Contacts of the helix formed by residues 607 - 623 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A SER* 3.8 0.7 + - - -
505A GLY* 3.9 1.6 + - - -
800A ATP 2.9 57.4 + - - -
606B LEU* 1.3 79.4 - - - +
608B GLY* 1.3 54.4 + - - +
610B GLN* 3.0 33.0 + - - +
611B ARG* 2.8 36.5 + - - +
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Residues in contact with GLY 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A GLN* 5.7 7.0 - - - -
800A ATP 3.7 12.8 + - - -
607B SER* 1.3 71.8 - - - +
609B GLY* 1.3 56.7 + - - +
611B ARG* 3.4 27.0 + - - +
612B GLN* 3.0 30.2 + - - +
635B ALA* 5.9 1.6 - - - -
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Residues in contact with GLY 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A SER* 3.2 11.0 - - - -
800A ATP 2.6 25.9 + - - -
608B GLY* 1.3 67.7 - - - -
610B GLN* 1.3 64.7 + - - +
612B GLN* 3.3 2.1 + - - +
613B ARG* 3.0 31.2 + - - -
635B ALA* 5.0 5.7 + - - -
636B LEU* 3.5 20.0 - - - -
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Residues in contact with GLN 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A SER* 3.3 4.2 + - - +
505A GLY* 4.4 9.5 - - - -
800A ATP 3.1 37.1 + - - -
587B PHE* 3.4 55.0 - - + +
591B LEU* 5.7 3.0 - - - +
606B LEU* 3.9 11.1 - - + +
607B SER* 3.0 30.6 + - - +
609B GLY* 1.3 76.5 - - - +
611B ARG* 1.3 62.1 + - - +
613B ARG* 3.3 15.0 + - - +
614B ILE* 3.2 28.1 + - - +
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B ASP* 3.8 14.6 + - - -
552B ASN* 3.1 32.4 + - + +
554B LEU* 4.4 23.3 - - + +
603B GLY 4.4 5.7 + - - -
604B ALA* 2.8 39.7 + - - +
606B LEU* 3.9 16.2 + - + +
607B SER 2.8 22.9 + - - +
608B GLY* 3.6 24.3 + - - +
610B GLN* 1.3 72.3 - - - +
612B GLN* 1.3 62.6 + - - +
614B ILE* 3.5 4.1 + - - +
615B ALA* 3.1 22.0 + - - +
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Residues in contact with GLN 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B VAL* 3.9 7.7 - - - +
549B LEU 2.6 28.7 + - - -
550B GLN 2.7 22.1 + - - +
552B ASN* 3.1 22.5 + - - +
608B GLY 3.0 18.6 + - - +
609B GLY* 3.5 5.4 - - - +
610B GLN 3.2 0.2 - - - -
611B ARG* 1.3 79.8 + - - +
613B ARG* 1.3 56.6 + - - +
615B ALA* 3.3 7.0 + - - +
616B ILE* 3.1 34.9 + - + +
632B ALA* 3.0 32.2 + - - +
635B ALA* 6.5 1.3 - - + -
636B LEU* 4.1 13.7 - - + -
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Residues in contact with ARG 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SER* 2.7 39.2 + - - -
582B ALA* 3.4 32.5 + - - +
583B GLY* 3.1 24.7 + - - -
584B ALA* 3.9 13.4 - - + +
586B ASP* 6.4 0.2 - - - +
587B PHE* 3.4 22.1 - - + +
609B GLY 3.0 19.5 + - - +
610B GLN* 3.3 22.0 + - - +
612B GLN* 1.3 73.2 - - - +
614B ILE* 1.3 60.5 + - - +
616B ILE* 3.3 6.9 + - - -
617B ALA* 3.0 24.3 + - - +
636B LEU* 3.9 27.8 - - + -
640B SER* 3.9 18.5 + - - -
644B ILE* 4.3 2.5 - - + -
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Residues in contact with ILE 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B LEU* 3.7 31.9 - - + -
559B ILE* 4.1 26.2 - - + -
562B ASN* 4.6 7.2 - - + -
563B ILE* 4.0 22.3 - - + +
584B ALA* 3.9 14.1 - - + +
587B PHE* 3.8 24.9 - - + -
588B ILE* 5.3 3.4 - - + -
606B LEU* 4.8 7.2 - - + -
610B GLN 3.2 15.7 + - - +
611B ARG* 3.6 7.6 - - - +
612B GLN 3.3 0.2 - - - -
613B ARG* 1.3 75.4 - - - +
615B ALA* 1.3 57.3 + - - +
617B ALA* 3.4 5.2 + - - +
618B ARG* 2.9 27.2 + - - +
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Residues in contact with ALA 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B VAL* 4.2 5.4 - - + +
552B ASN* 3.5 36.8 - - + +
554B LEU* 4.7 3.8 - - + +
611B ARG 3.1 12.6 + - - +
612B GLN 3.4 9.6 - - - +
614B ILE* 1.3 75.1 - - - +
616B ILE* 1.3 58.7 + - - +
618B ARG* 3.2 29.4 + - - +
619B ALA* 3.0 24.9 + - - +
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Residues in contact with ILE 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B VAL* 4.0 21.5 - - + -
581B LEU 5.6 0.4 - - - +
582B ALA* 3.9 16.8 - - + -
612B GLN* 3.1 21.3 + - + +
613B ARG* 3.6 10.5 - - - +
614B ILE 3.2 0.2 - - - -
615B ALA* 1.3 74.3 - - - +
617B ALA* 1.3 65.8 + - - +
619B ALA* 3.2 3.3 + - - +
620B LEU* 3.0 34.5 + - + +
629B PHE* 4.1 27.4 - - + -
632B ALA* 4.8 7.9 - - + +
633B THR* 4.3 16.8 - - + -
636B LEU* 5.2 1.1 - - + -
644B ILE* 3.8 30.1 - - + -
651B ILE* 5.6 1.6 - - + -
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Residues in contact with ALA 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B ILE* 3.8 22.0 - - + -
578B ALA* 3.9 23.8 - - - +
579B ALA* 4.0 15.7 - - + -
582B ALA* 3.8 1.3 - - + +
584B ALA* 5.3 1.1 - - + -
613B ARG 3.0 14.0 + - - +
614B ILE* 3.5 9.9 - - - +
616B ILE* 1.3 75.8 - - - +
618B ARG* 1.3 61.7 + - - +
620B LEU* 3.1 8.5 + - - +
621B VAL* 3.0 23.6 + - - +
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Residues in contact with ARG 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B VAL 5.2 4.9 + - - -
548B VAL* 5.1 4.0 - - - +
552B ASN* 4.1 15.6 - - - +
553B VAL 4.5 9.5 + - - -
554B LEU* 4.5 15.4 - - + +
562B ASN 3.4 25.8 + - - +
563B ILE* 3.6 18.5 - - - +
565B LEU* 3.8 24.1 - - + +
614B ILE* 2.9 19.5 + - + +
615B ALA* 3.2 41.4 + - - +
616B ILE 3.2 0.2 - - - -
617B ALA* 1.3 74.9 - - - +
619B ALA* 1.3 63.4 + - - +
621B VAL* 3.1 5.0 + - - +
622B ASN* 2.8 45.5 + - - +
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Residues in contact with ALA 619 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546B GLY* 5.6 4.3 - - - -
547B VAL 5.4 2.2 - - - +
548B VAL* 3.5 32.3 - - + -
615B ALA 3.0 10.6 + - - +
616B ILE 3.2 4.5 + - - +
618B ARG* 1.3 81.2 - - - +
620B LEU* 1.3 61.4 + - - +
622B ASN* 3.2 12.9 + - - +
623B ASN 3.1 17.2 + - - -
624B PRO* 3.3 10.0 - - - +
627B LEU* 3.9 15.7 - - + -
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B ALA* 3.7 30.7 - - + +
581B LEU* 3.9 26.5 - - + -
582B ALA 4.8 0.7 - - - +
616B ILE* 3.0 32.2 + - + +
617B ALA* 3.3 7.2 - - - +
619B ALA* 1.3 74.8 - - - +
621B VAL* 1.3 61.3 - - - +
623B ASN* 3.2 22.1 + - - +
624B PRO* 5.1 0.7 - - - -
627B LEU* 4.2 10.8 - - + -
651B ILE* 3.6 36.6 - - + +
655B ARG* 3.8 22.4 + - - +
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Residues in contact with VAL 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B ILE* 3.3 46.7 - - + +
564B SER* 4.2 3.6 - - - -
565B LEU 4.8 1.1 - - - +
566B ALA* 4.3 4.3 - - - +
567B ASN* 4.7 13.4 + - + +
570B MET* 3.6 37.9 - - + -
574B LYS 4.8 3.8 - - - +
575B VAL* 4.8 2.2 - - - -
578B ALA* 3.8 15.7 - - + -
617B ALA 3.0 9.1 + - - +
618B ARG 3.1 3.1 + - - +
620B LEU* 1.3 73.2 - - - +
622B ASN* 1.3 66.3 + - - +
623B ASN* 3.0 8.4 + - - +
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Residues in contact with ASN 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B ARG 5.7 0.5 - - - +
546B GLY* 6.1 3.4 - - - -
565B LEU* 4.1 8.1 + - - +
566B ALA* 3.5 38.5 + - - +
618B ARG* 2.8 37.8 + - - +
619B ALA* 3.3 14.6 - - - +
621B VAL* 1.3 74.7 - - - +
623B ASN* 1.3 67.2 + - - +
624B PRO* 3.8 5.3 - - + +
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Residues in contact with ASN 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B ARG 5.0 1.7 - - - +
619B ALA 3.1 2.8 + - - -
620B LEU 3.2 13.5 + - - +
621B VAL 3.0 7.7 - - - +
622B ASN* 1.3 80.7 - - - +
624B PRO* 1.3 70.9 + - - +
625B LYS* 5.7 4.0 + - - -
655B ARG* 3.1 29.3 - - - +
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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