Contacts of the helix formed by residues 668 - 684 (chain A) in PDB entry 2JKK
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 ARG 668 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A GLU* 3.6 21.8 - - - +
605A VAL* 4.4 2.5 - - - -
666A ARG 3.7 2.9 + - - +
667A PRO* 1.3 76.1 - - - +
669A PHE* 1.3 66.0 + - - +
670A THR* 3.1 7.4 - - - +
671A GLU* 3.1 25.8 + - + +
672A LEU* 3.0 21.0 + - - +
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Residues in contact with PHE 669 (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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531A SER* 4.4 5.9 - - - +
534A LEU* 3.7 44.2 - - + -
535A ALA* 3.6 25.7 - - - +
538A GLU* 2.9 27.4 + - + +
547A ILE* 4.6 0.2 - - + -
601A SER* 3.7 4.7 - - - -
604A ASP* 3.6 31.2 - - + -
605A VAL* 3.6 30.7 - - + +
608A PHE* 3.7 30.7 - + + -
668A ARG* 1.3 71.9 - - - +
670A THR* 1.3 56.9 + - - +
672A LEU* 3.6 14.4 - - + +
673A LYS* 3.0 31.5 + - - +
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Residues in contact with THR 670 (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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535A ALA* 4.3 12.5 + - - +
538A GLU* 3.1 15.0 + - - -
668A ARG* 3.1 7.4 - - - -
669A PHE* 1.3 79.4 - - - +
671A GLU* 1.3 62.1 + - + +
673A LYS* 3.7 12.9 + - - +
674A ALA* 3.4 19.8 + - - +
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Residues in contact with GLU 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ARG 4.8 1.2 - - - +
667A PRO* 3.6 19.1 - - + +
668A ARG* 3.1 39.3 + - + +
670A THR* 1.3 75.2 - - + +
672A LEU* 1.3 66.1 + - - +
674A ALA* 3.3 7.3 + - - +
675A GLN* 3.0 33.3 + - - +
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Residues in contact with LEU 672 (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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531A SER* 4.7 1.1 - - - -
605A VAL* 4.0 15.3 - - + -
608A PHE* 3.8 18.6 - - + -
612A MET* 5.0 2.2 - - + -
654A LEU* 3.4 34.8 - - + -
658A CYS* 3.8 22.4 - - - -
667A PRO* 3.8 11.9 - - + -
668A ARG 3.0 14.8 + - - +
669A PHE* 3.3 32.7 + - + +
671A GLU* 1.3 75.7 - - - +
673A LYS* 1.3 53.5 + - - +
675A GLN* 3.3 4.5 + - - +
676A LEU* 2.8 48.7 + - + +
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Residues in contact with LYS 673 (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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528A TYR* 3.5 21.0 - - + +
531A SER* 3.4 21.4 + - - +
532A THR* 3.6 28.2 + - + +
535A ALA* 3.9 22.2 - - - +
669A PHE 3.0 13.6 + - - +
670A THR* 4.0 15.3 - - - +
672A LEU* 1.3 75.2 - - - +
674A ALA* 1.3 57.7 + - - +
676A LEU* 4.6 0.2 - - - -
677A SER* 3.0 31.2 + - - -
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Residues in contact with ALA 674 (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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670A THR 3.4 10.2 + - - +
671A GLU* 3.3 10.7 + - - +
673A LYS* 1.3 78.9 - - - +
675A GLN* 1.3 64.2 + - - +
677A SER* 3.4 7.8 + - - -
678A THR* 3.2 25.7 + - - -
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Residues in contact with GLN 675 (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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654A LEU* 3.8 34.5 - - + +
657A LYS* 5.3 7.0 + - - +
667A PRO* 5.9 0.9 - - - +
671A GLU* 3.0 23.0 + - - +
672A LEU 3.5 3.8 - - - +
674A ALA* 1.3 80.4 - - - +
676A LEU* 1.3 62.8 + - - +
678A THR* 3.2 9.8 + - - -
679A ILE* 3.0 34.3 + - + +
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Residues in contact with LEU 676 (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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524A ILE* 4.3 13.0 - - + +
527A ALA* 3.8 22.0 - - + +
528A TYR* 4.2 15.4 - - + +
531A SER* 3.7 25.8 - - - +
608A PHE* 4.0 14.8 - - + -
612A MET* 4.1 9.0 - - - -
651A LEU* 3.6 31.0 - - + -
654A LEU* 3.9 12.1 - - + -
672A LEU* 2.8 25.1 + - + +
673A LYS 4.0 3.4 - - - +
675A GLN* 1.3 74.3 - - - +
677A SER* 1.3 57.3 + - - +
679A ILE* 3.8 4.6 - - + +
680A LEU* 2.9 32.1 + - - +
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Residues in contact with SER 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A TYR* 3.8 21.7 + - - -
673A LYS* 3.0 19.5 + - - -
674A ALA* 3.4 10.3 - - - -
675A GLN 3.2 0.2 - - - -
676A LEU* 1.3 76.6 - - - +
678A THR* 1.3 62.2 + - - +
680A LEU* 3.6 5.9 + - - +
681A GLU* 3.1 31.9 + - - +
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Residues in contact with THR 678 (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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674A ALA 3.2 11.4 + - - -
675A GLN* 3.6 12.2 + - - -
677A SER* 1.3 78.9 + - - +
679A ILE* 1.3 57.7 + - + +
681A GLU* 3.4 7.2 + - - +
682A GLU* 2.9 44.4 + - + +
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Residues in contact with ILE 679 (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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524A ILE* 3.9 27.4 - - + -
648A PRO* 4.8 4.0 - - + -
650A THR* 3.6 47.3 - - + +
651A LEU* 4.1 24.9 - - + -
654A LEU* 4.1 18.8 - - + -
675A GLN* 3.0 27.8 + - + +
676A LEU* 3.9 5.2 - - - +
678A THR* 1.3 72.7 - - + +
680A LEU* 1.3 61.2 + - - +
682A GLU* 3.4 12.8 + - - +
683A GLU* 3.0 26.9 + - - +
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ALA* 3.3 32.3 - - + +
524A ILE* 3.8 13.2 - - + +
525A LEU* 3.7 39.7 - - + +
528A TYR* 4.4 17.7 - - + -
676A LEU 2.9 16.6 + - - +
677A SER* 3.7 6.7 - - - +
679A ILE* 1.3 75.1 - - - +
681A GLU* 1.3 68.5 + - + +
683A GLU* 3.0 4.8 + - - +
684A LYS* 3.0 49.5 + - + +
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Residues in contact with GLU 681 (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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677A SER* 3.1 23.1 + - - +
678A THR* 3.7 6.7 - - + +
680A LEU* 1.3 79.0 - - + +
682A GLU* 1.3 63.2 + - - +
683A GLU 3.3 0.5 + - - -
684A LYS* 3.5 36.5 + - - +
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Residues in contact with GLU 682 (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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650A THR* 4.2 17.7 + - - +
678A THR* 2.9 29.1 + - + +
679A ILE* 3.5 20.0 - - - +
681A GLU* 1.3 75.6 - - + +
683A GLU* 1.3 64.0 + - - +
684A LYS 4.3 3.3 - - - +
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Residues in contact with GLU 683 (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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520A LEU* 3.6 40.5 - - + +
521A ALA* 4.3 15.0 - - - +
524A ILE* 3.7 17.5 - - + -
648A PRO* 4.2 12.0 - - - +
679A ILE* 3.0 17.6 + - + +
680A LEU* 3.0 4.4 + - - +
682A GLU* 1.3 79.3 - - - +
684A LYS* 1.3 63.0 + - - +
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Residues in contact with LYS 684 (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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521A ALA* 4.6 13.6 - - + +
525A LEU* 6.2 2.1 - - - +
680A LEU* 3.0 44.3 + - + +
681A GLU* 3.8 35.9 - - - +
682A GLU 3.5 4.1 - - - +
683A GLU* 1.3 81.7 - - - +
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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