Contacts of the helix formed by residues 571 - 584 (chain C) in PDB entry 3VI7
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 HIS 571 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525C PRO* 4.6 3.8 + - - +
528C MET* 3.7 24.4 - - + +
529C GLN* 3.3 43.1 + - + +
532C ASP* 2.7 31.3 + - - +
567C LEU 4.1 14.1 - - - -
568C LEU* 2.9 16.7 + - + +
570C ASN* 1.3 97.3 + - + +
572C PRO* 1.4 67.0 - - - +
573C ARG 3.1 3.1 - - - -
574C LEU* 2.9 31.3 + - + +
575C VAL* 3.4 8.8 + - - +
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Residues in contact with PRO 572 (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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532C ASP* 5.4 0.4 - - - +
568C LEU 4.1 1.1 - - - +
569C ASP 4.5 6.5 - - - +
570C ASN 3.5 7.4 - - - +
571C HIS* 1.4 88.5 - - - +
573C ARG* 1.3 69.1 + - + +
575C VAL* 3.2 13.1 + - + +
576C THR* 3.0 25.8 + - - +
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Residues in contact with ARG 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C GLN* 5.9 0.8 - - - +
532C ASP* 2.9 46.8 + - - +
533C THR* 4.7 3.2 - - - +
535C LEU* 3.9 16.4 - - + +
536C GLY* 3.3 36.3 + - - -
537C GLY* 3.7 9.6 - - - +
571C HIS* 3.1 2.2 - - - +
572C PRO* 1.3 85.4 - - + +
574C LEU* 1.3 62.0 + - - +
576C THR* 3.4 10.4 + - - +
577C LEU* 3.2 21.7 + - - +
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Residues in contact with LEU 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C MET* 3.5 30.1 - - - +
531C LEU* 4.1 16.8 - - + +
532C ASP* 3.9 22.4 - - + +
535C LEU* 4.4 16.2 - - + -
541C LEU* 5.5 2.2 - - + -
553C TRP* 3.3 42.8 + - + +
568C LEU* 4.2 13.9 - - + -
571C HIS* 2.9 28.5 + - + +
573C ARG* 1.3 78.1 - - - +
575C VAL* 1.3 58.8 + - - +
577C LEU* 3.4 6.3 + - + +
578C ARG* 3.1 23.7 + - - +
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Residues in contact with VAL 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C LEU* 3.7 36.8 - - + +
571C HIS 3.8 6.7 - - - +
572C PRO* 3.2 11.6 + - + +
574C LEU* 1.3 71.2 - - - +
576C THR* 1.3 67.3 + - - +
577C LEU 3.0 1.6 - - - -
578C ARG* 3.0 13.1 + - - +
579C LYS* 2.8 55.6 + - + +
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Residues in contact with THR 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C PRO* 3.0 15.7 + - - +
573C ARG* 3.6 13.7 - - - +
575C VAL* 1.3 75.0 - - - +
577C LEU* 1.3 64.3 + - - +
579C LYS* 3.2 11.0 + - - +
580C LYS* 3.0 35.8 + - + +
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Residues in contact with LEU 577 (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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535C LEU* 4.4 14.4 - - + -
539C GLU 3.8 15.3 - - - +
540C TRP* 3.8 22.9 - - + -
541C LEU* 3.4 38.1 - - + +
550C ASP* 3.5 22.9 - - + +
553C TRP* 3.4 23.6 - - + +
573C ARG 3.2 10.5 + - - +
574C LEU* 3.5 14.1 - - + +
575C VAL 3.0 0.2 - - - -
576C THR* 1.3 78.0 - - - +
578C ARG* 1.3 67.7 + - - +
580C LYS* 3.3 13.9 + - + +
581C VAL* 3.3 10.6 + - + +
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Residues in contact with ARG 578 (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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553C TRP* 3.4 22.2 - - + +
554C GLU* 3.2 27.7 + - - +
557C SER* 3.0 30.8 + - - +
558C THR* 3.3 20.8 + - - +
561C LEU* 3.4 23.6 - - - +
568C LEU* 3.7 23.3 - - - +
574C LEU 3.1 5.7 + - - +
575C VAL* 3.0 12.8 + - + +
577C LEU* 1.3 78.7 - - - +
579C LYS* 1.3 64.1 + - + +
581C VAL* 3.2 4.2 + - - +
582C GLN* 3.0 51.4 + - - +
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Residues in contact with LYS 579 (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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575C VAL* 2.8 43.5 + - + +
576C THR* 3.2 10.9 + - - +
578C ARG* 1.3 73.5 - - + +
580C LYS* 1.3 56.3 + - - +
582C GLN* 3.2 18.1 + - - +
583C ALA* 2.9 28.9 + - - +
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Residues in contact with LYS 580 (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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539C GLU* 3.3 56.5 + - - +
540C TRP* 3.7 34.6 - - + -
576C THR* 3.0 25.5 + - + +
577C LEU* 3.3 9.8 + - + +
579C LYS* 1.3 71.0 - - - +
581C VAL* 1.3 66.9 + - - +
583C ALA* 3.3 15.8 + - - +
584C ILE* 3.4 15.2 + - - +
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Residues in contact with VAL 581 (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* 4.4 3.1 - - + -
540C TRP* 4.3 8.3 - - + -
546C VAL* 4.7 0.9 - - + -
550C ASP* 3.6 39.9 - - + +
551C PHE* 3.8 27.8 - - + +
553C TRP* 6.1 0.2 - - + -
554C GLU* 3.8 22.2 - - + -
577C LEU* 3.3 12.1 + - + +
578C ARG 3.2 7.6 + - - +
580C LYS* 1.3 78.0 - - - +
582C GLN* 1.3 64.2 + - - +
583C ALA 3.1 1.2 + - - -
584C ILE* 3.2 24.2 + - - +
587C VAL* 3.7 18.4 - - + +
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Residues in contact with GLN 582 (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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554C GLU* 2.8 35.8 + - - +
558C THR* 4.9 0.2 + - - -
578C ARG* 3.0 50.4 + - - +
579C LYS* 3.2 21.0 + - - +
581C VAL* 1.3 75.8 - - - +
583C ALA* 1.3 57.2 - - - +
584C ILE 4.5 0.4 - - - -
587C VAL* 4.6 0.2 - - - -
588C ALA* 3.3 27.9 - - - +
591C ILE* 3.9 19.7 - - + +
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Residues in contact with ALA 583 (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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579C LYS 2.9 15.0 + - - +
580C LYS* 3.7 9.6 - - - +
581C VAL 3.1 0.8 - - - -
582C GLN* 1.3 77.3 - - - +
584C ILE* 1.3 66.3 + - - +
585C PRO* 3.1 10.2 - - - +
588C ALA* 4.7 2.8 - - - +
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Residues in contact with ILE 584 (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* 3.8 28.5 - - + -
540C TRP* 4.7 6.3 - - + -
546C VAL* 4.1 22.2 - - + -
551C PHE* 3.9 26.9 - - + -
580C LYS 3.4 8.9 + - - +
581C VAL* 3.2 24.3 + - - +
583C ALA* 1.3 74.5 - - - +
585C PRO* 1.4 76.0 - - + +
586C ALA* 4.1 3.8 - - + +
587C VAL* 2.9 16.6 + - + +
588C ALA 2.9 19.6 + - - -
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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