Contacts of the helix formed by residues 413 - 425 (chain C) in PDB entry 3OMA
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 THR 413 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409C TYR 3.4 19.5 - - - +
410C TYR* 2.6 26.2 + - - +
411C HIS 3.7 3.4 - - - +
412C ASP* 1.3 82.8 - - - +
414C TYR* 1.3 59.4 + - - +
415C TYR* 3.2 16.6 + - - +
416C VAL* 3.1 21.3 + - - +
417C VAL 3.6 0.9 + - - -
475C GLY* 3.7 16.6 + - - +
478C GLY* 4.6 11.9 - - - +
479C MET 3.2 16.4 - - - +
480C PRO* 4.9 1.1 - - + -
481C ARG* 3.3 15.9 - - - +
227D LYS* 4.1 4.5 - - - +
253D SER* 6.0 0.7 - - - +
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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
----------------------------------------------------------
1C HEA 3.4 47.0 + - + +
52C ARG* 4.3 4.5 - - - -
55C LEU* 3.4 22.6 - - + +
95C TRP* 4.5 0.3 - - - -
413C THR* 1.3 71.8 - - - +
415C TYR* 1.3 59.5 + - - +
416C VAL 3.3 0.2 - - - -
417C VAL* 3.5 17.4 - - + +
418C ALA* 2.9 23.9 + - - +
471C GLN* 3.3 52.1 - - + +
474C LEU* 4.2 8.3 - - + -
475C GLY* 4.0 8.4 - - - +
479C MET* 3.0 38.5 + - + +
480C PRO 3.5 25.4 - - - -
481C ARG* 4.2 9.6 - - - -
482C ARG 4.9 0.7 - - - -
483C TYR 5.1 1.8 + - - -
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Residues in contact with TYR 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C THR* 3.5 39.7 - - + +
400C VAL* 3.7 19.9 - - + +
401C LEU* 3.7 15.5 - - + -
410C TYR* 3.4 66.9 + + + -
413C THR* 3.1 7.1 + - - +
414C TYR* 1.3 75.2 - - - +
416C VAL* 1.3 64.9 + - - +
418C ALA* 3.4 5.0 + - - +
419C HIS* 3.1 19.8 + - - +
471C GLN 4.1 4.7 - - - -
472C HIS* 3.8 32.7 - + + -
475C GLY* 3.5 7.9 - - - -
476C ARG* 4.3 3.8 - - + -
3D TRD 4.3 16.5 - - + +
58D ASP* 5.0 0.7 + - - -
62D LEU* 5.9 0.5 - - - +
65D ILE* 4.9 0.7 - - - +
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Residues in contact with VAL 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.5 53.2 - - + +
401C LEU* 3.7 21.3 - - + -
410C TYR 3.4 22.2 - - - +
411C HIS* 4.2 2.0 - - - -
412C ASP 4.2 2.2 - - - +
413C THR 3.1 8.0 + - - +
415C TYR* 1.3 76.5 - - - +
417C VAL* 1.3 62.9 + - - +
419C HIS* 3.2 3.8 + - - +
420C PHE* 3.0 36.2 + - + +
481C ARG* 3.8 21.1 - - - +
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Residues in contact with VAL 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 4.0 15.0 - - + -
414C TYR* 3.3 34.7 + - + +
416C VAL* 1.3 77.4 - - - +
418C ALA* 1.3 61.5 + - - +
420C PHE* 3.6 13.1 - - + -
421C HIS* 3.0 53.2 + - + +
471C GLN* 3.3 17.9 - - - +
481C ARG* 3.6 37.9 - - + +
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Residues in contact with ALA 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C TYR 2.9 17.2 + - - +
415C TYR 3.6 4.9 - - - +
416C VAL 3.2 0.4 - - - -
417C VAL* 1.3 77.1 - - - +
419C HIS* 1.3 62.5 + - - +
421C HIS* 3.4 1.4 + - - +
422C TYR* 3.1 30.8 + - - -
468C PHE* 3.5 26.2 - - - +
471C GLN* 3.9 5.8 + - + -
472C HIS* 3.6 32.3 - - + +
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Residues in contact with HIS 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 2.3 69.9 + + + -
394C GLY* 2.7 28.9 + - - -
397C THR* 3.2 18.8 + - - +
398C GLY* 3.4 17.3 + - - -
401C LEU* 3.7 20.4 - - + -
415C TYR 3.1 12.7 + - - +
416C VAL 3.5 7.2 - - - +
418C ALA* 1.3 77.5 - - - +
420C PHE* 1.3 64.8 + - + +
422C TYR* 3.4 4.4 + - - +
423C VAL* 3.3 23.2 + - + +
472C HIS* 4.6 1.0 + - - -
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Residues in contact with PHE 420 (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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1C HEA 3.8 29.4 - + + -
2C HEA 3.3 59.5 - + + +
416C VAL* 3.0 23.7 + - + -
417C VAL* 3.6 25.6 - - + -
419C HIS* 1.3 77.5 - - + +
421C HIS* 1.3 89.0 + + - +
423C VAL* 3.7 5.2 - - - -
424C MET* 3.0 46.7 + - + +
481C ARG* 4.0 22.0 - - - -
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Residues in contact with HIS 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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1C HEA 1.9 94.1 + + + -
417C VAL* 3.0 33.8 + - + +
418C ALA 4.1 0.7 - - - +
420C PHE* 1.3 92.8 - + - +
422C TYR* 1.3 55.9 + - - +
424C MET* 4.8 0.2 - - - -
425C SER* 2.8 29.3 + - - +
426C LEU* 3.1 11.8 + - - +
468C PHE* 3.2 37.9 - + + -
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Residues in contact with TYR 422 (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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390C LEU* 3.7 28.9 - - + +
393C VAL* 3.9 18.6 - - + -
394C GLY* 3.5 20.6 - - - +
418C ALA 3.1 26.3 + - - +
419C HIS 3.4 0.4 + - - +
420C PHE 3.3 0.2 - - - -
421C HIS* 1.3 76.8 - - - +
423C VAL* 1.3 56.9 + - - +
426C LEU* 3.1 51.4 - - + +
427C GLY* 3.7 0.7 - - - -
465C ASN* 2.7 32.7 + - - -
468C PHE* 3.7 25.6 - - + -
469C PHE* 3.3 38.2 + + - +
472C HIS* 3.8 18.2 - + - -
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.4 53.0 - - + +
291C VAL* 4.7 0.7 - - - +
391C PHE* 3.9 30.9 - - + +
394C GLY* 3.5 31.0 - - - +
395C GLY* 3.6 6.7 - - - +
419C HIS* 3.3 19.0 + - + +
420C PHE* 3.6 8.1 - - - +
422C TYR* 1.3 78.0 - - - +
424C MET* 1.3 61.0 + - - +
427C GLY* 3.2 3.8 - - - -
428C ALA 3.1 18.0 + - - -
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Residues in contact with MET 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.5 48.4 - - + +
2C HEA 3.5 41.7 - - + -
107C MET* 3.6 29.4 - - - +
290C ILE* 4.0 13.9 - - + -
420C PHE* 3.0 36.7 + - + +
421C HIS* 4.8 0.7 - - - -
423C VAL* 1.3 75.8 - - - +
425C SER* 1.3 60.2 + - - +
426C LEU 3.3 1.3 - - - -
428C ALA* 3.1 10.1 + - + +
429C VAL* 3.0 31.6 + - - +
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Residues in contact with SER 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.5 59.2 - - - +
421C HIS* 2.8 29.0 + - - -
424C MET* 1.3 75.4 - - - +
426C LEU* 1.3 64.5 + - - +
427C GLY 3.5 0.2 - - - -
429C VAL* 3.7 11.4 - - - +
430C PHE* 3.8 1.2 - - - -
460C MET* 3.6 20.8 - - - +
468C PHE* 4.0 3.0 - - - -
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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