Contacts of the helix formed by residues 668 - 688 (chain B) in PDB entry 2IJM
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B GLU* 3.2 34.2 + - - +
601B SER* 3.1 30.6 + - - -
605B VAL* 4.5 2.5 - - + -
666B ARG 3.8 2.9 + - - +
667B PRO* 1.3 76.7 - - - +
669B PHE* 1.3 61.1 + - - +
670B THR* 3.4 7.2 - - - +
671B GLU* 3.3 10.6 + - + +
672B LEU* 3.1 26.1 + - - +
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Residues in contact with PHE 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B SER* 4.3 8.3 - - - +
534B LEU* 3.5 49.6 - - + -
535B ALA* 3.5 24.0 - - - +
538B GLU* 3.4 19.8 + - + +
601B SER* 4.4 2.2 - - - -
604B ASP* 4.0 15.0 - - + -
605B VAL* 3.5 32.1 - - + -
608B PHE* 3.6 37.2 - + + -
668B ARG* 1.3 73.6 - - - +
670B THR* 1.3 59.4 + - - +
672B LEU* 3.5 17.9 - - + -
673B LYS* 2.9 33.6 + - - +
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Residues in contact with THR 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ALA* 4.4 7.2 - - - +
538B GLU* 3.9 9.7 + - - -
668B ARG* 3.4 4.4 - - - +
669B PHE* 1.3 75.9 - - - +
671B GLU* 1.3 62.5 + - - +
673B LYS* 3.6 7.1 + - - +
674B ALA* 3.2 23.9 + - + +
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Residues in contact with GLU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B LEU* 5.9 0.4 - - + -
657B LYS* 4.2 9.0 + - - +
667B PRO* 3.8 27.0 - - + +
668B ARG* 3.3 13.8 + - + +
669B PHE 3.3 0.4 - - - -
670B THR* 1.3 76.6 - - - +
672B LEU* 1.3 64.1 + - - +
674B ALA* 3.3 6.4 + - - +
675B GLN* 2.8 56.8 + - + +
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Residues in contact with LEU 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B SER* 4.7 0.9 - - - -
605B VAL* 4.0 22.9 - - + -
608B PHE* 4.1 17.7 - - + -
612B MET* 5.0 0.2 - - + -
654B LEU* 3.7 28.0 - - + -
658B CYS* 3.5 23.6 - - - -
667B PRO* 3.9 10.5 - - + +
668B ARG 3.1 14.4 + - - +
669B PHE* 3.5 40.4 - - + +
671B GLU* 1.3 76.5 - - - +
673B LYS* 1.3 57.6 + - - +
675B GLN* 3.3 5.5 + - - +
676B LEU* 2.8 37.9 + - + +
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Residues in contact with LYS 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B TYR* 3.3 33.8 - - + -
531B SER* 3.4 21.5 + - - +
532B THR* 3.8 26.5 + - + +
535B ALA* 4.2 18.4 - - + +
669B PHE 2.9 20.5 + - - +
670B THR* 3.8 6.7 - - - +
672B LEU* 1.3 72.9 - - - +
674B ALA* 1.3 57.5 + - - +
676B LEU* 3.6 0.4 + - - -
677B SER* 3.0 24.6 + - - -
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Residues in contact with ALA 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B THR* 3.2 16.2 + - + +
671B GLU* 3.7 5.8 - - - +
673B LYS* 1.3 79.7 - - - +
675B GLN* 1.3 61.6 + - + +
677B SER* 3.4 8.0 - - - -
678B THR* 3.1 26.3 + - - -
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Residues in contact with GLN 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B LEU* 3.9 23.3 - - + +
657B LYS* 3.1 30.2 + - - +
671B GLU* 2.8 49.2 + - + +
672B LEU 3.8 3.4 - - - +
674B ALA* 1.3 74.3 - - + +
676B LEU* 1.3 61.4 + - - +
678B THR* 3.4 7.9 + - - -
679B ILE* 2.9 36.3 + - + +
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Residues in contact with LEU 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B ILE* 4.3 12.5 - - + +
527B ALA* 3.8 17.7 - - + +
528B TYR* 4.0 15.0 - - + +
531B SER* 3.7 14.1 - - - +
608B PHE* 3.7 34.8 - - + -
612B MET* 4.1 6.3 - - - -
651B LEU* 3.7 32.3 - - + -
654B LEU* 3.9 10.8 - - + -
672B LEU* 2.8 24.6 + - + +
673B LYS 4.0 2.9 - - - +
675B GLN* 1.3 70.4 - - - +
677B SER* 1.3 59.8 + - - +
679B ILE* 3.9 4.2 - - + +
680B LEU* 2.8 32.7 + - - +
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Residues in contact with SER 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B TYR* 3.6 22.7 + - - -
673B LYS 3.0 18.7 + - - -
674B ALA* 3.4 9.6 - - - -
675B GLN 3.3 0.2 - - - -
676B LEU* 1.3 76.6 - - - +
678B THR* 1.3 56.1 + - - -
680B LEU* 3.7 5.0 - - - +
681B GLU* 2.9 43.8 + - - +
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Residues in contact with THR 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B ALA 3.1 12.8 + - - -
675B GLN* 3.6 10.4 - - - -
676B LEU 3.3 0.2 - - - -
677B SER* 1.3 76.9 - - - +
679B ILE* 1.3 59.9 + - + +
681B GLU* 3.3 5.9 + - - +
682B GLU* 2.9 46.0 + - - +
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Residues in contact with ILE 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B ILE* 4.0 25.6 - - + -
648B PRO* 4.3 11.0 - - + -
650B THR* 3.7 24.7 - - - +
651B LEU* 3.7 38.8 - - + +
654B LEU* 4.0 16.8 - - + -
675B GLN* 2.9 24.5 + - + +
676B LEU* 3.3 5.8 + - - +
678B THR* 1.3 77.9 - - + +
680B LEU* 1.3 57.3 + - - +
682B GLU* 3.3 10.4 - - + +
683B GLU* 3.0 27.5 + - - +
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Residues in contact with LEU 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ALA* 3.3 28.7 - - - +
524B ILE* 3.8 15.9 - - + +
525B LEU* 3.7 37.7 - - + +
528B TYR* 4.4 18.4 - - + -
676B LEU 2.8 18.2 + - - +
677B SER* 3.7 3.8 - - - +
679B ILE* 1.3 75.3 - - - +
681B GLU* 1.3 75.5 + - - +
683B GLU* 3.4 2.5 + - - +
684B LYS* 2.9 47.3 + - + +
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Residues in contact with GLU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B SER* 2.9 28.5 + - - +
678B THR* 3.9 5.2 - - - +
680B LEU* 1.3 92.1 - - - +
682B GLU* 1.3 63.2 + - - +
684B LYS* 3.8 26.1 + - - +
685B ALA* 3.1 26.3 + - - +
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Residues in contact with GLU 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B THR* 5.5 8.3 - - - +
678B THR* 2.9 36.6 + - - +
679B ILE* 3.3 10.2 - - - +
681B GLU* 1.3 72.9 - - - +
683B GLU* 1.3 66.4 + - - +
685B ALA* 3.2 7.0 + - - +
686B GLN* 3.2 41.9 + - + +
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Residues in contact with GLU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU* 3.6 32.1 - - - +
521B ALA* 3.8 28.3 + - + +
524B ILE* 3.8 16.6 - - + -
648B PRO* 5.6 2.8 - - + +
679B ILE 3.0 13.6 + - - +
680B LEU* 3.8 3.6 - - - +
682B GLU* 1.3 79.6 - - - +
684B LYS* 1.3 61.9 + - - +
686B GLN* 3.3 19.1 + - - +
687B GLN* 3.1 47.6 + - - +
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Residues in contact with LYS 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ALA* 4.1 14.4 - - + -
525B LEU* 6.4 0.4 - - + -
680B LEU* 2.9 44.8 + - + +
681B GLU* 3.8 27.2 + - - +
683B GLU* 1.3 77.6 - - - +
685B ALA* 1.3 57.1 + - - +
687B GLN* 3.3 5.4 + - - +
688B GLU* 2.9 57.7 + - - +
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Residues in contact with ALA 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B GLU 3.1 19.3 + - - +
682B GLU* 3.2 5.8 + - - +
684B LYS* 1.3 73.9 - - - +
686B GLN* 1.3 64.6 + - + +
688B GLU* 3.5 8.3 + - - +
689B GLU* 3.2 23.9 + - - +
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Residues in contact with GLN 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B GLU* 3.2 33.6 + - + +
683B GLU* 3.5 19.7 + - - +
684B LYS 3.3 0.2 - - - -
685B ALA* 1.3 79.8 - - + +
687B GLN* 1.3 69.5 + - - +
689B GLU* 3.5 19.0 + - - +
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Residues in contact with GLN 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ASP* 5.1 13.0 - - - +
521B ALA* 4.9 8.7 - - + -
683B GLU* 3.1 40.5 + - + +
684B LYS* 3.3 7.2 + - - +
686B GLN* 1.3 83.4 + - - +
688B GLU* 1.3 62.1 + - + +
689B GLU 3.4 2.9 + - - -
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Residues in contact with GLU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B LYS* 2.9 46.0 + - - +
685B ALA* 3.8 6.8 - - - +
686B GLN 3.3 0.2 - - - -
687B GLN* 1.3 80.9 - - + +
689B GLU* 1.3 60.9 + - - +
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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
------------------------------------------------------------
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