - - - +
415B TRP* 3.2 71.1 + - - +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 2.9 45.8 + - + +
409B ILE* 3.0 13.2 + - + +
411B ASN* 1.3 81.1 - - + +
413B PHE* 1.3 60.7 + - + +
415B TRP* 5.2 0.4 - - - -
416B ILE* 2.9 39.8 + - + +
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Residues in contact with PHE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 3.6 35.7 - + + -
232B LEU* 4.1 32.3 - - + -
285B ILE* 5.0 16.4 - - + -
289B VAL* 5.9 7.0 - - + -
409B ILE* 2.9 27.1 + - + +
410B PHE 4.4 1.6 - - - +
412B LEU* 1.3 79.0 - - + +
414B TYR* 1.3 61.0 + - - +
415B TRP 3.5 0.2 - - - -
416B ILE* 4.0 10.8 - - + -
417B ILE* 2.9 48.5 + - + +
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Residues in contact with TYR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ILE* 6.3 1.3 - - + -
229B ILE* 5.5 4.9 - - + -
410B PHE* 3.1 40.1 + + + +
411B ASN* 3.8 8.5 + - - -
413B PHE* 1.3 78.3 - - - +
415B TRP* 1.3 78.8 - + - +
417B ILE* 3.7 5.7 + - + +
418B TYR* 3.4 60.6 + + - +
430B HIS* 5.4 4.9 - - - -
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Residues in contact with TRP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B ASN* 3.2 49.6 + - - +
412B LEU* 5.0 1.1 - - - +
414B TYR* 1.3 88.7 - + - +
416B ILE* 1.3 60.5 + - + +
417B ILE 3.3 0.2 - - - -
418B TYR* 3.7 1.4 + - - +
419B LYS* 2.9 61.2 + - - +
428B GLU* 4.6 0.3 - - - +
430B HIS* 3.3 46.3 + + + -
431B HIS* 4.4 28.7 - + + -
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B LEU* 2.9 33.4 + - + +
413B PHE* 4.4 13.0 - - + +
414B TYR 3.4 0.2 - - - -
415B TRP* 1.3 79.3 - - + +
417B ILE* 1.3 61.4 + - + +
419B LYS* 3.7 13.9 - - + +
420B ILE* 2.9 34.1 + - + +
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ILE* 3.5 65.7 - - + +
228B TYR* 5.2 7.4 - - + -
413B PHE* 2.9 40.9 + - + +
414B TYR* 3.9 7.6 - - + +
415B TRP 3.3 0.2 - - - -
416B ILE* 1.3 80.8 - - + +
418B TYR* 1.3 71.8 + - + +
419B LYS 3.2 0.4 - - - -
420B ILE* 3.0 23.3 - - + +
421B VAL* 3.2 13.9 - - + +
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Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ILE* 5.7 3.8 - - + -
414B TYR* 3.4 57.5 + + - +
415B TRP 4.3 0.2 - - - +
417B ILE* 1.3 90.6 - - + +
419B LYS* 1.3 58.0 + - - +
421B VAL* 4.4 2.2 - - - -
422B ARG* 3.1 57.1 + - - +
428B GLU* 3.1 14.0 - - - +
430B HIS* 4.2 14.6 - + + -
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B TRP* 2.9 58.2 + - - +
416B ILE* 3.7 17.5 - - + +
418B TYR* 1.3 78.3 - - - +
420B ILE* 1.3 57.2 + - - +
421B VAL 3.1 1.8 - - - -
422B ARG* 2.7 25.2 + - - +
423B ARG* 2.8 13.6 + - - -
425B ASP* 4.6 11.7 + - - +
428B GLU* 3.0 34.2 + - + +
430B HIS* 4.8 4.0 + - - +
431B HIS* 6.0 3.4 - - - +
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ILE* 6.2 1.3 - - + -
281B LYS* 6.2 3.4 - - + -
416B ILE* 2.9 23.1 + - + +
417B ILE* 3.0 22.9 - - - +
419B LYS* 1.3 75.1 - - - +
421B VAL* 1.3 74.7 + - + +
422B ARG 3.0 1.7 + - - -
423B ARG* 3.3 33.6 + - - +
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Residues in contact with VAL 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B TYR* 5.3 16.6 - - + +
225B ILE* 5.5 6.7 - - + -
417B ILE* 3.2 22.7 - - + +
418B TYR* 4.5 1.3 - - - +
419B LYS 3.1 0.4 - - - -
420B ILE* 1.3 81.1 - - + +
422B ARG* 1.3 85.6 + - - +
423B ARG* 6.0 0.2 - - - -
426B GLU* 5.7 0.2 - - - +
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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
------------------------------------------------------------
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