Contacts of the helix formed by residues 571 - 586 (chain C) in PDB entry 2IO1
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 GLN 571 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558C TYR* 4.9 2.4 + - - -
566C THR 4.5 0.9 - - - +
567C PHE* 3.2 19.9 - - - +
568C THR* 2.8 36.5 + - - +
569C GLN 3.1 1.2 - - - -
570C HIS* 1.3 86.1 - - + +
572C MET* 1.3 59.9 + - - +
573C PRO* 3.4 3.4 - - - -
574C LEU* 3.4 11.7 + - + +
575C PHE* 2.8 51.9 + - + -
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Residues in contact with MET 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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547C ASP* 3.7 14.8 - - - +
550C MET* 3.4 30.3 - - - -
551C PHE* 3.9 26.7 - - + -
554C LYS* 4.2 5.8 - - + -
567C PHE* 3.4 39.0 - - + -
568C THR 4.1 3.4 - - - +
569C GLN* 3.4 30.9 + - - +
571C GLN* 1.3 74.5 - - - +
573C PRO* 1.3 64.3 - - + +
575C PHE* 3.0 18.7 + - + +
576C ARG* 2.7 44.6 + - + +
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Residues in contact with PRO 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ASN* 4.3 26.1 + - - +
569C GLN* 4.0 6.3 - - - +
570C HIS 4.0 11.2 - - - +
571C GLN 3.4 4.3 - - - -
572C MET* 1.3 96.2 - - + +
574C LEU* 1.3 61.1 + - - +
576C ARG* 3.4 3.9 + - + +
577C LYS* 3.2 31.2 + - - +
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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
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366C LEU* 4.1 29.8 - - + +
367C GLU* 5.2 0.4 - - - -
368C LEU* 4.6 21.1 - - + +
571C GLN* 3.4 15.0 + - + +
572C MET 3.2 0.4 - - - -
573C PRO* 1.3 80.7 - - - +
575C PHE* 1.3 68.5 + - + +
577C LYS* 3.2 14.6 + - - +
578C LYS* 2.9 46.2 + - + -
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Residues in contact with PHE 575 (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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550C MET* 3.6 17.2 - - + +
554C LYS* 3.7 32.9 + - + +
558C TYR* 3.9 18.6 - - - -
567C PHE* 3.8 27.6 - + + -
571C GLN* 2.8 47.6 + - + +
572C MET* 3.0 24.2 + - + +
574C LEU* 1.3 89.9 - - + +
576C ARG* 1.3 57.9 + - - +
578C LYS* 3.3 14.9 + - - +
579C MET* 2.9 31.5 + - - +
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Residues in contact with ARG 576 (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 THR 3.6 2.0 + - - -
405C LEU* 3.3 39.4 + - + +
406C LYS 3.1 20.3 + - - -
407C ASN* 3.5 25.6 - - - +
408C TYR 4.3 5.6 - - - +
409C HIS 2.8 28.0 + - - +
411C LEU* 3.7 10.3 - - - +
546C SER* 3.2 11.1 + - - -
547C ASP* 2.8 32.3 + - - +
550C MET* 3.8 28.2 - - + +
572C MET* 2.7 26.1 + - - +
573C PRO* 3.6 5.6 - - + +
574C LEU 3.2 0.2 - - - -
575C PHE* 1.3 73.2 - - - +
577C LYS* 1.3 63.7 + - + +
579C MET* 3.4 2.8 + - - +
580C VAL* 3.2 21.9 + - - +
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Residues in contact with LYS 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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368C LEU* 3.6 18.5 - - + +
373C GLU* 4.2 18.6 - - - +
376C ILE* 3.2 33.9 - - + +
380C LEU* 5.2 6.7 - - + -
407C ASN* 6.2 2.5 - - - +
573C PRO* 3.2 23.0 + - - +
574C LEU* 3.2 16.9 + - - +
576C ARG* 1.3 77.5 - - + +
578C LYS* 1.3 66.2 + - - +
580C VAL* 3.0 20.6 - - + +
581C TRP 3.3 1.7 + - - -
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Residues in contact with LYS 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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366C LEU* 3.4 33.2 - - + -
368C LEU* 4.4 11.8 - - + +
372C MET* 6.2 0.2 - - + -
554C LYS* 4.6 14.4 - - - +
557C ASP* 5.8 0.8 + - - -
574C LEU* 2.9 27.8 + - + +
575C PHE* 3.7 16.4 - - + +
577C LYS* 1.3 79.2 - - - +
579C MET* 1.3 57.9 + - - +
581C TRP* 3.1 6.5 + - + +
582C GLU* 2.8 59.8 + - + +
589C LEU* 2.8 38.3 + - + +
369E THR* 3.7 9.0 - - - +
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Residues in contact with MET 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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405C LEU* 4.0 20.0 - - + -
411C LEU* 4.4 3.4 - - - -
415C VAL* 4.0 18.2 - - - -
419C TYR* 3.6 36.6 - - + -
550C MET* 3.3 33.0 - - + +
553C CYS* 3.9 22.2 - - + -
554C LYS* 4.3 7.2 - - + +
575C PHE 2.9 13.5 + - - +
576C ARG 3.8 4.7 - - - +
577C LYS 3.3 0.2 - - - -
578C LYS* 1.3 77.6 - - - +
580C VAL* 1.3 56.7 + - - +
582C GLU* 3.1 10.5 + - - +
583C ILE* 2.8 38.9 + - + +
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Residues in contact with VAL 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ILE* 3.7 24.7 - - + +
379C ALA* 4.2 10.1 - - + -
380C LEU* 4.4 15.5 - - + -
402C ILE* 4.1 24.4 - - + +
405C LEU* 4.3 13.1 - - + +
576C ARG 3.2 13.6 + - - +
577C LYS* 3.0 24.0 - - - +
579C MET* 1.3 76.0 - - - +
581C TRP* 1.3 62.1 + - - +
583C ILE* 3.3 1.0 + - - +
584C LEU* 3.0 41.0 + - + +
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Residues in contact with TRP 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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368C LEU* 5.4 0.2 - - + -
372C MET* 3.5 49.3 - - + +
375C GLU* 3.4 15.1 + - + -
376C ILE* 4.0 18.1 - - + +
577C LYS 3.3 5.6 + - - +
578C LYS* 3.1 11.9 + - + +
580C VAL* 1.3 78.4 - - - +
582C GLU* 1.3 73.3 + - + +
584C LEU* 3.1 5.0 + - + -
585C HIS* 3.0 75.5 + + + -
587C GLN* 4.2 24.0 - - + -
589C LEU* 3.6 40.8 - - + -
587E GLN* 4.2 9.6 - - - -
589E LEU* 4.4 11.4 - - + -
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Residues in contact with GLU 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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419C TYR* 3.8 14.3 + - + -
422C LEU* 3.7 5.6 - - + +
554C LYS* 4.7 2.1 + - - -
578C LYS* 2.8 51.8 + - + +
579C MET* 3.6 14.6 + - + +
581C TRP* 1.3 87.2 - - + +
583C ILE* 1.3 56.6 + - - +
586C GLN* 2.8 24.3 + - - -
587C GLN 3.1 28.0 + - - +
588C LEU* 3.2 27.1 - - + +
589C LEU* 2.8 26.8 + - + +
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Residues in contact with ILE 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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390C SER* 3.0 25.1 + - - -
397C ILE* 4.2 15.9 - - + -
402C ILE* 3.7 20.0 - - + -
405C LEU* 4.1 10.8 - - + -
415C VAL* 4.0 40.8 - - + +
418C PHE* 3.7 34.8 - - + -
419C TYR* 5.0 2.5 - - + +
422C LEU* 4.3 7.0 - - + -
579C MET* 2.8 34.2 + - + +
580C VAL 3.8 3.4 - - - +
582C GLU* 1.3 70.1 - - - +
584C LEU* 1.3 64.8 + - - +
586C GLN 3.4 7.1 + - - -
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Residues in contact with LEU 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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383A GLY 4.3 0.2 - - - +
384A PRO* 3.5 19.2 - - + +
385A GLN 4.5 1.9 + - - -
375C GLU* 3.9 22.7 - - + +
379C ALA* 3.7 23.1 - - + -
389C LEU* 3.7 44.7 - - + +
390C SER* 4.0 7.0 + - - -
402C ILE* 4.2 13.2 - - + -
580C VAL* 3.0 26.4 + - + +
581C TRP* 3.6 6.1 - - - +
583C ILE* 1.3 78.0 - - - +
585C HIS* 1.3 68.6 + - + +
586C GLN* 3.8 5.0 + - - +
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Residues in contact with HIS 585 (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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383A GLY* 3.4 14.4 - - - -
384A PRO* 3.7 33.5 - - + +
375C GLU* 2.8 37.5 + - - +
581C TRP* 3.0 67.4 + + + +
584C LEU* 1.3 85.1 - - + +
586C GLN* 1.3 74.9 + - - +
587C GLN* 3.2 14.5 + - + +
587E GLN* 5.4 1.6 + - - -
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Residues in contact with GLN 586 (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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381A GLY 4.7 0.7 - - - +
382A HIS* 3.4 32.4 + - + +
383A GLY 3.1 34.6 + - - +
385A GLN 5.9 0.4 - - - +
403A GLN* 5.2 1.9 - - - +
390C SER* 2.7 23.6 + - - +
391C SER 2.9 34.8 + - - +
392C ALA* 3.8 7.6 - - + +
418C PHE* 3.8 3.0 - - + -
422C LEU* 3.6 25.5 - - + +
429C LYS* 5.2 5.2 + - - -
582C GLU 2.8 10.7 + - - -
583C ILE 3.4 10.6 + - - +
584C LEU 3.8 2.6 + - - +
585C HIS* 1.3 81.0 - - - +
587C GLN* 1.3 58.5 + - - +
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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