Contacts of the helix formed by residues 398 - 421 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C TRP* 3.4 38.0 - - + -
242C PHE* 4.8 7.9 - - + -
243C TRP* 3.4 42.0 - - + -
300C GLU* 3.7 35.7 - - + +
396C ASP* 4.5 4.0 - - - -
397C LYS* 1.3 76.2 - - - +
399C SER* 1.3 60.1 + - - +
400C ARG 3.1 8.3 + - - -
401C ILE* 3.3 21.7 - - + +
402C GLY 3.4 3.8 + - - -
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Residues in contact with SER 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C TRP* 6.1 0.2 - - - -
240C ILE* 5.9 0.9 - - - -
243C TRP* 5.5 5.6 - - - -
396C ASP* 3.3 19.0 + - - +
397C LYS 3.3 0.2 - - - -
398C ILE* 1.3 81.7 - - - +
400C ARG* 1.3 62.4 + - - +
401C ILE 3.3 1.1 - - - -
402C GLY* 4.0 4.0 - - - +
403C PHE* 3.2 53.9 - - - +
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Residues in contact with ARG 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ASP 4.5 2.9 + - - +
397C LYS* 3.5 54.1 - - + +
398C ILE 3.1 0.6 - - - -
399C SER* 1.3 83.4 - - - +
401C ILE* 1.3 62.2 + - + +
403C PHE* 5.3 0.2 - - - -
404C PRO* 3.0 20.0 - - - +
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Residues in contact with ILE 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C TRP* 3.2 35.2 - - + -
296C SER* 5.3 6.1 - - - +
300C GLU* 5.7 0.4 - - - +
397C LYS 5.1 3.1 - - - +
398C ILE* 3.3 20.0 - - + +
400C ARG* 1.3 86.4 - - + +
402C GLY* 1.3 74.3 + - - +
403C PHE 3.4 0.2 - - - -
404C PRO* 3.3 6.6 - - - +
405C LEU* 2.9 37.1 + - + +
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Residues in contact with GLY 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C TRP* 4.1 19.3 - - - -
240C ILE* 6.0 2.2 - - - -
398C ILE 3.4 6.0 + - - -
399C SER* 4.7 1.6 - - - -
401C ILE* 1.3 91.0 - - - +
403C PHE* 1.3 66.8 + - - +
405C LEU* 2.9 22.1 + - - +
406C ALA* 2.9 15.6 + - - +
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Residues in contact with PHE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ILE* 3.4 33.4 - - + -
399C SER* 3.2 34.6 + - - +
400C ARG* 5.3 0.2 - - - -
402C GLY* 1.3 77.6 - - - +
404C PRO* 1.3 68.9 - - + +
405C LEU 3.2 0.3 + - - -
406C ALA* 3.3 11.8 + - - +
407C PHE* 3.4 12.6 + - - +
306D PHE* 6.2 4.0 - + - -
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Residues in contact with PRO 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C ARG* 3.0 28.9 - - - +
401C ILE* 3.3 12.3 - - - +
403C PHE* 1.3 99.5 - - + +
405C LEU* 1.3 57.8 + - - -
406C ALA 3.4 0.2 - - - -
407C PHE* 4.1 8.3 - - + +
408C LEU* 3.3 27.2 + - - +
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 6.4 1.1 - - - -
239C TRP* 5.1 23.8 - - + +
296C SER* 5.4 10.5 - - - +
401C ILE* 2.9 30.8 + - + +
402C GLY* 2.9 13.5 + - - +
404C PRO* 1.3 79.1 - - - +
406C ALA* 1.3 69.3 + - + +
408C LEU* 4.0 5.4 - - - +
409C ILE* 3.4 38.4 + - + +
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Residues in contact with ALA 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 3.2 53.2 - - + +
402C GLY 2.9 13.3 + - - +
403C PHE* 3.3 6.0 + - - +
405C LEU* 1.3 84.3 - - + +
407C PHE* 1.3 59.2 + - - +
409C ILE* 3.4 5.8 + - - +
410C PHE* 3.0 30.0 + - - +
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Residues in contact with PHE 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C PHE 3.4 12.2 + - - +
404C PRO* 4.4 7.6 - - + +
406C ALA* 1.3 76.4 - - - +
408C LEU* 1.3 63.4 + - + +
410C PHE* 4.4 15.7 - + - -
411C ASN* 3.0 41.2 + - + +
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Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C PRO 3.3 19.6 + - - +
405C LEU* 4.0 6.7 - - - +
406C ALA 3.3 0.6 - - - -
407C PHE* 1.3 82.3 - - + +
409C ILE* 1.3 57.4 + - + +
411C ASN* 3.8 2.8 - - - +
412C LEU* 2.9 52.8 + - + +
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Residues in contact with ILE 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 3.2 32.5 - - + -
235C VAL* 6.2 4.3 - - + -
236C ILE* 6.3 2.5 - - + -
289C VAL* 6.4 2.7 - - + -
405C LEU* 3.4 32.8 + - + +
406C ALA* 3.4 5.1 + - - +
407C PHE 3.3 0.2 - - - -
408C LEU* 1.3 80.2 - - + +
410C PHE* 1.3 60.1 + - - +
412C LEU* 3.5 11.8 - - + +
413C PHE* 2.9 40.4 + - + +
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Residues in contact with PHE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ILE* 3.6 31.4 - - + -
232C LEU* 5.1 17.0 - - + -
233C LEU* 5.6 15.3 - - + -
236C ILE* 4.7 10.8 - - + -
406C ALA 3.0 18.8 + - - +
407C PHE* 4.0 16.8 - + - +
409C ILE* 1.3 80.3 - - - +
411C ASN* 1.3 59.4 + - - +
413C PHE* 3.8 2.8 + - + +
414C TYR* 3.1 41.2 + + + +
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Residues in contact with ASN 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C PHE* 3.0 37.9 + - + +
408C LEU* 3.8 4.0 - - + +
410C PHE* 1.3 75.9 - - - +
412C LEU* 1.3 60.5 + - - +
413C PHE 3.4 0.2 - - - -
414C TYR* 3.9 8.3 - - - +
415C TRP* 3.2 71.0 + - - +
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Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C LEU* 2.9 46.3 + - + +
409C ILE* 3.0 14.1 + - + +
411C ASN* 1.3 80.5 - - - +
413C PHE* 1.3 59.2 + - + +
415C TRP* 5.2 0.7 - - - -
416C ILE* 2.9 40.8 + - + +
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Residues in contact with PHE 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C TYR* 3.6 35.9 - + - -
232C LEU* 4.0 33.9 - - + -
285C ILE* 5.0 15.9 - - + -
289C VAL* 5.9 7.4 - - + -
409C ILE* 2.9 26.0 + - + +
410C PHE* 4.4 2.0 - - + +
412C LEU* 1.3 79.0 - - + +
414C TYR* 1.3 59.7 + - - +
416C ILE* 4.0 10.8 - - + -
417C ILE* 2.9 48.7 + - + +
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Residues in contact with TYR 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ILE* 6.3 1.8 - - + -
229C ILE* 5.5 7.9 - - + -
410C PHE* 3.1 38.6 + + + +
411C ASN* 3.8 8.0 + - - -
412C LEU 3.4 0.2 - - - -
413C PHE* 1.3 77.9 - - - +
415C TRP* 1.3 78.3 + + - +
417C ILE* 3.7 5.4 + - + +
418C TYR* 3.4 61.5 + + - +
430C HIS* 5.0 0.6 + - - -
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Residues in contact with TRP 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ASN* 3.2 47.7 + - - +
412C LEU* 5.0 0.9 - - - +
414C TYR* 1.3 92.0 - + - +
416C ILE* 1.3 61.1 + - + +
418C TYR* 3.7 1.4 + - - +
419C LYS* 2.9 60.2 + - - +
430C HIS* 3.8 32.5 - + + -
431C HIS* 3.5 39.3 - + - -
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Residues in contact with ILE 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C LEU* 2.9 34.6 + - + +
413C PHE* 4.4 13.5 - - + +
414C TYR 3.4 0.2 - - - -
415C TRP* 1.3 79.3 - - + +
417C ILE* 1.3 61.1 + - + +
419C LYS* 3.7 14.3 - - + +
420C ILE* 2.9 34.9 + - + +
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Residues in contact with ILE 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C ILE* 3.5 66.2 - - + +
228C TYR* 5.2 7.6 - - + -
413C PHE* 2.9 40.7 + - + +
414C TYR* 3.9 7.4 - - + +
415C TRP 3.3 0.2 - - - -
416C ILE* 1.3 80.7 - - + +
418C TYR* 1.3 71.1 + - + +
419C LYS 3.1 0.4 - - - -
420C ILE* 3.0 23.3 - - + +
421C VAL* 3.2 14.2 - - + +
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Residues in contact with TYR 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C ILE* 5.6 3.8 - - + -
414C TYR* 3.4 55.9 + + - +
415C TRP 3.9 0.7 - - - +
417C ILE* 1.3 91.2 - - + +
419C LYS* 1.3 59.1 + - - +
421C VAL* 4.4 6.6 - - - +
422C ARG* 2.9 43.0 + - - +
428C GLU* 4.7 0.7 - - - +
430C HIS* 3.7 30.3 - + + +
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Residues in contact with LYS 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C TRP* 2.9 58.8 + - - +
416C ILE* 3.7 17.7 - - + +
417C ILE 3.1 0.2 - - - -
418C TYR* 1.3 78.2 - - - +
420C ILE* 1.3 57.1 + - - +
421C VAL 3.1 1.3 - - - -
422C ARG* 2.7 27.3 + - - +
423C ARG* 2.8 13.2 + - - -
425C ASP* 4.7 10.0 - - - +
428C GLU* 2.8 41.1 + - + +
430C HIS* 4.4 2.1 - - + +
431C HIS* 5.9 3.4 - - - +
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Residues in contact with ILE 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ILE* 6.2 1.6 - - + -
281C LYS* 4.2 24.5 - - - +
416C ILE* 2.9 22.2 + - + +
417C ILE* 3.0 23.3 - - + +
419C LYS* 1.3 75.8 - - - +
421C VAL* 1.3 75.8 + - + +
422C ARG 3.0 1.6 + - - -
423C ARG* 3.3 18.1 + - - +
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Residues in contact with VAL 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C TYR* 5.3 17.7 - - + +
225C ILE* 5.5 6.5 - - + -
417C ILE* 3.2 22.7 - - + +
418C TYR* 4.5 8.5 - - - +
419C LYS 3.1 0.6 - - - -
420C ILE* 1.3 81.6 - - + +
422C ARG* 1.3 69.3 + - + +
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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