Contacts of the helix formed by residues 604 - 622 (chain D) in PDB entry 2JJD
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 GLY 604 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601D PRO* 5.1 3.6 - - - +
603D GLU* 1.3 76.0 - - - +
605D LYS* 1.3 58.8 + - - +
606D GLY 3.1 3.2 - - - +
607D MET* 3.1 13.9 + - - +
608D ILE* 2.8 42.3 + - - +
681D PHE* 4.5 7.3 - - - -
685D VAL* 4.4 18.2 - - - -
688D ASP* 5.3 2.9 - - - -
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Residues in contact with LYS 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D GLU* 3.4 11.9 + - + +
604D GLY* 1.3 75.8 - - - +
606D GLY* 1.3 57.7 + - - +
608D ILE* 4.2 7.9 - - - +
609D ASP* 3.1 27.9 + - - +
688D ASP* 5.5 2.4 - - - +
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Residues in contact with GLY 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D ALA* 5.2 9.0 - - - -
564D ILE* 4.3 2.5 - - - +
592D PHE* 4.1 19.8 - - - -
603D GLU* 4.6 4.4 - - - +
604D GLY* 3.1 3.6 - - - +
605D LYS* 1.3 78.1 - - - +
607D MET* 1.3 58.7 + - - +
609D ASP* 3.4 6.2 + - - +
610D LEU* 3.0 27.5 + - - +
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Residues in contact with MET 607 (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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525D LEU* 5.2 0.7 - - + -
592D PHE* 3.3 33.3 - - + -
595D TRP* 3.4 30.7 - - + -
601D PRO* 4.7 3.1 - - + -
604D GLY* 3.1 10.4 + - - +
606D GLY* 1.3 74.1 - - - +
608D ILE* 1.3 64.5 + - - +
610D LEU* 3.3 19.2 + - - +
611D ILE* 3.1 31.6 + - + +
639D THR* 6.0 0.4 - - - -
640D PHE* 4.4 17.9 - - - -
643D LEU* 4.2 17.5 - - + -
681D PHE* 4.1 33.0 - - + -
685D VAL* 4.4 3.8 - - + -
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Residues in contact with ILE 608 (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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604D GLY 2.8 24.4 + - - +
605D LYS* 4.2 6.1 - - - +
607D MET* 1.3 75.7 - - - +
609D ASP* 1.3 58.1 + - - +
611D ILE* 3.4 7.6 + - - +
612D ALA* 3.0 31.4 + - + +
647D LEU* 4.6 4.0 - - + -
685D VAL* 3.5 23.8 - - + +
688D ASP* 4.0 8.1 - - + +
689D PHE* 3.6 62.1 - - + +
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Residues in contact with ASP 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D ILE* 4.7 9.1 - - + +
605D LYS 3.1 21.1 + - - +
606D GLY* 3.7 6.7 - - - +
607D MET 3.2 0.2 - - - -
608D ILE* 1.3 79.1 - - - +
610D LEU* 1.3 58.7 + - - +
612D ALA* 3.9 6.4 - - - +
613D ALA* 3.3 22.0 + - - +
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Residues in contact with LEU 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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523D VAL* 4.3 3.8 - - + -
525D LEU* 4.1 8.7 - - + -
564D ILE* 3.1 39.5 - - + +
590D PHE* 4.0 22.4 - - + -
592D PHE* 4.1 24.2 - - + -
606D GLY 3.0 15.7 + - - +
607D MET* 3.7 12.8 - - - +
608D ILE 3.2 0.4 - - - -
609D ASP* 1.3 75.1 - - - +
611D ILE* 1.3 65.3 + - - +
612D ALA 3.2 1.1 - - - -
613D ALA* 3.2 3.3 + - - +
614D VAL* 3.0 28.4 + - + +
640D PHE* 3.5 31.9 - - + -
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Residues in contact with ILE 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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607D MET* 3.1 29.9 + - + +
608D ILE 3.8 3.8 - - - +
610D LEU* 1.3 75.3 - - - +
612D ALA* 1.3 63.5 + - - +
614D VAL* 3.5 4.0 + - - +
615D GLN* 3.0 46.4 + - + +
640D PHE* 4.1 19.5 - - + +
643D LEU* 3.7 25.8 - - + -
644D SER* 3.8 28.7 - - - +
647D LEU* 3.6 33.4 - - + -
685D VAL* 5.5 0.7 - - + -
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Residues in contact with ALA 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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608D ILE* 3.0 21.0 + - + +
609D ASP* 3.9 7.6 - - - +
611D ILE* 1.3 77.1 - - - +
613D ALA* 1.3 58.4 + - - +
615D GLN* 2.8 30.1 + - - +
616D LYS* 3.0 13.8 + - - +
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Residues in contact with ALA 613 (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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564D ILE* 5.8 3.8 - - + -
566D ILE* 5.5 4.3 - - + -
590D PHE* 3.7 24.9 - - + -
609D ASP 3.3 17.3 + - - +
610D LEU* 3.2 7.3 + - + +
612D ALA* 1.3 78.7 - - - +
614D VAL* 1.3 62.7 + - - +
616D LYS* 3.4 7.2 + - - +
617D GLN* 3.0 23.0 + - - +
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Residues in contact with VAL 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D THR* 4.2 4.5 - - + -
523D VAL* 3.6 24.9 - - + -
590D PHE* 4.0 27.4 - - + -
610D LEU* 3.0 22.8 + - + +
611D ILE 3.9 4.0 - - - +
613D ALA* 1.3 75.7 - - - +
615D GLN* 1.3 59.2 + - + +
617D GLN* 3.4 2.4 + - - +
618D GLN* 2.9 27.7 + - - +
626D ILE* 3.6 39.7 - - + -
640D PHE* 4.2 15.3 - - + -
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Residues in contact with GLN 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D TYR* 5.7 3.8 - - - +
611D ILE* 3.0 34.6 + - + +
612D ALA* 2.8 16.4 + - - +
614D VAL* 1.3 77.0 - - + +
616D LYS* 1.3 58.8 + - - +
618D GLN* 3.3 7.1 + - - +
619D GLN* 2.9 28.6 + - - +
626D ILE* 6.2 0.2 - - - -
644D SER* 4.0 17.3 + - - +
647D LEU* 5.5 0.6 - - - +
648D GLU* 4.2 17.4 - - - +
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Residues in contact with LYS 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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612D ALA 3.0 11.7 + - - +
613D ALA* 3.9 8.1 - - - +
615D GLN* 1.3 73.2 - - - +
617D GLN* 1.3 66.4 + - - +
619D GLN* 3.2 6.9 + - - +
620D GLN* 3.1 38.2 + - - +
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Residues in contact with GLN 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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520D HIS* 3.7 11.9 + - - +
521D THR* 3.9 16.4 - - + +
586D VAL* 5.2 4.9 + - - +
588D ARG* 3.5 43.6 + - + +
590D PHE* 3.7 24.9 - - + -
613D ALA 3.0 14.1 + - - +
614D VAL 3.6 7.6 - - - +
615D GLN 3.3 0.2 - - - -
616D LYS* 1.3 77.0 - - - +
618D GLN* 1.3 58.2 + - - +
620D GLN* 3.4 9.5 + - - +
621D THR* 2.8 46.7 + - - -
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Residues in contact with GLN 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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495D TYR* 3.0 27.1 - - - +
520D HIS* 5.7 1.0 - - - +
521D THR* 2.7 36.9 + - - +
614D VAL 2.9 17.3 + - - +
615D GLN* 3.6 7.2 - - - +
617D GLN* 1.3 74.2 - - - +
619D GLN* 1.3 65.9 + - - +
621D THR* 3.7 3.9 - - - -
622D GLY* 2.9 26.0 + - - -
623D ASN* 3.1 21.6 - - - +
624D HIS* 2.8 30.0 + - - +
625D PRO 3.9 1.6 + - - -
626D ILE* 3.1 28.4 - - + +
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Residues in contact with GLN 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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615D GLN 2.9 16.8 + - - +
616D LYS* 3.2 9.6 + - - +
618D GLN* 1.3 75.5 - - - +
620D GLN* 1.3 62.6 + - + +
622D GLY* 3.7 7.8 + - - -
623D ASN* 3.8 10.7 + - - +
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Residues in contact with GLN 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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616D LYS* 3.1 27.6 + - - +
617D GLN* 3.9 9.2 + - - +
618D GLN 3.1 0.4 - - - -
619D GLN* 1.3 79.2 - - + +
621D THR* 1.3 58.5 + - - +
622D GLY 2.8 10.5 + - - -
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Residues in contact with THR 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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520D HIS* 4.2 23.5 + - - -
521D THR* 5.1 1.3 - - - -
586D VAL 6.1 0.2 - - - -
617D GLN* 2.8 41.6 + - - +
618D GLN* 3.7 4.9 - - - -
620D GLN* 1.3 71.0 - - - +
622D GLY* 1.3 66.0 + - - +
623D ASN* 4.1 0.7 - - - -
624D HIS* 3.5 13.9 + - - -
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Residues in contact with GLY 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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618D GLN 2.9 8.5 + - - -
619D GLN 3.8 8.5 - - - -
620D GLN 2.8 9.5 + - - -
621D THR* 1.3 82.5 - - - +
623D ASN* 1.3 62.4 + - - -
624D HIS* 3.3 12.6 + - - -
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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
------------------------------------------------------------
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