Contacts of the helix formed by residues 624 - 652 (chain A) in PDB entry 2YGG
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 624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A ALA 3.5 4.9 + - - -
623A LEU* 1.3 74.3 - - - +
625A LYS* 1.3 54.7 + - - +
626A ASP* 3.5 11.7 - - - +
627A LYS* 2.8 26.2 + - - +
628A GLU* 2.8 32.2 + - - +
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Residues in contact with LYS 625 (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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623A LEU 5.5 1.3 - - - +
624A SER* 1.3 74.3 - - - +
626A ASP* 1.3 57.4 + - - +
628A GLU* 3.1 32.2 - - - +
629A GLU* 3.0 29.6 + - - +
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Residues in contact with ASP 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A SER* 3.5 10.3 + - - +
625A LYS* 1.3 78.9 - - - +
627A LYS* 1.3 63.6 + - + +
629A GLU* 3.4 7.6 + - - +
630A GLU* 3.1 24.8 + - - +
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Residues in contact with LYS 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A PHE* 6.0 2.0 - - + -
623A LEU* 3.7 27.1 - - + -
624A SER* 2.8 26.4 + - - +
626A ASP* 1.3 78.3 - - + +
628A GLU* 1.3 67.1 + - - +
630A GLU* 3.0 34.6 + - - +
631A ILE* 2.8 32.3 + - + +
1686A MPD 4.0 24.2 - - + +
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Residues in contact with GLU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LEU* 4.4 9.7 - - + +
624A SER 2.8 14.6 + - - +
625A LYS* 3.1 39.7 - - - +
627A LYS* 1.3 72.4 - - - +
629A GLU* 1.3 58.1 + - - +
631A ILE* 3.1 10.9 + - - +
632A ARG* 2.9 28.8 + - + +
1687A TAM 5.1 7.4 + - - +
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Residues in contact with GLU 629 (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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625A LYS 3.0 16.6 + - - +
626A ASP* 3.6 8.1 - - - +
627A LYS 3.2 0.2 - - - -
628A GLU* 1.3 72.7 - - - +
630A GLU* 1.3 66.1 + - - +
632A ARG* 2.8 46.6 + - - +
633A LYS* 2.9 54.1 + - - +
1687A TAM 3.3 22.9 + - - +
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Residues in contact with GLU 630 (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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626A ASP* 3.1 14.3 + - - +
627A LYS* 3.0 34.4 + - - +
629A GLU* 1.3 76.9 - - - +
631A ILE* 1.3 65.2 + - + +
633A LYS* 3.2 10.1 + - + +
634A ILE* 3.2 34.8 + - + +
1686A MPD 3.0 30.8 - - + +
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Residues in contact with ILE 631 (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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623A LEU* 4.8 12.8 - - + -
627A LYS* 2.8 44.6 + - + +
628A GLU* 3.5 9.4 - - - +
630A GLU* 1.3 76.5 - - + +
632A ARG* 1.3 66.2 + - - +
634A ILE* 3.1 8.8 + - + +
635A LEU* 3.0 43.4 + - + +
1686A MPD 3.5 25.1 - - - +
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Residues in contact with ARG 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A GLU* 2.9 15.4 + - + +
629A GLU* 2.8 43.8 + - - +
631A ILE* 1.3 79.4 - - - +
633A LYS* 1.3 63.4 + - - +
635A LEU* 4.2 3.1 - - - +
636A ARG* 2.8 50.5 + - + +
1687A TAM 3.1 57.1 + - - +
124B GLU* 4.9 1.6 + - - -
127B ARG* 3.8 6.1 - - - +
128B GLU* 2.5 42.6 + - - -
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Residues in contact with LYS 633 (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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629A GLU* 2.9 50.2 + - - +
630A GLU* 3.7 9.8 - - + +
631A ILE 3.2 0.4 - - - -
632A ARG* 1.3 80.9 - - - +
634A ILE* 1.3 61.8 + - + +
636A ARG* 3.7 6.5 - - - +
637A ASN* 2.8 32.8 + - - +
124B GLU* 5.1 0.4 - - - -
127B ARG* 3.3 47.7 - - - +
128B GLU* 4.8 0.7 - - - +
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Residues in contact with ILE 634 (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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630A GLU* 3.2 28.2 + - + +
631A ILE* 3.1 10.1 + - + +
633A LYS* 1.3 80.3 - - + +
635A LEU* 1.3 63.1 + - + +
637A ASN* 3.3 6.7 + - - +
638A ASN* 2.9 28.0 + - + +
1686A MPD 4.1 34.8 - - + +
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Residues in contact with LEU 635 (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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631A ILE* 3.0 35.6 + - + +
632A ARG* 4.2 3.4 - - - +
634A ILE* 1.3 80.0 - - + +
636A ARG* 1.3 62.2 + - - +
638A ASN* 3.1 17.1 + - + +
639A LEU* 2.9 28.6 + - - +
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Residues in contact with ARG 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ARG* 2.8 35.7 + - + +
633A LYS* 3.8 5.8 - - - +
635A LEU* 1.3 77.2 - - - +
637A ASN* 1.3 62.9 + - - +
639A LEU* 3.1 14.9 + - + +
640A GLN* 2.9 51.8 + - + +
643A ARG* 5.8 4.0 - - - +
1687A TAM 5.8 1.6 + - - -
128B GLU* 3.1 60.1 + - - +
129B ALA* 4.7 2.2 - - - +
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Residues in contact with ASN 637 (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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633A LYS 2.8 19.0 + - - +
634A ILE* 3.5 6.8 - - - +
636A ARG* 1.3 77.6 - - - +
638A ASN* 1.3 62.8 + - - +
640A GLN* 3.2 13.9 + - - +
641A LYS* 2.7 48.9 + - - +
130B ASP 4.3 4.0 + - - -
131B ILE* 3.0 36.2 + - - +
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Residues in contact with ASN 638 (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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634A ILE* 2.9 15.7 + - + +
635A LEU* 3.1 22.6 + - + +
637A ASN* 1.3 78.5 + - - +
639A LEU* 1.3 56.9 + - - +
641A LYS* 3.4 8.1 + - - +
642A THR* 3.0 38.3 + - - -
645A ARG* 5.0 1.6 + - - -
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Residues in contact with LEU 639 (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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635A LEU 2.9 12.7 + - - +
636A ARG* 3.4 19.1 - - + +
638A ASN* 1.3 79.3 + - - +
640A GLN* 1.3 58.1 + - + +
642A THR* 3.0 17.2 + - + -
643A ARG* 2.9 71.5 + - + +
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Residues in contact with GLN 640 (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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636A ARG* 2.9 54.2 + - + +
637A ASN* 3.2 24.1 + - - +
639A LEU* 1.3 75.0 - - + +
641A LYS* 1.3 61.3 + - - +
643A ARG* 3.3 4.0 + - - +
644A GLN* 2.9 24.6 + - - +
128B GLU 3.5 10.7 + - - +
129B ALA* 4.1 6.5 + - - +
130B ASP 4.5 4.3 - - - +
131B ILE* 3.6 32.1 - - + +
144B GLN* 3.0 36.7 + - - +
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Residues in contact with LYS 641 (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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637A ASN* 2.7 46.5 + - - +
638A ASN* 3.8 7.0 - - - +
640A GLN* 1.3 76.0 - - - +
642A THR* 1.3 52.5 + - - +
644A GLN* 3.2 9.4 + - - +
645A ARG* 2.7 50.6 + - + +
131B ILE* 3.5 32.0 + - + -
132B ASP* 5.1 4.8 - - - +
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Residues in contact with THR 642 (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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638A ASN* 3.0 24.7 + - - -
639A LEU* 3.0 21.4 + - + +
641A LYS* 1.3 78.0 - - - +
643A ARG* 1.3 59.4 + - + +
645A ARG* 3.1 30.8 + - - +
646A LEU* 2.9 46.3 + - + +
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Residues in contact with ARG 643 (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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636A ARG* 5.8 3.4 - - - +
639A LEU* 2.9 53.1 + - + +
640A GLN* 3.7 9.5 - - - +
641A LYS 3.3 0.4 - - - -
642A THR* 1.3 78.5 - - + +
644A GLN* 1.3 62.3 + - - +
646A LEU* 3.5 10.3 + - + +
647A ARG* 3.1 30.6 + - - +
144B GLN* 3.7 27.8 + - + +
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Residues in contact with GLN 644 (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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640A GLN 2.9 15.6 + - - +
641A LYS* 3.5 7.7 - - - +
642A THR 3.2 0.2 - - - -
643A ARG* 1.3 77.8 - - - +
645A ARG* 1.3 61.3 + - - +
647A ARG* 3.4 2.6 + - - +
648A SER* 3.2 21.2 + - - -
651A ARG* 5.0 1.0 + - - +
131B ILE* 3.8 29.6 - - - +
138B ASN* 5.3 5.1 - - - +
140B GLU* 3.8 43.3 - - + +
141B GLU* 5.3 1.2 - - - +
144B GLN* 3.6 7.8 - - - +
1156B TAM 5.2 3.2 + - - -
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Residues in contact with ARG 645 (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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638A ASN* 5.0 2.2 + - - -
641A LYS* 2.7 37.6 + - + +
642A THR* 3.1 33.8 + - - +
644A GLN* 1.3 74.7 - - - +
646A LEU* 1.3 56.7 + - - +
648A SER* 3.1 10.5 + - - +
649A TYR* 2.8 64.4 + - + -
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Residues in contact with LEU 646 (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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642A THR* 2.9 41.5 + - + +
643A ARG* 3.9 10.8 - - + +
644A GLN 3.4 0.2 - - - -
645A ARG* 1.3 73.6 - - + +
647A ARG* 1.3 62.5 + - + +
649A TYR* 3.4 25.4 + - + +
650A ASN* 3.1 23.7 + - - +
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Residues in contact with ARG 647 (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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643A ARG* 3.1 22.5 + - - +
644A GLN* 3.9 4.3 - - - +
645A ARG 3.3 0.2 - - - -
646A LEU* 1.3 76.1 - - - +
648A SER* 1.3 61.4 + - - +
650A ASN* 3.4 6.9 + - - +
651A ARG* 3.2 40.0 + - - +
83B GLU* 3.1 41.0 + - - -
139B TYR* 4.1 2.4 - - - -
140B GLU* 3.0 39.3 + - - +
143B VAL* 3.6 32.3 - - - +
144B GLN* 5.4 6.7 - - - -
1156B TAM 4.9 0.2 + - - -
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Residues in contact with SER 648 (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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644A GLN* 3.2 9.3 + - - -
645A ARG* 3.1 14.3 + - - -
647A ARG* 1.3 75.9 - - - +
649A TYR* 1.3 72.7 + - - +
650A ASN 2.9 2.3 + - - -
651A ARG* 3.4 27.5 + - - +
652A HIS* 3.2 33.1 + - - +
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Residues in contact with TYR 649 (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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645A ARG* 2.8 61.8 + - + +
646A LEU* 3.7 28.7 - - + +
648A SER* 1.3 79.1 + - - +
650A ASN* 1.3 57.8 + - - +
652A HIS* 3.9 1.1 - - - -
653A THR* 3.1 34.0 + - - -
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Residues in contact with ASN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A LEU 3.1 15.4 + - - +
647A ARG* 3.5 8.2 + - - +
648A SER 2.9 0.6 - - - -
649A TYR* 1.3 80.3 - - - +
651A ARG* 1.3 67.9 + - - +
653A THR* 3.2 19.4 - - - +
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Residues in contact with ARG 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A GLN* 5.0 1.4 + - - +
647A ARG* 3.2 29.5 + - - +
648A SER* 3.6 30.1 - - - +
650A ASN* 1.3 83.6 - - - +
652A HIS* 1.3 98.2 + - + +
653A THR 3.5 3.9 + - - +
83B GLU* 5.5 0.6 + - - -
140B GLU* 3.6 26.7 + - - +
1156B TAM 3.6 28.3 + - - +
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Residues in contact with HIS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A SER* 3.2 18.3 + - - +
649A TYR* 3.9 2.5 - - - -
651A ARG* 1.3 112.6 + - + +
653A THR* 1.3 65.0 + - - +
654A LEU* 3.9 10.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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