Contacts of the helix formed by residues 607 - 623 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C GLY* 3.8 4.5 + - - -
802C ATP 3.1 65.1 + - - -
606D LEU* 1.3 76.6 - - - +
608D GLY* 1.3 53.1 + - - +
610D GLN* 2.8 34.5 + - - +
611D ARG* 2.8 33.0 + - - +
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Residues in contact with GLY 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802C ATP 4.0 7.7 + - - -
606D LEU 3.8 1.2 + - - -
607D SER* 1.3 71.6 - - - +
609D GLY* 1.3 51.4 + - - +
611D ARG* 3.3 30.6 + - - +
612D GLN* 2.8 36.7 + - - +
635D ALA* 6.5 0.9 - - - -
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Residues in contact with GLY 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C SER* 3.4 10.8 - - - -
802C ATP 2.8 25.7 + - - -
608D GLY* 1.3 70.7 - - - -
610D GLN* 1.3 58.8 + - - +
612D GLN* 3.8 2.2 - - - -
613D ARG* 2.9 32.4 + - - -
635D ALA* 5.1 6.7 + - - +
636D LEU* 3.7 20.5 - - - +
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Residues in contact with GLN 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C SER* 4.2 3.1 + - - +
505C GLY* 4.2 9.9 + - - -
802C ATP 2.7 39.4 + - - -
587D PHE* 3.7 51.5 - - + +
606D LEU* 3.7 12.7 - - + +
607D SER* 2.8 29.3 + - - +
609D GLY* 1.3 73.4 - - - +
611D ARG* 1.3 67.9 + - - +
612D GLN 3.1 1.3 - - - -
613D ARG* 3.3 13.2 + - - +
614D ILE* 3.1 29.8 + - - +
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Residues in contact with ARG 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D ASP* 3.2 23.9 + - - -
552D ASN* 3.0 33.1 + - + +
553D VAL* 4.8 2.6 - - - +
554D LEU* 4.2 36.2 - - + +
606D LEU* 4.3 19.2 + - + +
607D SER 2.8 10.3 + - - +
608D GLY* 3.3 29.4 + - - +
610D GLN* 1.3 75.1 - - - +
612D GLN* 1.3 59.2 + - - +
614D ILE* 3.5 3.7 - - - +
615D ALA* 3.1 26.5 + - - +
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Residues in contact with GLN 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C GLN* 5.7 0.6 - - - +
548D VAL* 5.1 1.3 - - - -
549D LEU 3.2 15.4 + - - -
550D GLN* 2.7 33.8 + - - +
552D ASN* 3.0 26.6 + - - +
608D GLY 2.8 17.1 + - - +
609D GLY* 4.0 6.7 - - - +
610D GLN 3.1 0.6 - - - -
611D ARG* 1.3 76.7 - - - +
613D ARG* 1.3 64.5 + - - +
615D ALA* 3.1 5.2 + - - +
616D ILE* 3.0 28.6 + - + +
631D GLU 4.5 0.4 + - - -
632D ALA* 2.7 33.1 + - - +
635D ALA* 6.1 2.6 - - + +
636D LEU* 4.1 13.7 - - + -
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Residues in contact with ARG 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C SER* 2.8 38.4 + - - -
582D ALA* 3.3 31.7 + - - +
583D GLY* 3.1 25.3 + - - -
584D ALA* 3.9 13.0 - - + -
586D ASP* 6.0 1.6 - - - +
587D PHE* 3.2 30.4 - - + +
609D GLY 2.9 18.1 + - - +
610D GLN* 3.3 10.6 + - - +
612D GLN* 1.3 76.2 - - - +
614D ILE* 1.3 59.8 + - - +
616D ILE* 3.2 7.7 + - - +
617D ALA* 2.9 24.9 + - - +
636D LEU* 4.3 15.0 - - + -
640D SER* 3.8 17.8 + - - -
644D ILE* 4.1 11.9 - - + -
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Residues in contact with ILE 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D LEU* 3.9 24.7 - - + -
559D ILE* 4.0 12.8 - - + -
562D ASN* 4.5 10.1 - - + -
563D ILE* 3.9 19.8 - - + +
584D ALA* 3.7 5.2 - - + -
587D PHE* 3.7 17.3 - - + -
588D ILE* 3.6 31.4 - - + -
606D LEU* 4.6 11.2 - - + -
610D GLN 3.1 15.9 + - - +
611D ARG* 3.5 10.8 - - - +
613D ARG* 1.3 77.4 - - - +
615D ALA* 1.3 51.6 + - - +
617D ALA* 3.3 6.8 + - - +
618D ARG* 2.8 32.9 + - + +
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Residues in contact with ALA 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D VAL* 4.2 7.5 - - + +
552D ASN* 3.5 40.4 - - + +
554D LEU* 5.5 0.7 - - + -
611D ARG 3.1 12.7 + - - +
612D GLN 3.1 10.0 + - - +
614D ILE* 1.3 72.8 - - - +
616D ILE* 1.3 61.3 + - - +
618D ARG* 3.2 22.2 + - - +
619D ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D VAL* 3.9 22.2 - - + -
582D ALA* 3.8 17.3 - - + -
612D GLN* 3.0 20.8 + - + +
613D ARG* 3.2 7.6 + - - +
615D ALA* 1.3 72.4 - - - +
617D ALA* 1.3 65.0 + - - +
619D ALA* 3.1 4.3 + - - +
620D LEU* 3.1 33.6 + - + +
627D LEU* 6.0 0.2 - - - +
629D PHE* 3.9 29.1 - - + -
632D ALA* 4.6 9.4 - - + +
633D THR* 3.9 19.7 - - + -
636D LEU* 5.6 0.7 - - + -
644D ILE* 3.8 31.0 - - + -
651D ILE* 5.7 0.7 - - + -
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Residues in contact with ALA 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D ILE* 3.9 19.9 - - + +
578D ALA* 3.9 14.6 - - - +
579D ALA* 4.1 9.9 - - - -
582D ALA* 3.6 15.2 - - + +
584D ALA* 5.1 1.1 - - + -
613D ARG 2.9 13.8 + - - +
614D ILE* 3.3 13.0 - - - +
616D ILE* 1.3 76.7 - - - +
618D ARG* 1.3 63.2 + - - +
620D LEU* 3.3 13.6 + - - +
621D VAL* 3.3 17.0 + - - +
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Residues in contact with ARG 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D VAL 5.7 3.0 + - - -
548D VAL* 5.8 1.4 - - - +
552D ASN* 3.8 23.4 - - - +
553D VAL 4.1 17.0 + - - -
554D LEU* 4.4 9.9 - - - +
562D ASN* 3.0 30.4 + - - +
563D ILE* 3.5 16.4 - - - +
565D LEU* 4.7 21.6 - - + +
566D ALA* 5.5 2.6 - - + +
614D ILE* 2.8 18.3 + - + +
615D ALA* 3.2 33.6 + - - +
617D ALA* 1.3 72.2 - - - +
619D ALA* 1.3 65.0 + - - +
621D VAL* 3.1 15.6 + - - +
622D ASN* 3.4 18.6 + - - +
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Residues in contact with ALA 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D GLY* 5.7 2.0 - - - -
547D VAL 4.7 4.9 - - - +
548D VAL* 3.4 33.4 - - + -
615D ALA 2.9 8.3 + - - +
616D ILE 3.1 4.0 + - - +
618D ARG* 1.3 79.4 - - - +
620D LEU* 1.3 58.8 + - - +
622D ASN* 3.1 28.8 - - - +
624D PRO* 3.4 14.1 - - + +
627D LEU* 3.9 16.1 - - + +
629D PHE* 5.5 0.2 - - + -
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Residues in contact with LEU 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ALA* 3.9 18.6 - - + +
581D LEU* 3.9 35.2 - - + -
582D ALA 4.6 1.3 - - - +
616D ILE* 3.1 31.5 + - + +
617D ALA* 3.6 7.9 - - - +
618D ARG 3.2 0.4 - - - -
619D ALA* 1.3 76.1 - - - +
621D VAL* 1.3 57.5 - - - +
623D ASN* 2.8 33.6 + - - +
624D PRO* 5.2 0.2 - - - -
627D LEU* 3.8 16.2 - - + -
629D PHE* 5.6 0.2 - - + -
651D ILE* 3.6 38.4 - - + +
655D ARG* 4.2 12.8 - - - +
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Residues in contact with VAL 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D ILE* 3.6 30.5 - - + +
564D SER* 4.3 5.2 - - - +
566D ALA* 4.9 1.6 - - + -
567D ASN* 3.7 40.4 + - + +
570D MET* 3.8 33.6 - - + +
575D VAL* 5.1 0.2 - - - -
578D ALA* 3.9 11.4 - - + -
617D ALA 3.3 14.3 + - - +
618D ARG 3.1 6.9 + - - +
620D LEU* 1.3 71.9 - - - +
622D ASN* 1.3 67.6 + - - +
623D ASN* 3.0 6.3 + - - +
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Residues in contact with ASN 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542D ARG 6.0 0.4 + - - -
543D ARG* 5.6 4.9 + - - +
566D ALA* 3.8 26.2 - - - +
618D ARG* 3.4 20.3 + - - +
619D ALA* 3.1 20.2 - - - +
621D VAL* 1.3 77.9 - - - +
623D ASN* 1.3 67.2 + - - +
624D PRO* 3.4 14.6 - - + +
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Residues in contact with ASN 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D LEU* 2.8 18.3 + - - +
621D VAL 4.0 4.5 - - - +
622D ASN* 1.3 79.5 - - - +
624D PRO* 1.3 72.0 - - - +
653D LYS 5.7 0.9 - - - +
655D ARG* 3.0 33.6 + - - +
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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