Contacts of the helix formed by residues 416 - 428 (chain C) in PDB entry 5DO7
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 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C LEU* 3.9 8.5 + - + +
415C ALA* 1.3 75.8 - - - +
417C GLN* 1.3 83.9 - - + +
418C ASP 3.3 0.7 - - - -
419C ARG* 2.9 6.7 + - - +
420C VAL* 2.8 36.1 + - + +
580C PHE* 3.8 20.9 - - + -
585C PHE* 3.4 33.0 - - + -
599C MET* 3.6 36.1 - - + -
601C ALA* 5.0 11.4 - - + +
602C PHE 6.1 0.2 - - - +
608C PHE* 4.5 24.5 - - + -
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Residues in contact with GLN 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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412C LEU 5.2 0.2 - - - +
413C LYS 4.5 3.6 - - - +
414C GLY 3.6 1.2 + - - -
416C ILE* 1.3 91.4 - - + +
418C ASP* 1.3 61.4 + - - +
420C VAL* 3.5 19.3 - - + +
421C GLY 3.6 0.2 + - - -
599C MET* 3.2 28.5 - - + +
575D GLY 4.2 1.0 + - - -
576D PHE* 3.4 33.9 + - - +
577D MET 3.4 15.4 - - - +
578D ILE* 4.4 0.4 - - - -
579D ASN* 3.5 46.7 + - + +
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Residues in contact with ASP 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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404C VAL* 4.7 23.1 - - + +
406C ARG 5.7 0.2 - - - +
407C VAL* 4.9 12.5 - - + +
408C ARG* 4.6 9.9 + - - +
414C GLY* 2.8 41.7 + - - +
417C GLN* 1.3 75.8 - - - +
419C ARG* 1.3 60.2 + - - +
421C GLY* 4.1 0.9 - - - -
422C LEU* 3.4 23.7 + - - +
577D MET 5.1 0.2 - - - -
578D ILE* 2.9 35.0 - - - +
579D ASN* 3.9 4.7 - - - +
582D SER* 4.0 15.2 + - - +
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Residues in contact with ARG 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C VAL* 3.7 35.2 - - + +
408C ARG 4.3 3.4 + - - -
409C SER* 4.6 9.9 + - - +
414C GLY 4.3 0.2 + - - -
415C ALA* 2.5 32.7 + - - +
416C ILE* 2.9 9.7 + - - +
418C ASP* 1.3 75.6 - - - +
420C VAL* 1.3 69.1 + - - +
421C GLY 3.1 1.3 - - - -
422C LEU* 2.8 16.9 + - + +
423C LEU* 2.8 28.5 + - + +
491C GLY 5.2 5.3 + - - -
492C LEU* 4.8 9.0 - - + -
493C HIS 5.3 0.4 - - - +
579C GLU* 3.5 28.9 + - - -
580C PHE* 4.5 9.3 - - + -
583C LEU* 3.0 29.0 - - - +
585C PHE* 3.2 31.6 - - - -
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Residues in contact with VAL 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ILE* 2.8 14.4 + - + +
417C GLN* 3.5 20.4 - - + +
419C ARG* 1.3 75.6 - - - +
421C GLY* 1.3 70.4 + - - +
423C LEU* 3.3 6.7 + - - +
424C TYR* 2.8 32.2 + - + +
548C PHE* 3.2 46.4 - - + +
549C LEU* 6.2 2.7 - - + -
580C PHE* 5.5 1.4 - - - -
608C PHE* 3.9 22.7 - - + -
576D PHE* 5.6 7.9 - - + +
577D MET* 4.7 6.1 - - - +
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Residues in contact with GLY 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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417C GLN 3.6 4.2 + - - -
418C ASP 4.0 1.3 + - - -
419C ARG 3.1 0.8 - - - -
420C VAL* 1.3 84.8 - - - +
422C LEU* 1.3 52.9 + - - +
424C TYR* 3.3 3.4 - - - +
425C GLN* 2.8 35.7 + - - +
577D MET* 3.5 40.7 - - - +
578D ILE* 4.9 4.7 - - - -
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Residues in contact with LEU 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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400C LEU* 4.7 13.5 - - + -
404C VAL* 3.9 26.9 - - + +
407C VAL* 5.1 4.0 - - + -
418C ASP 3.4 12.3 + - - +
419C ARG* 2.8 13.4 + - - +
421C GLY* 1.3 74.6 - - - +
423C LEU* 1.3 67.6 + - + +
425C GLN* 3.2 6.9 + - - +
426C PHE* 2.8 55.5 + - + -
490C LEU* 3.9 30.5 - - + -
492C LEU* 3.8 35.2 - - + -
578D ILE* 5.5 0.6 - - - +
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Residues in contact with LEU 423 (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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419C ARG* 2.8 31.5 + - + +
420C VAL* 3.8 5.4 - - - +
422C LEU* 1.3 76.7 - - + +
424C TYR* 1.3 66.8 + - - +
426C PHE* 2.9 10.5 + - + +
427C VAL* 2.8 26.2 + - - +
492C LEU* 4.9 7.0 - - + -
502C PHE* 4.6 13.7 - - + -
548C PHE* 4.3 20.2 - - + -
575C LEU* 3.5 51.1 - - + +
576C VAL* 4.9 4.0 - - - -
579C GLU* 5.0 6.3 - - + +
580C PHE* 4.4 22.2 - - + -
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Residues in contact with TYR 424 (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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420C VAL* 2.8 20.2 + - + +
421C GLY* 3.3 7.2 - - - +
423C LEU* 1.3 76.9 - - - +
425C GLN* 1.3 67.6 + - - +
427C VAL* 3.1 8.7 - - - +
428C GLY* 2.8 22.2 + - - -
539C ILE* 4.6 2.9 + - - +
542C VAL* 3.1 46.6 - - + +
543C LEU* 3.7 20.6 - - - +
546C SER* 4.0 10.3 - - - -
548C PHE* 4.1 14.4 - + + -
549C LEU* 3.5 34.2 - - + +
454D MET* 5.5 3.3 - - - +
571D TYR* 3.1 26.9 - - - -
577D MET* 3.6 15.3 - - + -
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Residues in contact with GLN 425 (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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396C MET* 4.9 10.2 - - - -
400C LEU* 3.8 32.1 - - + -
421C GLY 2.8 18.9 + - - +
422C LEU 3.6 4.3 - - - +
424C TYR* 1.3 75.1 - - - +
426C PHE* 1.3 66.1 + - - +
428C GLY* 3.1 5.3 + - - +
429C ALA* 2.8 31.1 + - + +
568D ASN* 3.1 28.4 + - - +
571D TYR* 3.0 35.3 + - - -
572D LEU* 4.3 6.3 - - + +
577D MET* 3.5 10.8 - - + +
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Residues in contact with PHE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C MET* 4.9 4.9 - - + -
397C GLY* 4.3 6.3 - - - -
400C LEU* 3.5 27.4 - - + -
422C LEU* 2.8 49.3 + - + -
423C LEU* 2.9 10.7 + - + +
425C GLN* 1.3 73.8 - - - +
427C VAL* 1.3 53.4 + - - +
429C ALA* 4.6 2.0 - - - -
430C THR* 2.6 44.4 + - + -
482C PHE* 3.1 36.8 - + + -
486C CYS* 5.0 2.0 - - + -
490C LEU* 4.2 15.7 - - + -
502C PHE* 3.5 33.9 - + - -
506C LEU* 3.9 17.3 - - + -
575C LEU* 5.1 1.1 - - + -
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Residues in contact with VAL 427 (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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423C LEU 2.8 15.9 + - - +
424C TYR* 3.1 24.5 - - - +
426C PHE* 1.3 74.5 - - - +
428C GLY* 1.3 56.7 + - - +
430C THR* 3.8 4.9 + - - -
431C PRO* 3.2 19.8 - - - +
506C LEU* 4.4 3.1 - - - +
509C PRO* 4.8 4.4 - - + +
542C VAL* 3.6 18.2 - - + +
546C SER* 4.5 3.1 - - - +
567C PHE* 4.6 1.8 - - + -
568C GLN* 4.3 18.8 - - + +
571C CYS* 3.6 35.9 - - + -
572C SER* 3.7 21.1 - - - +
575C LEU* 4.9 4.0 - - + -
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Residues in contact with GLY 428 (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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424C TYR* 2.8 12.9 + - - -
425C GLN* 3.4 7.9 + - - -
427C VAL* 1.3 76.7 - - - +
429C ALA* 1.3 56.6 + - - +
431C PRO* 4.2 3.6 - - - -
432C TYR* 4.7 6.2 - - - +
538C SER* 4.0 9.1 + - - +
539C ILE* 4.1 20.1 - - - +
542C VAL* 3.4 22.7 - - - -
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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