Contacts of the helix formed by residues 406 - 418 (chain C) in PDB entry 2DB3
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 ASP 406 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402C ASP 3.2 15.0 + - - +
403C ARG* 3.4 26.3 + - - +
405C LEU* 1.3 78.8 - - - +
407C MET* 1.3 95.2 + - - +
408C GLY 3.3 3.4 - - - +
409C PHE 3.2 3.9 + - - -
410C SER* 2.9 21.2 + - - -
439C ILE* 3.6 22.1 - - - +
442C MET* 5.5 2.0 - - - -
569C LYS* 5.3 10.4 + - - +
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Residues in contact with MET 407 (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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406C ASP* 1.3 93.0 + - - +
408C GLY* 1.3 62.4 + - - +
410C SER* 3.2 20.1 + - - -
411C GLU* 4.7 2.3 + - - +
442C MET* 5.8 1.4 - - - +
1G U 5.1 10.1 - - - +
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Residues in contact with GLY 408 (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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403C ARG* 6.2 3.1 - - - -
406C ASP* 3.2 3.8 + - - +
407C MET* 1.3 79.9 - - - +
409C PHE* 1.3 66.2 + - - +
411C GLU* 5.2 2.3 + - - +
412C ASP* 5.9 1.6 - - - -
4G U 5.5 7.1 - - - +
5G U 5.7 1.4 - - - +
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Residues in contact with PHE 409 (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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326C PRO* 3.5 37.2 - - + -
376C PRO* 3.7 25.1 - - + -
403C ARG* 3.5 30.2 + - + +
404C MET* 3.3 31.0 - - + +
406C ASP 3.2 3.0 + - - -
408C GLY* 1.3 78.9 - - - +
410C SER* 1.3 66.0 + - - +
411C GLU 3.3 3.0 + - - -
412C ASP* 3.4 10.3 + - + +
413C MET* 2.9 21.6 + - + +
4G U 3.7 19.3 - - - -
5G U 3.5 44.9 - - - -
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Residues in contact with SER 410 (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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404C MET 4.0 2.7 + - - -
405C LEU* 3.7 14.1 - - - +
406C ASP 2.9 15.7 + - - -
407C MET* 3.2 19.8 + - - -
409C PHE* 1.3 74.8 - - - +
411C GLU* 1.3 59.9 + - - +
413C MET* 3.3 7.0 + - - +
414C ARG* 2.8 39.1 + - - +
442C MET* 4.9 9.4 - - - -
446C PHE* 5.9 0.2 - - - -
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Residues in contact with GLU 411 (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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407C MET 4.7 2.7 + - - +
408C GLY 5.2 1.8 + - - +
409C PHE 3.4 1.0 - - - -
410C SER* 1.3 82.6 + - - +
412C ASP* 1.3 64.7 + - - +
414C ARG* 2.9 9.7 + - - +
415C ARG* 2.8 36.0 + - + +
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Residues in contact with ASP 412 (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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376C PRO* 4.2 20.9 - - + +
377C GLY* 4.6 7.4 + - - -
380C LEU* 3.4 28.3 - - + +
409C PHE* 3.4 11.9 + - + +
411C GLU* 1.3 81.2 - - - +
413C MET* 1.3 64.2 + - - +
415C ARG* 3.1 13.5 + - - +
416C ILE* 3.0 28.7 + - - +
5G U 4.7 5.5 + - - +
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Residues in contact with MET 413 (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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324C VAL* 3.9 9.6 - - + -
376C PRO* 3.6 19.7 - - + -
398C LEU* 3.5 28.7 - - + -
404C MET* 3.3 50.9 - - + +
405C LEU* 4.4 7.6 - - + -
409C PHE* 2.9 19.1 + - + +
410C SER* 3.6 5.6 - - - +
412C ASP* 1.3 75.9 - - - +
414C ARG* 1.3 61.4 + - - +
416C ILE* 3.3 14.6 + - + +
417C MET* 3.1 44.6 + - + +
446C PHE* 5.5 1.1 - - + -
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Residues in contact with ARG 414 (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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410C SER* 2.8 23.4 + - - +
411C GLU* 2.9 10.5 + - - +
413C MET* 1.3 77.0 - - - +
415C ARG* 1.3 57.8 + - + +
418C THR* 3.0 50.8 + - + +
442C MET* 6.3 1.2 - - - +
445C GLU* 2.3 45.3 + - - -
446C PHE* 3.5 34.8 - - + -
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Residues in contact with ARG 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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380C LEU* 3.5 33.2 - - + +
383C VAL* 5.6 1.6 - - - +
384C ASP* 2.7 38.8 + - - -
411C GLU* 2.8 22.4 + - + +
412C ASP* 3.1 19.8 + - - +
414C ARG* 1.3 78.3 - - + +
416C ILE* 1.3 61.6 + - - +
418C THR* 4.2 1.7 - - - -
419C HIS* 3.4 32.7 + - - +
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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
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322C VAL* 5.1 6.1 - - + -
324C VAL* 4.6 8.1 - - + -
376C PRO* 4.6 8.3 - - + -
379C LEU* 3.5 28.3 - - + -
380C LEU* 3.6 24.9 - - + -
390C PHE* 4.0 26.0 - - + -
396C VAL* 5.6 3.1 - - + -
412C ASP 3.0 15.6 + - - +
413C MET* 3.6 27.1 - - + +
414C ARG 3.2 0.2 - - - -
415C ARG* 1.3 76.3 - - - +
417C MET* 1.3 74.0 + - - +
419C HIS* 3.2 19.8 + - - +
422C MET* 3.4 14.0 - - + +
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Residues in contact with MET 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C VAL* 3.8 28.5 - - - -
398C LEU* 3.6 34.1 - - + -
405C LEU* 4.9 0.7 - - + -
413C MET* 3.1 28.7 + - + +
414C ARG 4.1 0.2 - - - +
416C ILE* 1.3 84.0 - - - +
418C THR* 1.3 58.9 + - - +
419C HIS 3.3 0.2 - - - -
422C MET* 3.5 28.2 - - + +
426C HIS* 4.9 13.8 + - + -
428C THR* 5.0 4.5 - - + +
430C MET* 4.9 1.3 - - + -
446C PHE* 3.6 52.0 - - + -
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Residues in contact with THR 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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414C ARG* 3.0 29.9 + - + +
415C ARG* 4.2 2.9 - - - -
417C MET* 1.3 75.6 - - - +
419C HIS* 1.3 66.8 + - - +
420C VAL* 3.6 1.4 + - - -
422C MET* 5.0 0.2 - - - -
446C PHE* 4.2 14.9 - - - -
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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