Contacts of the helix formed by residues 608 - 623 (chain A) in PDB entry 2RD0
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 ASP 608 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A HIS* 4.1 16.0 - - + +
397A PRO* 5.2 1.2 - - - +
398A ARG 3.7 12.8 + - - +
574A TRP* 4.2 7.8 - - + -
580A VAL* 5.2 0.2 - - - +
584A TYR* 3.0 29.8 + - - -
606A TYR 3.3 4.9 + - - -
607A PRO* 1.3 77.5 - - + +
609A PRO* 1.3 64.3 - - - +
610A MET* 2.7 49.7 + - - +
611A VAL* 3.0 33.0 + - + +
612A ARG* 3.0 18.2 + - - +
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Residues in contact with PRO 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ARG* 4.0 41.1 - - + +
399A ALA* 4.5 5.2 - - + -
584A TYR* 4.9 1.1 - - - +
608A ASP* 1.3 92.3 - - - +
610A MET* 1.3 73.5 + - + +
612A ARG* 4.1 7.7 - - + +
613A GLY* 3.3 18.5 + - - -
643A GLN* 5.5 2.7 - - - +
644A TYR* 5.8 4.0 - - + -
648A LEU* 4.3 8.8 - - + +
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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
----------------------------------------------------------
398A ARG* 6.1 3.1 - - + -
488A ASP* 4.2 19.7 - - - +
584A TYR* 3.7 57.2 - - + +
587A VAL* 3.6 20.0 - - + +
608A ASP* 2.7 16.6 + - - +
609A PRO* 1.3 93.0 - - + +
611A VAL* 1.3 64.8 + - + +
612A ARG 3.4 0.3 + - - -
613A GLY* 3.4 7.8 + - - -
614A PHE 3.5 7.8 + - - -
617A ARG* 5.0 3.1 + - - -
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Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU* 6.3 0.2 - - + -
569A LEU* 3.8 45.5 - - + -
574A TRP* 4.4 8.1 - - + -
587A VAL* 4.6 9.6 - - + +
601A LEU* 4.0 15.2 - - + +
606A TYR* 4.0 26.7 - - + -
608A ASP* 3.0 26.4 + - + +
610A MET* 1.3 79.8 - - + +
612A ARG* 1.3 64.8 + - + +
614A PHE* 3.3 8.5 + - - +
615A ALA* 3.2 17.8 + - - +
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Residues in contact with ARG 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A LEU 3.9 5.6 - - - +
602A LEU* 2.7 42.2 + - + +
603A ASP 2.7 31.5 + - - -
604A CYS* 4.5 0.8 - - - +
606A TYR 2.7 24.9 + - - +
607A PRO* 4.0 6.0 - - - +
608A ASP 3.0 21.3 + - - +
609A PRO* 4.4 5.4 - - + +
611A VAL* 1.3 74.5 - - - +
613A GLY* 1.3 55.4 + - - +
615A ALA* 3.1 9.4 - - - +
616A VAL* 2.7 41.3 + - + +
638A VAL* 4.1 8.1 + - - +
641A TYR* 4.2 17.9 + - - +
642A GLU* 2.6 44.4 + - - +
648A LEU* 4.9 1.8 - - + -
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Residues in contact with GLY 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PRO 3.3 11.3 + - - -
610A MET 3.4 1.5 + - - -
611A VAL 3.3 0.6 - - - -
612A ARG* 1.3 79.1 - - - +
614A PHE* 1.3 51.3 + - - +
616A VAL* 3.3 3.9 + - - +
617A ARG* 2.7 50.5 + - - +
648A LEU* 3.3 30.4 - - - +
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Residues in contact with PHE 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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565A LEU* 3.4 31.0 - - + -
587A VAL* 4.1 20.6 - - + -
590A TRP* 3.4 22.9 - + + -
591A PRO 3.2 29.8 - - - -
592A PRO* 4.1 4.0 - - + -
593A ILE* 4.3 9.2 - - + -
601A LEU* 4.1 14.6 - - + -
610A MET 3.5 7.9 + - - +
611A VAL* 3.3 9.4 + - - +
613A GLY* 1.3 72.5 - - - +
615A ALA* 1.3 56.4 + - - +
617A ARG* 3.0 30.4 + - + +
618A CYS* 2.7 60.1 + - - -
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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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598A ALA 3.5 21.9 - - - +
601A LEU* 3.8 13.7 - - + -
602A LEU* 3.7 20.6 - - + -
611A VAL 3.2 9.1 + - - +
612A ARG 3.1 10.2 + - - +
614A PHE* 1.3 81.9 - - - +
616A VAL* 1.3 63.6 + - - +
618A CYS* 3.0 19.4 + - - +
619A LEU* 3.1 18.5 + - - +
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Residues in contact with VAL 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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602A LEU* 4.7 7.6 - - + -
612A ARG* 2.7 25.2 + - + +
613A GLY 3.7 5.2 - - - +
615A ALA* 1.3 72.2 - - - +
617A ARG* 1.3 57.5 + - + +
619A LEU* 3.0 10.8 + - - +
620A GLU* 2.9 43.6 + - + +
642A GLU* 5.2 0.4 - - - +
648A LEU* 4.0 18.8 - - + +
649A LEU* 3.7 36.8 - - + +
652A PHE* 3.8 31.2 - - + -
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Residues in contact with ARG 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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587A VAL* 4.4 4.9 + - - +
588A LYS* 4.4 16.6 + - - +
610A MET* 5.0 2.8 + - - -
613A GLY* 2.7 41.2 + - - +
614A PHE* 3.0 32.4 + - + +
616A VAL* 1.3 71.2 - - + +
618A CYS* 1.3 59.4 + - - +
620A GLU* 3.8 22.4 - - + +
621A LYS* 3.0 27.5 + - - +
648A LEU* 5.1 6.8 - - - +
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Residues in contact with CYS 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A PRO* 4.5 3.4 - - - -
593A ILE 3.7 24.5 - - - +
595A PRO* 4.5 1.9 - - + +
598A ALA* 3.5 25.6 - - + -
614A PHE* 2.7 58.4 + - - -
615A ALA 3.0 8.3 + - - +
617A ARG* 1.3 72.7 - - - +
619A LEU* 1.3 58.9 + - - +
621A LYS* 3.2 6.4 + - - +
622A TYR* 3.0 33.8 + - - -
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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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595A PRO* 3.9 36.3 - - + +
598A ALA* 4.4 9.0 - - + +
599A MET* 4.6 5.8 - - + -
602A LEU* 3.8 28.5 - - + -
615A ALA 3.1 16.4 + - - +
616A VAL* 3.0 13.5 + - - +
618A CYS* 1.3 75.3 - - - +
620A GLU* 1.3 65.1 + - - +
623A LEU* 3.2 41.2 + - + +
635A LEU* 4.3 14.1 - - + -
649A LEU* 4.8 1.8 - - + -
652A PHE* 3.7 33.9 - - + -
656A LYS* 5.9 0.2 + - - -
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Residues in contact with GLU 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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616A VAL* 2.9 30.7 + - + +
617A ARG* 3.9 22.3 - - + +
619A LEU* 1.3 76.5 - - - +
621A LYS* 1.3 65.0 + - - +
622A TYR* 4.6 0.2 - - - -
623A LEU 5.0 0.7 + - - +
648A LEU* 5.9 2.4 - - - +
652A PHE* 3.8 33.4 - - + +
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Residues in contact with LYS 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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592A PRO* 4.5 18.6 - - + -
617A ARG 3.0 20.3 + - - +
618A CYS* 3.2 7.4 + - - +
620A GLU* 1.3 79.5 - - - +
622A TYR* 1.3 101.6 + - + +
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Residues in contact with TYR 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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592A PRO* 3.1 32.8 + - + +
593A ILE 3.2 27.2 - - - -
594A LYS* 4.2 2.4 + - - -
595A PRO* 2.7 37.3 - - + +
618A CYS 3.0 10.8 + - - -
621A LYS* 1.3 112.9 - - + +
623A LEU* 1.3 54.2 + - - +
624A THR* 4.1 6.1 - - + -
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Residues in contact with LEU 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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595A PRO* 3.6 28.0 - - + -
599A MET* 5.0 3.1 - - + -
619A LEU* 3.2 35.7 + - + +
620A GLU 5.0 0.7 + - - +
621A LYS 4.1 0.4 - - - -
622A TYR* 1.3 74.8 - - - +
624A THR* 1.3 62.7 + - - +
625A ASP 4.0 0.5 + - - -
627A LYS* 3.8 30.3 - - + +
628A LEU* 3.5 40.3 - - + +
631A TYR* 4.3 11.2 - - + -
635A LEU* 4.9 2.5 - - + -
652A PHE* 4.4 12.1 - - + -
656A LYS* 4.5 11.1 + - - +
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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