Contacts of the helix formed by residues 567 - 583 (chain H) in PDB entry 6V3O
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 ARG 567 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536H MET* 3.9 33.3 - - + +
538H THR* 4.9 9.0 - - - +
566H GLU* 1.3 80.4 - - - +
568H LEU* 1.3 61.1 + - - +
569H ALA* 3.2 8.1 - - + +
570H ASP* 2.9 32.3 + - - +
571H LEU* 2.9 26.2 + - - +
607H ASP* 3.3 27.8 - - + +
770H THR* 4.8 19.9 - - - +
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Residues in contact with LEU 568 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566H GLU 3.9 0.4 + - - -
567H ARG* 1.3 71.9 - - - +
569H ALA* 1.3 64.8 + - - +
571H LEU* 3.2 11.3 + - + +
572H GLN* 2.6 53.6 + - - +
604H SER* 5.2 5.5 - - - +
607H ASP* 2.8 17.8 + - + +
608H ALA* 4.4 17.0 - - + -
612H SER* 4.2 25.1 - - - +
613H ALA* 4.9 3.1 - - - +
616H GLN* 3.8 30.3 - - + +
721H ALA* 6.5 0.4 - - + -
725H THR* 5.0 2.9 - - + +
729H ARG* 5.4 5.6 - - - +
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Residues in contact with ALA 569 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567H ARG* 3.2 7.0 - - + +
568H LEU* 1.3 80.1 - - + +
570H ASP* 1.3 68.9 + - - +
572H GLN* 3.3 21.5 + - - +
573H SER* 3.4 15.1 + - - -
607H ASP* 4.4 1.4 + - - -
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Residues in contact with ASP 570 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536H MET* 5.0 5.0 - - - +
537H ALA 3.8 15.4 - - - +
538H THR* 3.4 39.5 - - - +
565H PHE* 3.8 16.6 - - + -
566H GLU 4.3 1.8 + - - +
567H ARG* 2.9 44.2 + - - +
569H ALA* 1.3 79.7 - - - +
571H LEU* 1.3 64.6 + - - +
573H SER* 3.8 3.7 + - - +
574H ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 571 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565H PHE* 4.1 25.8 - - + +
567H ARG 2.9 13.4 + - - +
568H LEU* 3.2 11.2 + - + +
570H ASP* 1.3 76.1 - - - +
572H GLN* 1.3 65.0 + - - +
574H ALA* 3.3 18.4 + - + +
575H PRO* 3.6 1.9 - - - +
599H VAL* 4.5 10.1 - - + -
604H SER* 3.6 26.9 - - - +
613H ALA* 4.6 1.8 - - - +
616H GLN* 3.8 22.6 - - + +
617H LEU* 3.9 34.8 - - + +
620H ALA* 3.6 30.6 - - + +
624H MET* 5.8 0.9 - - + -
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Residues in contact with GLN 572 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568H LEU* 2.6 44.1 + - - +
569H ALA* 3.3 11.0 + - - +
571H LEU* 1.3 77.5 - - - +
573H SER* 1.3 57.7 + - - +
575H PRO* 3.5 13.2 - - - +
616H GLN* 3.3 31.4 + - - +
619H ARG* 5.3 4.0 - - - +
623H GLU* 4.7 4.7 - - - +
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Residues in contact with SER 573 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538H THR 4.8 6.5 + - - -
569H ALA 3.4 12.5 + - - -
570H ASP* 4.0 3.1 - - - -
571H LEU 3.3 0.4 - - - -
572H GLN* 1.3 76.8 - - - +
574H ALA* 1.3 59.6 + - - +
575H PRO* 3.3 2.5 - - - -
576H ALA* 2.9 17.5 + - - +
577H SER* 2.8 32.4 + - - -
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Residues in contact with ALA 574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565H PHE* 3.6 34.1 - - + -
570H ASP 3.1 16.4 + - - +
571H LEU* 3.4 17.3 - - + +
573H SER* 1.3 75.8 - - - +
575H PRO* 1.3 61.1 - - + +
577H SER* 3.2 3.1 + - - -
578H VAL* 2.9 35.1 + - - +
620H ALA* 5.0 3.6 - - + -
624H MET* 4.2 11.4 - - + -
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Residues in contact with PRO 575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571H LEU 3.6 5.6 - - - +
572H GLN 3.5 15.5 - - - +
573H SER 3.5 1.1 - - - -
574H ALA* 1.3 94.3 - - + +
576H ALA* 1.3 56.5 + - - +
578H VAL* 3.3 3.6 + - + +
579H GLU* 2.9 29.5 + - - +
620H ALA* 4.2 6.5 - - - +
623H GLU* 3.4 46.7 - - + +
624H MET* 4.0 22.0 - - + +
627H VAL* 4.1 10.9 - - + +
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Residues in contact with ALA 576 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572H GLN 5.3 0.2 + - - -
573H SER* 2.9 20.4 + - - +
575H PRO* 1.3 75.5 - - - +
577H SER* 1.3 66.3 + - - +
579H GLU* 3.2 9.6 + - - +
580H ARG* 3.1 23.9 + - - +
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Residues in contact with SER 577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538H THR 3.6 16.8 + - - -
539H ALA* 3.7 2.2 - - - -
540H PRO* 3.3 35.3 - - - +
565H PHE* 4.4 13.8 - - - -
573H SER* 2.8 18.3 + - - -
574H ALA* 3.6 11.2 - - - -
576H ALA* 1.3 76.8 - - - +
578H VAL* 1.3 62.6 + - - +
579H GLU 3.3 0.2 + - - -
580H ARG 3.3 0.5 + - - -
581H LEU* 3.2 29.8 + - - +
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Residues in contact with VAL 578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563H PRO* 5.8 1.3 - - + -
565H PHE* 4.7 9.2 - - + -
574H ALA 2.9 21.0 + - - +
575H PRO* 3.7 6.1 - - + +
577H SER* 1.3 75.7 - - - +
579H GLU* 1.3 62.5 + - - +
581H LEU* 3.5 10.0 + - + +
582H PHE* 3.1 58.0 + - + -
595H GLN* 5.4 2.0 - - + -
597H VAL* 4.5 13.9 - - + -
624H MET* 4.1 27.8 - - + +
627H VAL* 4.2 8.3 - - + -
635H LEU* 5.3 7.0 - - + -
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Residues in contact with GLU 579 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575H PRO 2.9 16.9 + - - +
576H ALA* 3.7 8.7 - - - +
577H SER 3.2 0.4 - - - -
578H VAL* 1.3 75.8 - - - +
580H ARG* 1.3 66.5 + - - +
582H PHE* 3.2 4.3 + - - +
583H SER* 3.0 22.4 + - - -
627H VAL* 3.8 15.6 - - + +
630H ARG* 3.0 38.1 + - - -
631H TYR* 3.5 21.8 + - + +
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Residues in contact with ARG 580 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487H GLN* 2.7 35.3 + - - +
491H LEU* 4.7 14.0 - - - +
540H PRO* 4.2 13.0 - - + -
576H ALA 3.1 16.2 + - - +
577H SER 3.3 3.3 + - - +
579H GLU* 1.3 77.8 - - - +
581H LEU* 1.3 62.7 + - - +
583H SER* 3.2 26.9 + - - +
584H VAL* 3.0 36.2 - - - +
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Residues in contact with LEU 581 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540H PRO* 3.9 23.8 - - + +
543H VAL* 4.0 29.8 - - + -
544H LEU* 3.9 35.7 - - + -
563H PRO* 5.9 3.4 - - + -
565H PHE* 6.6 0.4 - - + -
577H SER* 3.2 22.7 + - - +
578H VAL* 3.8 10.3 - - + +
580H ARG* 1.3 76.6 - - - +
582H PHE* 1.3 62.1 + - + +
584H VAL* 3.2 21.6 + - + +
587H TYR* 3.5 40.9 - - + +
595H GLN* 5.4 3.8 - - - +
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Residues in contact with PHE 582 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578H VAL* 3.1 44.7 + - + +
579H GLU 3.2 5.1 + - - +
581H LEU* 1.3 81.4 - - + +
583H SER* 1.3 57.7 + - - +
584H VAL 3.3 0.2 - - - -
587H TYR* 4.6 2.2 - + - -
588H MET* 3.1 30.3 - - - +
591H ILE* 3.9 26.7 - - + -
595H GLN* 3.9 22.2 - - + -
627H VAL* 4.0 6.1 - - + -
628H ALA* 3.8 24.0 - - + -
631H TYR* 3.7 45.6 - + + -
633H VAL* 3.7 22.2 - - + -
635H LEU* 5.3 1.8 - - + -
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Residues in contact with SER 583 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579H GLU* 3.0 15.2 + - - -
580H ARG* 3.3 27.8 + - - +
581H LEU 3.2 0.8 - - - -
582H PHE* 1.3 76.2 - - - +
584H VAL* 1.3 59.3 + - - +
585H ASP* 3.8 8.4 + - - +
631H TYR* 3.8 19.7 - - - -
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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
------------------------------------------------------------
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