Contacts of the helix formed by residues 567 - 583 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536F MET* 4.6 32.2 - - + +
538F THR* 4.1 14.3 - - - +
566F GLU* 1.3 81.1 - - + +
568F LEU* 1.3 67.3 + - - +
569F ALA* 3.2 14.2 - - - +
570F ASP* 2.8 49.5 + - - +
571F LEU* 3.0 22.2 + - - +
607F ASP* 3.4 27.1 + - + +
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Residues in contact with LEU 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566F GLU 3.9 0.6 + - - -
567F ARG* 1.3 71.4 - - - +
569F ALA* 1.3 64.3 + - - +
571F LEU* 3.2 9.9 + - + +
572F GLN* 3.0 28.8 + - - +
604F SER* 5.0 3.7 - - - +
607F ASP* 2.9 19.0 + - + +
608F ALA* 3.7 25.8 - - + -
612F SER* 3.9 15.3 - - - +
613F ALA* 3.9 15.7 - - + +
616F GLN* 3.5 37.0 - - + +
725F THR* 4.2 12.6 - - + +
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Residues in contact with ALA 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567F ARG* 3.2 14.8 - - + +
568F LEU* 1.3 78.3 - - - +
570F ASP* 1.3 68.0 + - - +
572F GLN* 3.4 9.9 + - - +
573F SER* 3.2 23.2 + - - -
607F ASP* 4.5 1.0 + - - -
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Residues in contact with ASP 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536F MET* 5.1 2.8 - - - -
537F ALA 3.6 24.6 - - - +
538F THR* 3.5 15.6 - - - +
565F PHE* 3.9 16.1 - - + -
566F GLU* 4.4 2.3 + - - +
567F ARG* 2.8 63.1 + - - +
569F ALA* 1.3 78.8 - - - +
571F LEU* 1.3 59.6 + - - +
573F SER* 3.4 8.5 + - - -
574F ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565F PHE* 4.0 26.5 - - + +
567F ARG 3.0 12.8 + - - +
568F LEU* 3.2 11.2 + - + +
570F ASP* 1.3 73.8 - - - +
572F GLN* 1.3 67.3 + - - +
574F ALA* 3.2 18.8 + - + +
575F PRO* 3.6 5.2 - - - +
599F VAL* 4.5 8.7 - - + -
600F GLY 5.2 2.0 - - - +
604F SER* 3.7 27.1 - - - +
613F ALA 4.5 4.9 - - - +
616F GLN* 3.8 22.1 - - + +
617F LEU* 4.4 31.2 - - + +
620F ALA* 3.7 28.2 - - + +
624F MET* 5.9 0.4 - - + -
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Residues in contact with GLN 572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568F LEU* 3.0 22.6 + - - +
569F ALA* 3.6 9.2 - - - +
571F LEU* 1.3 78.9 - - - +
573F SER* 1.3 58.8 + - - +
575F PRO* 3.4 10.4 - - - +
576F ALA* 5.8 0.2 - - - +
616F GLN* 3.4 31.3 + - - +
619F ARG* 5.3 8.2 - - - +
623F GLU* 4.8 4.0 - - - +
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Residues in contact with SER 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538F THR 3.9 14.6 + - - -
569F ALA 3.2 11.2 + - - -
570F ASP* 3.4 12.0 + - - -
571F LEU 3.3 0.2 - - - -
572F GLN* 1.3 76.7 - - - +
574F ALA* 1.3 66.5 + - - +
575F PRO* 3.3 2.2 - - - -
576F ALA* 2.9 24.3 + - - +
577F SER* 3.0 15.0 + - - -
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Residues in contact with ALA 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F PHE* 3.7 32.1 - - + -
570F ASP 3.0 14.9 + - - +
571F LEU* 3.2 17.7 + - + +
573F SER* 1.3 75.2 - - - +
575F PRO* 1.3 65.2 - - + +
577F SER* 3.2 6.6 + - - -
578F VAL* 3.0 29.5 + - - +
620F ALA* 4.9 4.3 - - + -
624F MET* 4.3 10.8 - - + -
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Residues in contact with PRO 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571F LEU 3.6 5.2 - - - +
572F GLN 3.4 15.3 - - - +
573F SER 3.5 1.3 - - - -
574F ALA* 1.3 93.8 - - + +
576F ALA* 1.3 56.5 + - - +
578F VAL* 4.0 2.8 - - + +
579F GLU* 3.0 30.4 + - - +
620F ALA* 4.2 6.5 - - - +
623F GLU* 3.3 51.4 - - + +
624F MET* 4.0 17.2 - - + +
627F VAL* 4.3 7.7 - - + +
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Residues in contact with ALA 576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573F SER* 2.9 17.9 + - - +
575F PRO* 1.3 80.0 - - - +
577F SER* 1.3 62.8 + - - +
579F GLU* 3.2 8.8 + - - +
580F ARG* 3.1 27.1 + - - +
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Residues in contact with SER 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538F THR 3.9 14.8 + - - -
539F ALA* 4.3 3.3 - - - -
540F PRO* 3.6 33.7 - - - +
565F PHE* 4.6 13.0 - - - -
573F SER* 3.0 19.3 + - - -
574F ALA* 3.7 7.9 - - - -
576F ALA* 1.3 77.6 - - - +
578F VAL* 1.3 63.1 + - - +
580F ARG 3.4 1.0 + - - -
581F LEU* 3.1 29.1 + - - +
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Residues in contact with VAL 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563F PRO* 5.9 1.8 - - + -
565F PHE* 4.6 12.8 - - + -
574F ALA 3.0 17.1 + - - +
575F PRO* 4.1 4.7 - - + +
577F SER* 1.3 75.5 - - - +
579F GLU* 1.3 58.3 + - - +
581F LEU* 3.4 10.9 + - + +
582F PHE* 2.9 64.4 + - + -
595F GLN* 5.0 7.0 - - + -
597F VAL* 4.7 8.5 - - + -
624F MET* 4.0 26.5 - - + +
627F VAL* 4.9 7.4 - - + -
635F LEU* 5.4 4.0 - - + -
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Residues in contact with GLU 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575F PRO 3.0 19.9 + - - +
576F ALA* 3.2 8.2 + - - +
578F VAL* 1.3 77.7 - - - +
580F ARG* 1.3 65.4 + - - +
582F PHE* 3.3 5.3 + - - +
583F SER* 2.8 28.0 + - - +
627F VAL* 3.6 16.1 - - + +
630F ARG* 2.8 36.5 + - - -
631F TYR* 3.3 23.6 + - + +
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Residues in contact with ARG 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484F ASP* 5.8 3.1 + - - -
487F GLN* 3.5 28.4 - - - +
540F PRO* 4.5 10.5 - - + -
576F ALA* 3.1 17.7 + - - +
577F SER 4.2 2.5 - - - +
578F VAL 3.3 0.2 - - - -
579F GLU* 1.3 79.8 - - - +
581F LEU* 1.3 67.1 + - - +
583F SER* 3.1 20.2 + - - -
584F VAL* 3.3 21.6 + - + +
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Residues in contact with LEU 581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540F PRO* 3.8 35.4 - - + +
543F VAL* 4.1 32.8 - - + -
544F LEU* 4.0 24.5 - - + -
563F PRO* 5.7 3.8 - - + -
565F PHE* 6.5 1.1 - - + -
577F SER* 3.1 23.3 + - - +
578F VAL* 3.6 13.9 - - + +
580F ARG* 1.3 79.1 - - - +
582F PHE* 1.3 63.9 + - + +
583F SER 3.3 0.5 + - - -
584F VAL* 3.4 11.6 + - + +
587F TYR* 3.6 41.3 - - + +
588F MET* 4.8 0.2 - - - +
595F GLN* 5.4 4.7 - - - +
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Residues in contact with PHE 582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F VAL* 2.9 43.9 + - + +
579F GLU 3.6 6.1 - - - +
580F ARG 3.2 0.2 - - - -
581F LEU* 1.3 80.8 - - + +
583F SER* 1.3 57.5 + - - +
584F VAL 3.3 0.9 - - - -
587F TYR* 4.6 2.5 - + - -
588F MET* 3.1 29.6 - - - +
591F ILE* 4.0 18.6 - - + -
595F GLN* 3.9 26.7 - - + -
627F VAL* 4.4 4.3 - - + -
628F ALA* 3.9 21.8 - - + -
631F TYR* 3.5 45.2 - + + -
633F VAL* 3.6 32.1 - - + -
635F LEU* 5.2 2.0 - - + -
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Residues in contact with SER 583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579F GLU* 2.8 16.7 + - - +
580F ARG* 3.1 19.4 + - - -
582F PHE* 1.3 76.0 - - - +
584F VAL* 1.3 61.5 - - - +
585F ASP 3.8 1.7 + - - -
588F MET* 5.3 0.2 - - - -
631F TYR* 2.6 32.4 + - - -
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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