Contacts of the helix formed by residues 415 - 426 (chain C) in PDB entry 1V40
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 ALA 415 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406C LEU* 4.4 9.0 - - + -
408C TYR* 3.5 40.4 - - + -
412C ARG 3.2 1.4 + - - -
414C ARG* 1.3 77.6 - - - +
416C GLU* 1.3 65.5 + - - +
417C ILE 3.2 3.1 - - - -
418C ILE* 2.9 21.0 + - - +
419C ARG* 3.1 24.4 + - - +
452C PRO* 4.0 13.2 - - + -
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Residues in contact with GLU 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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412C ARG* 2.9 39.5 + - + +
413C GLY 3.9 5.6 - - - +
414C ARG 3.5 0.8 - - - -
415C ALA* 1.3 77.5 - - - +
417C ILE* 1.3 57.2 + - - +
419C ARG* 3.0 32.1 + - - +
420C TYR* 2.8 46.9 + - + -
433C ARG* 4.8 1.0 + - - -
555C ILE* 3.7 17.5 - - + -
590C TRP* 2.7 32.8 + - - -
594C ARG* 2.8 25.4 + - - +
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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
----------------------------------------------------------
413C GLY 5.1 0.2 + - - -
414C ARG 3.9 17.8 + - - +
416C GLU* 1.3 76.8 - - - +
418C ILE* 1.3 73.2 + - + +
420C TYR* 3.4 1.4 + - - +
421C ILE* 3.1 28.4 + - + +
464C SER* 4.5 4.9 - - - +
465C LEU* 4.6 6.1 - - + -
468C ALA* 4.2 11.9 - - + -
548C TRP* 3.7 35.9 - - + +
551C PHE* 3.6 32.5 - - + -
552C TYR* 3.8 38.4 - - + +
555C ILE* 3.4 11.1 - - + +
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Residues in contact with ILE 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C LEU* 4.0 28.9 - - + -
415C ALA* 2.9 10.2 + - - +
417C ILE* 1.3 81.8 - - + +
419C ARG* 1.3 61.8 + - - +
421C ILE* 3.2 10.4 + - - +
422C PHE* 3.1 48.4 + - + -
452C PRO* 4.3 9.0 - - + -
454C LEU* 5.1 0.7 - - + -
464C SER* 3.9 25.4 - - - +
467C ILE* 3.7 37.0 - - + -
468C ALA* 4.3 5.8 - - - +
471C LEU* 3.7 10.3 - - + -
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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
----------------------------------------------------------
406C LEU* 3.7 11.4 - - + +
408C TYR* 4.0 16.2 - - - +
409C PHE 3.6 15.2 + - - -
411C MET 2.9 28.3 + - - -
412C ARG* 3.4 9.1 + - - +
415C ALA* 3.1 14.7 + - - +
416C GLU* 3.0 29.7 + - - +
418C ILE* 1.3 78.1 - - - +
420C TYR* 1.3 61.6 + - - +
422C PHE* 3.5 2.3 + - - +
423C ALA* 3.0 23.6 + - - +
429C TYR* 3.2 26.6 + - - +
431C ASP* 2.8 22.3 + - - -
432C HIS 5.4 0.4 + - - -
433C ARG* 3.3 21.5 - - - +
590C TRP* 3.4 36.7 - - + +
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Residues in contact with TYR 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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416C GLU* 2.8 42.9 + - + +
417C ILE 3.6 9.9 - - - +
418C ILE 3.3 0.2 - - - -
419C ARG* 1.3 76.1 - - - +
421C ILE* 1.3 57.5 + - - +
423C ALA* 3.2 6.6 + - - +
424C TYR* 2.8 31.5 + - - +
551C PHE* 3.9 32.1 - + + -
554C GLU* 2.6 35.9 + - - -
555C ILE* 3.5 21.8 - - + +
558C THR* 5.2 0.9 + - - -
581C VAL* 4.6 3.1 - - + -
587C VAL* 4.0 25.7 - - + +
590C TRP* 3.7 17.5 - + - -
591C ILE* 3.7 10.6 - - + +
594C ARG* 3.2 19.0 + - - -
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Residues in contact with ILE 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ILE* 3.1 21.7 + - + +
418C ILE* 3.2 8.6 + - - +
420C TYR* 1.3 73.2 - - - +
422C PHE* 1.3 65.8 + - + +
424C TYR* 3.3 4.7 + - - +
425C LEU* 2.9 46.5 + - + +
468C ALA* 3.6 43.1 - - + +
471C LEU* 3.7 21.8 - - + -
472C THR* 3.6 19.7 - - + -
477C LEU* 4.5 2.5 - - + -
548C TRP* 4.4 6.5 - - + -
551C PHE* 4.4 14.8 - - + -
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Residues in contact with PHE 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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404C TYR* 3.9 20.2 - + - -
406C LEU* 4.9 0.4 - - + -
418C ILE* 3.1 41.9 + - + -
419C ARG 3.8 2.5 - - - +
421C ILE* 1.3 77.0 - - + +
423C ALA* 1.3 57.6 + - - +
425C LEU* 3.4 0.8 + - - -
426C ASP* 2.9 9.9 + - - -
427C ILE* 2.9 63.7 + - + +
429C TYR* 3.4 56.5 - + + -
454C LEU* 4.0 23.1 - - + -
471C LEU* 3.6 27.6 - - + -
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Residues in contact with ALA 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 3.0 18.8 + - - +
420C TYR* 3.4 5.8 - - - +
422C PHE* 1.3 77.5 - - - +
424C TYR* 1.3 64.4 + - - +
426C ASP* 3.1 13.6 + - - +
429C TYR* 5.2 1.3 - - + -
586C ALA* 3.5 22.8 - - - +
587C VAL* 5.3 1.8 - - - -
590C TRP* 3.9 31.0 - - + -
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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 TYR 2.8 20.1 + - - +
421C ILE 3.8 3.1 - - - +
423C ALA* 1.3 73.3 - - - +
425C LEU* 1.3 70.8 + - + +
426C ASP* 3.4 2.4 + - - +
476C ASP* 3.3 34.5 + - - -
477C LEU* 3.4 26.5 - - + -
546C VAL* 3.9 23.1 - - + +
551C PHE* 3.6 26.7 - + + -
584C ILE* 4.1 26.5 - - + -
586C ALA* 4.0 14.7 - - + +
587C VAL* 4.6 3.3 - - + +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ILE* 2.9 34.7 + - + +
422C PHE 4.1 0.2 - - - +
424C TYR* 1.3 97.9 - - + +
426C ASP* 1.3 71.6 + - - +
427C ILE* 3.6 32.3 - - + +
471C LEU* 3.5 24.7 - - + +
475C THR* 4.1 29.6 - - + +
476C ASP* 5.0 1.3 - - - +
477C LEU* 4.3 4.0 - - + -
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Residues in contact with ASP 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C PHE 2.9 6.2 + - - -
423C ALA* 3.1 11.5 + - - +
424C TYR 3.2 2.2 - - - +
425C LEU* 1.3 81.8 - - - +
427C ILE* 1.3 61.3 + - - +
428C GLN* 4.2 12.6 + - - +
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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