Contacts of the helix formed by residues 667 - 690 (chain D) in PDB entry 1NYE
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 ASN 667 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425C LYS* 3.1 41.6 + - - +
445C GLU* 6.1 0.2 - - - +
478C ALA* 5.8 0.4 - - - -
654D TYR* 5.0 6.3 - - - -
658D THR* 3.5 10.0 - - - +
659D ARG* 4.1 12.6 - - + -
665D GLY 3.1 18.9 - - - +
666D THR* 1.3 78.1 - - - +
668D PRO* 1.3 79.0 - - + +
669D GLU* 3.4 6.9 - - - +
670D GLU* 2.9 39.6 + - - +
671D LEU* 3.4 21.6 + - - +
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Residues in contact with PRO 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C ALA* 3.7 33.2 - - + +
478C ALA* 4.3 7.1 - - + -
479C CYS* 3.8 10.5 - - + +
547C VAL* 4.0 16.6 - - + -
654D TYR* 5.0 6.3 - - + -
659D ARG* 3.2 47.6 - - - +
667D ASN* 1.3 79.8 - - - +
669D GLU* 1.3 68.6 + - - +
671D LEU* 2.9 14.9 + - + +
672D ILE* 3.0 16.6 + - - +
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Residues in contact with GLU 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C ILE* 5.6 0.4 - - + +
425C LYS* 3.6 18.9 + - + -
659D ARG* 2.7 49.7 + - - +
667D ASN* 3.4 10.7 + - - +
668D PRO* 1.3 73.7 - - - +
670D GLU* 1.3 52.4 + - - +
672D ILE* 3.1 8.4 + - - +
673D GLY 2.7 31.0 + - - -
704D VAL* 3.6 30.2 - - + +
706D LEU* 3.5 38.4 - - + +
715D ILE* 3.6 12.6 - - - +
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Residues in contact with GLU 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LYS* 3.9 11.8 - - + +
426C LYS 4.0 15.3 - - - +
427C GLY* 4.2 2.4 - - - -
444C THR* 2.9 40.4 + - - +
445C GLU* 3.4 10.6 - - - +
446C SER* 3.0 32.2 + - - -
448C VAL* 4.7 0.3 - - - +
665D GLY 4.5 0.7 - - - +
666D THR* 3.3 28.3 - - - +
667D ASN* 2.9 26.1 - - - +
669D GLU* 1.3 72.5 - - - +
671D LEU* 1.3 62.1 + - + +
673D GLY* 3.5 1.0 - - - +
674D ALA* 2.8 28.9 + - - +
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Residues in contact with LEU 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C THR* 4.5 7.0 - - - +
448C VAL* 6.2 0.4 - - + -
449C LEU* 5.2 6.7 - - + -
471C LEU* 3.9 25.0 - - + +
474C ALA* 4.4 7.6 - - + +
475C ALA* 3.5 29.2 - - + +
478C ALA* 5.3 0.2 - - + -
642D VAL* 4.9 8.5 - - + -
649D LEU* 4.1 22.4 - - + -
666D THR* 3.9 28.3 - - + -
667D ASN 3.4 20.7 + - - +
668D PRO* 2.9 7.4 + - + +
670D GLU* 1.3 85.5 - - + +
672D ILE* 1.3 64.9 + - - +
674D ALA* 2.9 7.3 + - - +
675D ALA* 2.8 24.2 + - - +
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Residues in contact with ILE 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ILE* 4.2 29.6 - - + -
475C ALA* 3.6 18.8 - - + -
547C VAL* 4.5 15.0 - - + -
551C LEU* 5.8 1.8 - - + -
668D PRO 3.0 19.6 + - - +
669D GLU* 3.3 10.3 - - - +
671D LEU* 1.3 74.0 - - - +
673D GLY* 1.3 63.4 + - - +
675D ALA* 3.4 7.0 + - - +
676D HIS* 2.9 22.1 + - + +
704D VAL* 4.8 4.0 - - + -
715D ILE* 4.7 15.0 - - + -
718D ILE* 4.2 22.9 - - + -
747D VAL* 5.0 1.7 - - + +
751D LEU* 4.3 21.1 - - + -
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Residues in contact with GLY 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C GLY* 4.0 8.3 - - - -
669D GLU 2.7 14.9 + - - -
670D GLU* 3.5 4.3 - - - -
671D LEU 3.0 0.4 - - - -
672D ILE* 1.3 77.5 - - - +
674D ALA* 1.3 63.5 + - - +
676D HIS* 2.9 15.5 + - - +
677D ALA* 2.9 11.8 + - - +
702D ALA* 3.6 17.0 - - - +
704D VAL* 3.7 17.7 - - - -
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Residues in contact with ALA 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C GLY* 3.6 11.8 - - - -
428C GLN 4.3 5.5 - - - +
442C VAL* 4.5 5.0 - - + +
443C SER 3.5 20.6 - - - +
444C THR* 4.4 2.7 - - - +
449C LEU* 4.3 10.5 - - + -
471C LEU* 4.1 15.5 - - + -
670D GLU 2.8 15.7 + - - +
671D LEU* 3.3 10.3 - - - +
673D GLY* 1.3 71.1 - - - +
675D ALA* 1.3 63.2 + - - +
677D ALA* 3.5 2.0 + - - +
678D ALA* 3.0 25.4 + - - +
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Residues in contact with ALA 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C PRO* 3.6 33.6 - - + +
471C LEU* 3.8 10.9 - - + +
472C ILE* 3.7 20.6 - - + -
671D LEU 2.8 11.7 + - - +
672D ILE 3.6 7.9 - - - +
674D ALA* 1.3 77.9 - - - +
676D HIS* 1.3 53.8 + - - +
678D ALA* 3.2 3.3 + - - +
679D CYS* 2.7 37.2 + - - +
747D VAL* 4.3 1.8 - - + -
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Residues in contact with HIS 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672D ILE 2.9 16.7 + - - +
673D GLY* 2.9 6.4 + - - +
675D ALA* 1.3 77.8 - - - +
677D ALA* 1.3 53.7 + - - +
680D PHE* 2.7 40.6 + - + +
702D ALA* 4.3 5.4 - - + -
718D ILE* 3.3 29.1 - - + +
720D LEU* 3.9 14.3 - - + +
745D CYS* 4.4 4.9 - - - -
747D VAL* 3.4 28.2 - - + +
748D SER* 2.9 27.9 + - - -
751D LEU* 4.0 6.0 - - + +
755D ILE* 3.7 37.2 - - + -
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Residues in contact with ALA 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C GLY 4.3 0.2 - - - +
428C GLN* 3.9 7.0 - - - -
429C ALA* 3.3 18.4 - - + +
673D GLY 2.9 14.1 + - - +
674D ALA 3.9 2.7 - - - +
676D HIS* 1.3 76.0 - - - +
678D ALA* 1.3 56.6 + - - +
680D PHE* 3.8 2.2 - - - +
681D SER* 2.8 37.2 + - - -
700D THR* 3.4 29.2 - - - +
702D ALA* 4.1 13.8 - - + +
720D LEU* 4.9 1.3 - - - -
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Residues in contact with ALA 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ALA* 3.3 11.1 - - - +
442C VAL* 3.3 25.1 - - + -
454C TYR* 2.8 29.1 + - + -
467C ASN* 5.8 0.4 - - - -
468C PRO* 4.1 12.8 - - + -
471C LEU* 5.6 1.3 - - + -
674D ALA 3.0 19.3 + - - +
675D ALA* 3.4 5.6 - - - +
677D ALA* 1.3 77.8 - - - +
679D CYS* 1.3 62.0 + - - +
682D MET* 3.1 14.6 + - - +
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Residues in contact with CYS 679 (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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459C ARG* 3.1 32.3 + - - +
468C PRO* 3.6 6.7 - - + +
675D ALA 2.7 12.7 + - - +
678D ALA* 1.3 70.5 - - - +
680D PHE* 1.3 68.4 + - - +
682D MET* 3.6 2.8 + - - +
683D ALA* 3.2 18.0 + - - +
745D CYS* 3.8 4.3 - - - -
746D PRO* 3.3 29.4 - - - -
747D VAL* 3.3 40.4 - - + -
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Residues in contact with PHE 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676D HIS* 2.7 29.9 + - + +
677D ALA* 3.8 2.5 - - - +
679D CYS* 1.3 72.5 - - - +
681D SER* 1.3 67.0 + - - +
683D ALA* 3.0 6.6 + - - +
684D LEU* 2.9 28.7 + - + +
700D THR* 4.2 17.3 - - + -
720D LEU* 4.2 16.4 - - + -
722D SER* 4.0 24.9 - - - -
738D ILE* 4.0 24.2 - - + -
741D ALA* 3.6 15.3 - - + -
742D LYS* 3.3 39.9 - - + -
745D CYS* 3.8 14.5 - - - -
757D LEU* 4.6 15.5 - - + -
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Residues in contact with SER 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ALA* 3.8 9.8 + - - +
431C TRP* 4.3 16.9 - - - -
454C TYR* 3.7 10.1 - - - -
677D ALA 2.8 28.0 + - - -
678D ALA 3.6 3.8 - - - -
680D PHE* 1.3 77.5 - - - +
682D MET* 1.3 63.1 + - - +
684D LEU* 3.0 17.6 + - - +
685D SER* 3.2 10.2 + - - -
698D ILE* 4.1 10.2 - - - +
700D THR* 2.8 28.4 - - - +
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Residues in contact with MET 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C TRP* 3.3 37.5 - - + -
435C ILE* 5.1 10.3 - - + +
454C TYR* 3.2 37.8 + - + -
455C GLY 3.7 18.2 - - - +
456C PHE* 4.1 4.7 - - + +
459C ARG* 3.7 36.1 - - + +
460C PHE* 4.4 10.3 - - + -
678D ALA 3.1 13.3 + - - +
679D CYS* 3.9 4.7 - - - +
681D SER* 1.3 78.2 - - - +
683D ALA* 1.3 63.7 + - - +
685D SER* 2.9 16.2 + - - -
686D LEU* 3.0 11.5 + - + +
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Residues in contact with ALA 683 (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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679D CYS 3.2 10.8 + - - +
680D PHE 3.0 9.7 + - - +
682D MET* 1.3 78.7 - - - +
684D LEU* 1.3 58.4 + - - +
686D LEU* 3.1 8.1 + - - +
687D MET* 2.9 39.4 + - + +
741D ALA* 4.1 10.8 - - + -
745D CYS* 3.5 25.4 - - + +
746D PRO* 5.2 2.5 - - + -
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Residues in contact with LEU 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680D PHE* 2.9 22.3 + - + +
681D SER* 3.0 12.7 + - - +
683D ALA* 1.3 76.9 - - - +
685D SER* 1.3 59.3 + - - +
687D MET* 4.8 0.2 - - - -
688D LEU* 2.9 48.3 + - + +
698D ILE* 3.5 26.5 - - + -
722D SER* 4.8 0.2 - - - +
724D VAL* 3.6 23.3 - - + -
734D PHE* 4.4 6.1 - - + -
737D ILE* 3.9 13.7 - - + -
738D ILE* 3.5 36.1 - - + -
741D ALA* 4.0 10.3 - - + +
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Residues in contact with SER 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C TRP* 3.6 26.0 - - - -
433C GLY 2.8 24.7 + - - -
434C ASP 3.2 13.0 + - - -
435C ILE* 3.4 10.4 - - - +
681D SER 3.2 5.5 + - - -
682D MET 2.9 9.5 + - - -
684D LEU* 1.3 74.7 - - - +
686D LEU* 1.3 61.7 + - - +
688D LEU* 3.6 2.3 - - - +
689D GLY* 2.8 23.7 + - - -
693D PHE 4.7 0.9 - - - +
695D PRO* 4.0 16.0 - - - +
698D ILE* 4.3 0.8 - - - +
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Residues in contact with LEU 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ILE* 3.3 33.8 - - + +
456C PHE* 6.0 2.5 - - + -
682D MET* 3.0 11.1 + - + +
683D ALA* 3.3 13.7 - - - +
685D SER* 1.3 73.4 - - - +
687D MET* 1.3 67.4 + - - +
689D GLY* 2.6 25.8 + - - -
690D GLU* 3.1 54.2 + - + +
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Residues in contact with MET 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D ALA* 2.9 23.0 + - - +
684D LEU* 4.3 1.3 - - - +
686D LEU* 1.3 83.2 - - - +
688D LEU* 1.3 62.0 + - - +
690D GLU* 3.4 23.0 + - - +
691D ALA* 3.3 18.7 + - - +
737D ILE* 3.8 24.6 - - + +
740D LYS* 3.1 48.2 - - + +
741D ALA* 4.0 20.6 - - + +
744D GLY* 6.3 1.3 - - - -
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Residues in contact with LEU 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D LEU* 2.9 37.1 + - + +
685D SER 3.6 3.1 - - - +
686D LEU 2.9 0.6 + - - -
687D MET* 1.3 75.0 - - - +
689D GLY* 1.3 58.7 + - - +
691D ALA* 2.7 26.7 + - - +
693D PHE* 3.0 40.6 + - + +
695D PRO* 3.8 33.7 - - + -
698D ILE* 4.6 0.2 - - + -
726D VAL* 4.4 13.9 - - + -
729D ILE* 5.2 1.6 - - + -
734D PHE* 3.9 21.5 - - + -
737D ILE* 3.5 27.4 - - + -
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Residues in contact with GLY 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ILE* 3.9 15.5 - - - -
685D SER 2.8 12.0 + - - -
686D LEU 2.6 14.5 + - - -
688D LEU* 1.3 70.8 - - - +
690D GLU* 1.3 55.2 + - - -
692D GLY* 2.9 20.8 + - - -
693D PHE 3.1 13.6 + - - -
694D THR* 5.5 0.7 - - - -
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Residues in contact with GLU 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686D LEU* 3.1 41.6 + - + +
687D MET* 3.7 21.6 - - - +
688D LEU 3.2 0.2 - - - -
689D GLY* 1.3 74.2 - - - +
691D ALA* 1.3 56.6 + - - +
692D GLY 3.2 1.7 + - - -
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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
------------------------------------------------------------
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