Contacts of the helix formed by residues 408 - 421 (chain C) in PDB entry 1M6X
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 SER 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PRO 5.1 0.4 + - - -
201C LYS 5.7 2.5 + - - -
203C PHE* 3.6 24.8 + - - +
406C ILE 3.6 4.0 + - - -
407C ILE* 1.3 76.7 - - - +
409C GLN* 1.3 65.2 + - - +
410C GLU* 3.3 24.8 + - - +
411C VAL* 3.1 12.0 + - - +
412C LEU* 3.0 17.3 + - - +
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Residues in contact with GLN 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU 5.1 3.8 - - - +
397C SER* 4.1 24.4 + - - +
407C ILE 3.3 4.2 + - - -
408C SER* 1.3 69.8 + - - +
410C GLU* 1.3 69.3 + - - +
411C VAL 2.9 0.3 + - - -
412C LEU* 3.0 11.6 + - + -
413C ASP* 2.8 47.4 + - - +
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Residues in contact with GLU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LYS* 5.4 1.4 - - - -
205C LEU* 3.6 41.3 + - + +
408C SER* 3.2 12.5 + - - +
409C GLN* 1.3 77.6 - - - +
411C VAL* 1.3 56.5 + - - +
413C ASP* 3.7 10.1 + - - +
414C TYR* 3.2 18.9 + - - +
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Residues in contact with VAL 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C PHE* 3.8 23.6 - - + +
204C LYS* 3.9 16.4 - - - +
205C LEU* 4.2 11.2 - - + +
215C ILE* 4.2 31.6 - - + -
245C LEU* 6.1 0.4 - - + -
407C ILE* 4.1 16.2 - - + -
408C SER* 3.1 25.5 + - - +
409C GLN 2.9 0.2 - - - -
410C GLU* 1.3 76.7 - - + +
412C LEU* 1.3 68.7 + - + +
413C ASP 3.0 2.3 + - - -
414C TYR* 3.0 3.3 + - - +
415C LEU* 2.9 25.9 + - + +
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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
----------------------------------------------------------
249C LEU* 4.6 6.3 - - + -
396C GLY* 3.6 12.3 - - - -
397C SER* 4.7 5.4 - - - +
400C TYR* 3.6 41.8 - - + +
403C TRP* 3.9 15.3 - - + +
404C ASN* 4.2 17.5 - - - +
405C GLY 4.9 0.7 - - - +
407C ILE* 3.1 46.0 - - + +
408C SER 3.0 9.1 + - - +
409C GLN* 3.0 13.3 + - + +
411C VAL* 1.3 75.8 - - + +
413C ASP* 1.3 57.7 + - - +
415C LEU* 4.8 2.0 - - + +
416C SER* 2.9 29.6 + - - -
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Residues in contact with ASP 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU* 4.4 4.5 + - + +
396C GLY* 3.3 21.8 + - - +
409C GLN* 2.8 47.6 + - - +
410C GLU* 3.7 8.4 - - - +
412C LEU* 1.3 76.0 - - - +
414C TYR* 1.3 58.0 + - - +
416C SER* 3.1 5.0 + - - -
417C SER* 2.7 41.3 + - - +
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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
----------------------------------------------------------
205C LEU* 3.6 28.0 - - + -
211C LEU 5.4 1.2 + - - -
213C VAL* 3.8 28.4 + - + +
214C ILE* 5.6 0.2 - - - -
215C ILE* 4.2 24.2 - - + -
234C SER* 4.9 3.8 + - - -
242C LEU* 4.0 25.6 - - + +
384C TRP* 3.8 30.7 - + + +
387C ILE* 4.0 25.5 - - + +
410C GLU 3.2 12.2 + - - +
411C VAL 3.0 7.1 + - - +
413C ASP* 1.3 79.8 - - - +
415C LEU* 1.3 59.0 + - - +
417C SER* 3.6 4.5 - - - -
418C TYR* 2.9 42.5 + + + +
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Residues in contact with LEU 415 (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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215C ILE* 4.5 6.7 - - + -
242C LEU* 3.6 46.4 - - + +
245C LEU* 3.8 19.3 - - + -
246C ASP* 4.0 7.4 - - - -
249C LEU* 3.7 28.7 - - + -
400C TYR* 3.2 22.4 - - + +
411C VAL* 2.9 16.5 + - + +
412C LEU* 4.1 4.0 - - - +
414C TYR* 1.3 77.3 - - + +
416C SER* 1.3 68.2 - - - +
417C SER 3.2 0.3 + - - -
418C TYR* 3.5 5.1 - - + +
419C ILE* 2.9 32.9 + - + +
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Residues in contact with SER 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU* 3.8 13.9 + - - +
396C GLY* 3.6 21.7 + - - -
399C ARG* 3.8 14.2 - - - +
400C TYR* 3.8 13.6 + - - -
412C LEU 2.9 23.2 + - - -
413C ASP* 3.4 4.0 - - - -
415C LEU* 1.3 78.5 - - - +
417C SER* 1.3 65.9 + - - +
419C ILE* 3.3 2.4 + - - +
420C ASN* 2.9 34.8 + - - -
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Residues in contact with SER 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C ILE* 3.4 31.2 + - - +
395C GLU* 6.1 1.9 - - - +
413C ASP* 2.7 26.9 + - - +
414C TYR* 3.6 0.6 - - - -
416C SER* 1.3 72.8 - - - +
418C TYR* 1.3 66.6 + - - +
419C ILE 2.8 1.6 + - - -
420C ASN* 3.6 5.5 - - - +
421C ARG* 2.6 29.2 + - - -
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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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234C SER* 2.7 33.9 + - - -
240C ASP* 2.4 29.6 + - - -
242C LEU* 3.5 33.4 - - + -
243C VAL* 4.8 1.8 - - + -
383C GLU* 4.1 16.9 + - - -
387C ILE* 3.6 28.3 - - + +
414C TYR* 2.9 29.0 + - + +
415C LEU* 3.5 7.0 - - + +
417C SER* 1.3 76.0 - - - +
419C ILE* 1.3 79.0 + - + +
421C ARG* 3.4 4.0 - - - +
422C ARG* 2.9 44.5 + - + +
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Residues in contact with ILE 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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242C LEU 4.0 10.1 - - - +
243C VAL* 4.4 12.3 - - + -
246C ASP* 3.5 25.4 - - + +
399C ARG* 3.3 32.8 - - - +
400C TYR* 3.8 17.0 - - - +
415C LEU* 2.9 23.8 + - + +
416C SER 3.4 7.4 - - - +
417C SER 2.8 3.2 + - - -
418C TYR* 1.3 84.3 - - + +
420C ASN* 1.3 66.1 + - - +
422C ARG* 2.9 24.8 + - - +
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Residues in contact with ASN 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU* 4.7 12.3 + - - +
399C ARG* 4.0 19.6 + - - +
416C SER* 2.9 32.5 + - - -
417C SER* 2.9 8.1 + - - +
419C ILE* 1.3 77.5 - - - +
421C ARG* 1.3 55.4 + - - +
422C ARG 2.7 21.0 + - - +
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Residues in contact with ARG 421 (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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383C GLU* 3.2 44.3 + - - +
386C HIS* 2.7 45.7 + - - +
387C ILE* 3.9 16.8 - - + -
417C SER* 2.6 26.0 + - - +
418C TYR* 3.4 9.0 - - - +
420C ASN* 1.3 71.7 - - - +
422C ARG* 1.3 58.7 + - - +
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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
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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