Contacts of the helix formed by residues 607 - 623 (chain A) in PDB entry 2FGJ
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 SER 607 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LEU* 1.3 78.9 - - - +
608A GLY* 1.3 65.4 + - - +
610A GLN* 3.1 33.8 + - - +
611A ARG* 3.0 24.4 + - - +
504B SER* 3.7 1.0 + - - -
505B GLY* 3.9 2.1 + - - -
801B ATP 3.0 60.4 + - - -
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Residues in contact with GLY 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A SER* 1.3 72.3 - - - +
609A GLY* 1.3 51.7 + - - +
611A ARG* 3.2 22.3 + - - +
612A GLN* 2.7 38.4 + - - +
635A ALA* 6.6 0.4 - - - -
550B GLN* 4.8 14.1 - - - -
801B ATP 3.5 9.7 + - - -
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Residues in contact with GLY 609 (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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608A GLY* 1.3 70.2 - - - +
610A GLN* 1.3 54.0 + - - -
612A GLN* 3.3 5.1 + - - +
613A ARG* 2.9 35.2 + - - -
635A ALA* 5.2 6.0 + - - +
636A LEU* 3.6 18.1 - - - +
504B SER* 3.2 10.5 - - - -
801B ATP 2.8 25.0 + - - -
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Residues in contact with GLN 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A PHE* 3.5 57.8 - - + +
606A LEU* 3.8 9.5 - - + +
607A SER* 3.1 30.3 + - - +
609A GLY* 1.3 73.2 - - - +
611A ARG* 1.3 66.2 + - - +
613A ARG* 3.0 23.5 + - - +
614A ILE* 3.1 17.7 + - - +
504B SER* 3.4 2.5 + - - +
505B GLY* 3.8 18.0 + - - -
801B ATP 2.8 33.4 + - - -
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Residues in contact with ARG 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ASP* 3.7 22.4 + - - -
552A ASN* 3.7 21.4 + - - +
553A VAL 4.6 4.4 + - - -
554A LEU* 3.7 32.1 - - + +
599A VAL* 6.1 1.3 - - - -
600A GLY 6.3 1.1 - - - +
606A LEU* 3.7 30.4 + - + +
607A SER 3.0 20.4 + - - +
608A GLY* 3.5 18.0 - - - +
610A GLN* 1.3 75.6 - - - +
612A GLN* 1.3 62.6 + - - +
614A ILE* 3.3 7.7 + - - +
615A ALA* 3.2 21.0 + - - +
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Residues in contact with GLN 612 (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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548A VAL* 4.2 2.5 - - - +
549A LEU 2.8 26.7 + - - -
550A GLN 3.0 22.4 + - - +
551A ASP* 4.2 2.3 - - - +
552A ASN* 3.3 21.2 + - - +
608A GLY 2.7 21.2 + - - +
609A GLY* 3.4 10.1 - - - +
610A GLN 3.2 0.2 - - - -
611A ARG* 1.3 73.6 - - - +
613A ARG* 1.3 59.5 + - - +
615A ALA* 3.4 4.0 + - - +
616A ILE* 3.2 33.7 + - + +
632A ALA* 2.8 35.7 + - - +
636A LEU* 4.5 8.7 - - + -
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Residues in contact with ARG 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA* 3.4 29.3 - - - +
583A GLY 3.1 25.4 + - - -
584A ALA* 4.0 12.9 - - + +
586A ASP* 6.1 1.2 - - - +
587A PHE* 3.1 31.5 - - + +
609A GLY 2.9 18.4 + - - +
610A GLN* 3.0 17.0 + - - +
612A GLN* 1.3 75.0 - - - +
614A ILE* 1.3 58.2 + - - +
616A ILE* 3.4 4.9 + - - -
617A ALA* 3.0 24.9 + - - +
636A LEU* 4.0 14.6 - - + -
640A SER* 4.1 16.2 + - - -
644A ILE* 4.2 12.1 - - + -
504B SER* 2.8 42.0 + - - -
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Residues in contact with ILE 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A LEU* 3.7 28.5 - - + -
559A ILE* 3.7 20.9 - - + -
562A ASN* 4.7 4.7 - - + -
563A ILE* 4.0 19.5 - - + +
584A ALA* 4.1 4.0 - - + -
587A PHE* 3.7 15.7 - - + -
588A ILE* 3.5 33.2 - - + -
599A VAL* 6.0 0.4 - - + -
606A LEU* 4.7 9.4 - - + -
610A GLN 3.1 14.0 + - - +
611A ARG* 3.5 10.1 - - - +
613A ARG* 1.3 73.1 - - - +
615A ALA* 1.3 60.9 + - - +
617A ALA* 3.3 6.7 + - - +
618A ARG* 2.8 28.4 + - + +
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Residues in contact with ALA 615 (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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548A VAL* 4.2 6.4 - - + +
552A ASN* 3.8 38.8 - - + +
554A LEU* 5.2 1.8 - - + +
611A ARG 3.2 10.0 + - - +
612A GLN* 3.5 10.8 - - - +
614A ILE* 1.3 81.0 - - - +
616A ILE* 1.3 55.0 + - - +
618A ARG* 3.3 27.8 + - - +
619A ALA* 2.9 25.3 + - - +
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Residues in contact with ILE 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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548A VAL* 3.9 17.9 - - + -
582A ALA* 3.9 13.2 - - + -
612A GLN* 3.2 31.0 + - + +
613A ARG* 3.8 5.2 - - - +
614A ILE 3.2 0.4 - - - -
615A ALA* 1.3 73.5 - - - +
617A ALA* 1.3 60.3 + - - +
619A ALA* 3.1 7.4 + - - +
620A LEU* 2.8 42.7 + - + +
629A PHE* 4.2 17.5 - - + -
632A ALA* 4.5 5.4 - - + +
633A THR* 4.3 16.6 - - + -
636A LEU* 5.0 1.6 - - + -
644A ILE* 3.8 41.5 - - + -
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Residues in contact with ALA 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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563A ILE* 4.1 19.7 - - + -
578A ALA* 3.4 30.9 - - + +
579A ALA* 4.1 4.3 - - - -
582A ALA* 3.5 6.8 - - + +
584A ALA* 5.2 0.9 - - + -
613A ARG 3.0 15.1 + - - +
614A ILE* 3.5 9.6 - - - +
616A ILE* 1.3 75.4 - - - +
618A ARG* 1.3 62.7 + - - +
620A LEU* 3.1 13.9 + - - +
621A VAL* 3.1 19.6 + - - +
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Residues in contact with ARG 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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547A VAL 5.2 5.9 + - - -
548A VAL* 5.3 1.4 - - - +
552A ASN* 4.0 21.0 - - - +
553A VAL* 4.5 14.9 - - - +
554A LEU* 4.7 15.2 - - - +
562A ASN* 3.3 27.6 + - - +
563A ILE* 3.6 23.0 - - - +
565A LEU* 4.3 19.7 - - + +
566A ALA* 3.2 31.8 - - + +
614A ILE* 2.8 15.3 + - + +
615A ALA* 3.3 47.3 + - - +
616A ILE 3.2 0.2 - - - -
617A ALA* 1.3 76.3 - - - +
619A ALA* 1.3 67.3 + - - +
621A VAL* 3.4 3.5 + - - +
622A ASN* 3.4 0.5 + - - +
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Residues in contact with ALA 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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546A GLY* 5.9 0.9 - - - -
547A VAL 5.2 2.9 - - - +
548A VAL* 3.3 35.2 - - + -
615A ALA 2.9 7.8 + - - +
616A ILE* 3.1 7.2 + - - +
618A ARG* 1.3 80.1 - - - +
620A LEU* 1.3 63.6 + - + +
622A ASN* 3.3 20.8 + - - +
623A ASN 3.7 4.3 + - - -
624A PRO* 3.8 9.0 - - - +
627A LEU* 4.1 17.4 - - + +
629A PHE* 5.4 1.1 - - + -
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Residues in contact with LEU 620 (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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578A ALA* 4.1 9.4 - - + +
581A LEU* 3.7 42.8 - - + +
582A ALA* 4.1 16.2 - - + +
616A ILE* 2.8 32.3 + - + +
617A ALA* 3.1 6.5 + - - +
619A ALA* 1.3 77.3 - - + +
621A VAL* 1.3 61.9 + - - +
623A ASN* 3.3 22.9 + - - +
624A PRO* 5.7 0.2 - - - -
627A LEU* 4.5 12.3 - - + -
629A PHE* 5.3 0.9 - - + -
644A ILE* 5.9 0.7 - - + -
648A MET* 4.9 3.4 - - + -
651A ILE* 3.5 42.0 - - + -
655A ARG* 4.1 6.6 + - - +
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Residues in contact with VAL 621 (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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563A ILE* 3.8 12.3 - - + +
566A ALA* 3.9 7.8 - - + +
567A ASN* 3.6 22.5 + - + +
570A MET* 3.3 41.5 - - + -
574A LYS* 6.1 1.8 - - + -
578A ALA* 3.4 23.8 - - + -
617A ALA 3.1 14.7 + - - +
618A ARG 3.7 6.3 - - - +
619A ALA 3.3 0.2 - - - -
620A LEU* 1.3 75.0 - - - +
622A ASN* 1.3 62.4 + - - +
623A ASN* 2.8 19.4 + - - +
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Residues in contact with ASN 622 (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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542A ARG 5.5 1.9 - - - +
543A ARG* 5.2 5.0 + - - +
545A VAL 4.9 2.1 - - - +
546A GLY* 4.4 9.5 - - - -
566A ALA* 3.4 31.6 + - + +
618A ARG 3.4 3.9 + - - +
619A ALA* 3.3 14.5 + - - +
620A LEU 3.3 0.6 - - - -
621A VAL* 1.3 78.6 - - - +
623A ASN* 1.3 65.3 + - - +
624A PRO* 4.2 18.6 - - + +
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Residues in contact with ASN 623 (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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620A LEU 3.3 15.0 + - - +
621A VAL* 2.8 24.0 + - - +
622A ASN* 1.3 79.3 - - - +
624A PRO* 1.3 73.4 - - - +
625A LYS* 3.9 10.4 + - - +
655A ARG* 3.0 33.0 + - - +
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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