Contacts of the helix formed by residues 603 - 620 (chain A) in PDB entry 3FZP
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 THR 603 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A VAL* 3.8 13.6 - - - +
595A GLU* 4.7 5.4 + - + +
601A ARG* 5.0 14.1 - - + +
602A PHE* 1.3 82.9 - - - +
604A THR* 1.3 64.9 + - - +
605A ALA* 3.3 11.2 + - - +
606A SER* 2.9 30.3 + - - -
607A ASP* 3.1 11.1 + - - +
666A PRO* 5.4 1.6 - - - +
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Residues in contact with THR 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLU* 4.4 30.5 + - + +
544A ASN* 4.3 29.0 + - + +
545A CYS 4.5 6.5 - - - +
546A VAL* 4.0 12.5 - - + +
603A THR* 1.3 74.3 - - - +
605A ALA* 1.3 59.4 + - - +
607A ASP* 3.2 11.3 + - - +
608A VAL* 2.9 29.8 + - - +
671A ARG* 3.9 18.8 + - - +
672A PHE* 3.9 4.2 - - + -
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Residues in contact with ALA 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A THR* 3.1 8.6 + - - +
604A THR* 1.3 83.9 + - - +
606A SER* 1.3 60.0 + - - +
608A VAL* 3.2 12.3 + - - +
609A TRP 3.1 14.7 + - - -
666A PRO* 3.6 37.7 - - + +
669A ARG* 3.1 19.2 + - + +
670A PRO 5.9 0.7 - - - +
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Residues in contact with SER 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A SER* 3.2 25.7 + - - -
595A GLU* 3.6 6.9 + - - -
596A SER* 3.5 10.7 + - - -
601A ARG 4.3 2.0 - - - -
602A PHE* 3.4 12.0 - - - +
603A THR* 2.9 35.4 + - - -
605A ALA* 1.3 74.1 - - - +
607A ASP* 1.3 63.9 + - - +
609A TRP* 3.3 4.5 + - - +
610A MET* 3.0 27.1 + - - +
669A ARG* 3.8 8.9 - - - +
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Residues in contact with ASP 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A MET* 3.3 11.6 - - - +
545A CYS 4.3 1.0 - - - +
546A VAL* 3.5 7.9 - - - +
547A HIS 2.2 50.1 + - - +
548A ARG* 4.0 5.5 - - - +
550A ILE* 3.7 15.9 - - + +
602A PHE* 5.8 0.5 - - - +
603A THR 3.1 9.5 + - - +
604A THR* 3.3 12.3 - - - +
606A SER* 1.3 84.0 + - - +
608A VAL* 1.3 51.3 + - - +
610A MET* 3.2 6.7 + - - +
611A PHE* 2.7 37.1 + - - +
672A PHE* 3.7 12.0 - - + -
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Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLU* 4.8 1.1 - - - +
604A THR 2.9 12.9 + - - +
605A ALA* 3.5 12.1 - - - +
606A SER 3.2 0.4 - - - -
607A ASP* 1.3 73.2 - - - +
609A TRP* 1.3 66.9 + - - +
611A PHE* 3.3 2.9 + - - +
612A ALA* 3.1 22.7 + - - +
661A CYS* 3.6 32.4 - - + +
669A ARG* 4.1 7.0 - - + -
670A PRO* 3.3 28.3 - - + +
671A ARG* 4.4 0.9 - - - -
672A PHE* 3.6 43.5 - - + +
675A LEU* 4.0 5.6 - - + -
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Residues in contact with TRP 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LYS 5.7 0.2 + - - -
591A TRP 3.7 8.2 + - - -
592A MET 3.2 11.3 + - - -
593A SER* 3.5 30.3 - - - -
594A PRO* 3.4 23.3 - - + -
605A ALA 3.1 6.9 + - - -
606A SER 3.4 8.5 - - - +
608A VAL* 1.3 76.0 - - - +
610A MET* 1.3 67.0 + - - +
612A ALA 3.2 1.0 + - - -
613A VAL* 3.1 29.2 + - + +
626A PHE* 6.1 1.6 - + - -
638A LEU* 3.7 31.2 - - + +
643A ARG* 3.9 20.0 - - - -
661A CYS 3.5 12.7 + - - +
662A TRP* 3.2 56.6 + + + -
663A ASP 3.8 5.4 - - - -
669A ARG* 3.5 23.6 - - - +
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Residues in contact with MET 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A HIS 4.5 1.6 - - - +
548A ARG* 3.1 33.4 - - - +
549A ASP* 3.7 6.1 - - - +
550A ILE* 3.3 44.8 - - + +
551A ALA* 5.2 0.7 - - + -
588A PRO* 3.8 13.9 - - + -
591A TRP* 3.5 47.3 - - + +
592A MET* 5.2 5.6 - - + -
606A SER 3.0 16.7 + - - +
607A ASP* 3.7 7.4 - - - +
609A TRP* 1.3 76.3 - - - +
611A PHE* 1.3 64.2 + - - +
613A VAL* 3.0 5.6 + - - +
614A CYS 3.0 18.0 + - - -
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Residues in contact with PHE 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A SER* 3.3 21.1 - - - -
533A ILE* 3.8 22.9 - - + -
534A CYS* 3.2 44.2 - - + -
537A MET* 4.6 1.1 - - + -
550A ILE* 4.1 16.3 - - + +
607A ASP 2.7 20.2 + - - +
608A VAL 3.6 5.2 - - - +
610A MET* 1.3 74.4 - - - +
612A ALA* 1.3 58.5 + - + +
614A CYS* 3.2 7.3 + - + +
615A MET* 3.0 56.0 + - + +
618A ILE* 6.4 0.4 - - + -
661A CYS* 5.2 0.4 - - - -
672A PHE* 3.7 25.4 - + + -
675A LEU* 4.2 13.7 - - + -
679A LEU* 3.7 7.9 - - + -
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Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A VAL 3.1 6.5 + - - -
609A TRP 3.2 2.0 + - - +
611A PHE* 1.3 73.1 - - - +
613A VAL* 1.3 66.6 + - - +
615A MET* 3.2 15.7 + - + +
616A TRP 3.0 18.0 + - - -
658A MET* 4.0 10.7 - - - +
661A CYS* 3.2 39.0 - - + -
662A TRP* 3.4 27.6 - - + +
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Residues in contact with VAL 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LYS 4.0 5.6 - - - +
591A TRP* 3.6 41.3 - - + +
609A TRP* 3.1 25.6 + - - +
610A MET 3.0 8.1 + - - +
612A ALA* 1.3 78.1 - - - +
614A CYS* 1.3 55.8 + - - +
616A TRP* 3.2 5.2 + - - +
617A GLU* 2.9 25.3 + - - +
625A PRO* 3.6 32.1 - - + -
626A PHE* 6.1 0.7 - - + -
644A LEU* 4.0 10.3 - - + -
662A TRP* 3.5 17.0 - - - +
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Residues in contact with CYS 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A ILE* 5.0 4.7 - - - -
550A ILE* 3.5 28.6 + - + +
551A ALA* 4.1 14.6 - - - -
552A VAL* 4.1 5.2 - - - -
555A ILE* 3.5 32.5 - - - -
610A MET 3.0 7.1 + - - +
611A PHE* 3.2 12.3 - - + +
613A VAL* 1.3 72.4 - - - +
615A MET* 1.3 59.1 + - - +
617A GLU* 3.0 14.7 + - - +
618A ILE* 2.9 38.7 + - - +
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Residues in contact with MET 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A SER* 3.5 30.3 - - - +
611A PHE* 3.0 49.0 + - + +
612A ALA* 3.4 19.3 - - + +
614A CYS* 1.3 73.9 - - - +
616A TRP* 1.3 51.5 + - - +
618A ILE* 3.2 3.3 + - + +
619A LEU* 2.8 41.4 + - + +
654A LEU* 4.2 11.2 - - + -
657A LEU* 5.0 4.0 - - + -
658A MET* 3.5 40.8 - - + +
661A CYS* 4.9 4.5 - - - -
675A LEU* 5.9 1.8 - - + -
679A LEU* 4.1 17.0 - - + -
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Residues in contact with TRP 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SO4 5.2 3.8 - - - -
612A ALA 3.0 12.4 + - - +
613A VAL 3.2 13.2 + - - +
615A MET* 1.3 72.8 - - - +
617A GLU* 1.3 63.0 + - + +
619A LEU* 3.9 0.3 - - - -
620A SER* 2.5 54.8 + - - -
623A LYS* 3.4 32.5 - - + -
624A GLN 3.8 10.8 - - - -
625A PRO* 3.5 28.5 - - + -
627A PHE* 4.6 10.3 - + - -
628A TRP* 4.6 5.6 - + - -
644A LEU* 3.5 34.1 - - + +
645A PRO* 2.8 41.2 + - + -
647A PRO* 3.5 20.0 - - + +
655A TYR* 5.2 0.2 - + - -
658A MET* 3.9 9.7 - - - +
662A TRP* 4.3 10.8 - + + -
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Residues in contact with GLU 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LEU* 4.0 0.2 - - - +
551A ALA* 3.2 5.7 - - - +
552A VAL* 2.8 51.4 + - + +
553A ARG 5.0 0.7 + - - -
591A TRP* 2.8 42.8 + - - +
613A VAL 2.9 16.9 + - - +
614A CYS* 3.0 12.4 + - - +
616A TRP* 1.3 78.3 - - + +
618A ILE* 1.3 64.3 + - - +
620A SER* 3.5 1.0 + - - -
621A PHE 3.2 2.3 + - - -
622A GLY* 2.7 32.1 + - - +
623A LYS 3.7 19.2 - - - +
624A GLN* 5.0 1.0 - - - -
625A PRO* 4.1 7.8 - - + +
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Residues in contact with ILE 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A LEU* 3.8 19.7 - - + -
514A LEU* 3.8 11.9 - - + +
526A LEU* 3.6 52.2 - - + +
529A TYR* 4.1 9.6 - - + +
530A SER* 3.9 28.5 - - - +
533A ILE* 4.9 5.4 - - + -
552A VAL* 3.6 15.9 - - + -
611A PHE* 6.4 0.7 - - + -
614A CYS* 2.9 29.2 + - - +
615A MET* 3.6 7.4 - - + +
617A GLU* 1.3 77.0 - - - +
619A LEU* 1.3 61.8 + - + +
621A PHE* 3.0 18.7 + - - -
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Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SO4 4.3 2.9 + - - -
523A VAL* 4.6 6.1 - - + -
526A LEU* 3.8 29.8 - - + +
527A VAL* 5.0 0.9 - - + -
530A SER* 4.1 11.0 - - - +
615A MET* 2.8 28.6 + - + +
618A ILE* 1.3 86.1 - - + +
620A SER* 1.3 56.3 + - - +
621A PHE* 3.3 16.1 + - - -
647A PRO* 3.7 28.8 - - + +
649A LEU* 4.2 13.7 - - - +
650A CYS* 4.0 24.2 - - + +
651A PRO* 4.6 2.2 - - + -
654A LEU* 4.1 18.4 - - + -
658A MET* 4.0 11.9 - - + -
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Residues in contact with SER 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SO4 3.7 18.2 + - - -
616A TRP* 2.5 45.3 + - - -
617A GLU 3.9 3.4 - - - -
618A ILE 3.2 0.2 - - - -
619A LEU* 1.3 75.8 - - - +
621A PHE* 1.3 73.4 + - - +
622A GLY 3.1 0.7 + - - -
623A LYS* 3.4 41.1 + - - +
647A PRO* 3.5 8.4 - - - +
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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
------------------------------------------------------------
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