Contacts of the helix formed by residues 638 - 661 (chain M) in PDB entry 2JA7
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 GLY 638 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633M VAL 3.3 0.6 + - - -
634M THR 3.2 20.1 + - - +
635M ARG 5.1 0.7 - - - -
636M GLU 3.5 0.9 - - - -
637M LYS* 1.3 80.5 - - - +
639M PRO* 1.3 74.8 - - - +
640M GLN 3.4 1.6 - - - -
641M VAL* 4.0 5.6 - - - -
642M CYS* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 639 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508M PRO* 3.7 28.7 - - + +
509M LEU* 4.2 20.2 - - + -
511M ILE* 4.2 2.6 - - + +
634M THR* 4.1 12.9 - - + +
638M GLY* 1.3 83.1 - - - +
640M GLN* 1.3 75.3 + - + +
642M CYS* 3.7 2.1 - - + +
643M ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 640 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362M ASP* 4.2 15.6 + - - +
508M PRO* 4.6 11.8 - - + +
639M PRO* 1.3 90.6 - - + +
641M VAL* 1.3 66.1 + - + +
643M ALA* 3.2 7.1 + - - +
644M LYS* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 641 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583M PRO* 4.7 13.9 - - + -
633M VAL* 4.6 5.2 - - + -
637M LYS* 3.5 50.0 - - + +
638M GLY* 3.7 4.0 + - - +
639M PRO 3.3 0.6 - - - -
640M GLN* 1.3 77.7 - - + +
642M CYS* 1.3 61.7 + - - +
644M LYS* 3.4 11.6 + - - +
645M LEU* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 642 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511M ILE* 3.6 15.7 - - + -
630M ILE* 3.7 20.4 - - - -
633M VAL* 3.9 15.0 - - + +
634M THR* 2.9 39.7 - - + +
638M GLY 3.1 16.2 + - - +
639M PRO 3.7 3.1 - - - +
641M VAL* 1.3 75.3 - - - +
643M ALA* 1.3 67.7 + - - +
645M LEU* 3.0 18.8 + - - +
646M PHE* 3.3 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 643 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360M GLU* 6.1 0.4 - - - +
361M LEU* 4.3 22.6 + - + +
362M ASP* 4.9 4.7 - - - +
508M PRO* 4.0 25.8 - - + -
511M ILE* 4.0 8.7 - - - +
639M PRO 2.9 14.4 + - - +
640M GLN* 3.2 12.8 + - - +
642M CYS* 1.3 77.9 - - - +
644M LYS* 1.3 64.0 + - - +
645M LEU 3.0 0.9 + - - -
646M PHE* 3.1 18.3 + - - +
647M GLY* 3.6 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 644 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360M GLU* 5.1 13.9 - - - +
554M PRO* 5.4 5.2 - - + -
555M ASP* 3.3 39.8 + - - +
640M GLN 3.1 9.1 + - - +
641M VAL* 3.5 12.6 - - + +
642M CYS 3.2 0.2 - - - -
643M ALA* 1.3 79.0 - - - +
645M LEU* 1.3 63.2 + - - +
647M GLY* 3.0 12.7 + - - +
648M ASN* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 645 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581M ALA* 4.1 26.2 - - + +
582M ILE* 4.5 4.7 - - + +
583M PRO* 4.8 6.5 - - + -
629M LEU* 4.3 12.6 - - + -
630M ILE* 5.0 13.5 - - + -
633M VAL* 3.8 33.4 - - + -
641M VAL 3.3 7.0 + - - +
642M CYS* 3.0 17.8 + - - +
644M LYS* 1.3 76.7 - - - +
646M PHE* 1.3 71.5 + - + +
648M ASN* 4.3 5.4 - - - +
649M ILE* 3.1 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 646 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M LEU* 4.0 20.2 - - + -
471M ASN* 5.4 0.2 - - - +
473M SER* 3.4 21.1 - - - +
511M ILE* 4.0 12.8 - - + -
521M MET* 3.8 15.9 - - + -
522M GLY* 2.8 33.4 - - - -
523M ILE* 4.4 6.3 - - + -
630M ILE* 3.1 34.1 - - + -
642M CYS* 3.3 34.3 - - - -
643M ALA 3.1 9.2 + - - +
645M LEU* 1.3 82.7 - - + +
647M GLY* 1.3 63.1 + - - +
649M ILE* 3.6 5.7 - - - +
650M GLN* 2.7 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 647 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359M LEU 5.4 0.9 - - - -
360M GLU* 4.5 15.9 - - - -
361M LEU 5.4 1.8 - - - +
643M ALA 3.6 3.6 + - - -
644M LYS* 3.0 10.8 + - - -
646M PHE* 1.3 81.4 - - - +
648M ASN* 1.3 67.5 + - - +
650M GLN* 3.3 9.7 + - - +
651M LYS* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 648 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360M GLU* 5.6 1.0 - - - +
553M VAL* 3.7 30.0 - - + +
554M PRO* 3.2 26.8 - - - +
555M ASP* 3.6 16.6 + - - +
581M ALA* 3.9 19.8 + - + -
644M LYS* 3.1 22.7 + - - +
645M LEU* 3.9 6.2 - - - +
647M GLY* 1.3 76.0 - - - +
649M ILE* 1.3 69.4 + - - +
651M LYS* 2.7 17.8 + - - +
652M VAL* 3.0 14.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 649 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523M ILE* 3.4 32.8 - - + -
527M THR* 4.4 1.6 - - + -
531M ILE* 4.0 21.1 - - + -
578M LEU* 4.3 9.6 - - + -
581M ALA* 3.9 13.6 - - + +
582M ILE* 5.7 2.0 - - + -
622M VAL* 4.0 12.8 - - + -
629M LEU* 4.7 7.2 - - + -
630M ILE* 6.2 0.4 - - + -
645M LEU* 3.1 51.4 + - + +
646M PHE* 3.6 3.8 - - - +
648M ASN* 1.3 74.4 - - - +
650M GLN* 1.3 66.0 + - - +
652M VAL* 3.3 2.2 + - - +
653M VAL* 2.9 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 650 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357M PRO* 5.3 10.0 - - - +
359M LEU 4.6 2.1 - - - +
471M ASN* 3.3 29.9 + - - -
472M LEU* 4.5 8.1 - - - +
473M SER* 3.0 29.7 + - - +
523M ILE* 5.2 3.9 - - + +
524M VAL 5.9 0.8 - - - +
527M THR* 3.3 26.3 + - + +
646M PHE* 2.7 32.4 + - - +
647M GLY* 3.3 7.2 - - - +
648M ASN 2.8 3.2 + - - -
649M ILE* 1.3 71.4 - - + +
651M LYS* 1.3 56.9 + - + +
654M ASN* 2.5 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 651 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357M PRO 4.5 7.7 + - - +
358M ASN* 3.7 33.3 + - - +
359M LEU 4.5 3.8 + - - -
360M GLU* 3.9 25.2 + - - -
552M TRP* 3.5 50.9 - - + +
554M PRO* 4.3 14.4 - - + -
647M GLY* 3.1 25.0 - - - +
648M ASN* 2.7 11.9 + - - +
650M GLN* 1.3 73.4 - - + +
652M VAL* 1.3 68.1 + - + +
654M ASN* 3.9 4.4 - - - +
655M PHE* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 652 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534M LEU* 4.6 10.5 - - + -
549M MET* 4.2 18.2 - - + +
552M TRP* 5.0 4.2 - - + +
553M VAL* 3.2 35.9 - - + +
577M ILE* 4.1 30.7 - - + +
578M LEU* 4.7 9.0 - - + -
581M ALA* 5.1 5.2 - - + -
648M ASN 3.0 13.1 + - - +
649M ILE* 3.6 7.0 - - - +
651M LYS* 1.3 77.2 - - - +
653M VAL* 1.3 75.6 + - + +
655M PHE* 2.8 9.7 + - - +
656M TRP* 2.8 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 653 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526M ASP 4.5 0.4 - - - +
527M THR* 3.4 19.5 - - + +
530M GLY* 3.5 13.0 - - - -
531M ILE* 3.3 51.6 - - + +
534M LEU* 4.2 13.0 - - + -
578M LEU* 4.2 4.7 - - + -
649M ILE* 2.9 27.1 + - + +
650M GLN 3.9 1.1 - - - +
652M VAL* 1.3 76.5 - - - +
654M ASN* 1.3 68.1 + - - +
656M TRP* 2.7 10.2 + - + +
657M LEU* 2.7 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 654 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357M PRO* 4.1 23.8 + - + +
526M ASP* 4.0 8.2 - - - +
527M THR* 3.0 29.9 + - - -
552M TRP* 6.2 0.7 - - + -
650M GLN* 2.5 54.2 + - - +
651M LYS* 3.6 4.5 - - - +
653M VAL* 1.3 75.9 - - - +
655M PHE* 1.3 51.2 + - - +
657M LEU* 3.0 7.1 + - - +
658M LEU* 2.6 38.4 + - - +
831N SER 4.6 14.4 - - - +
832N GLY* 5.3 1.0 - - - -
835N GLN* 4.6 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 655 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545M GLN* 4.7 10.3 - - + -
548M ASN* 3.8 33.4 - - + -
549M MET* 3.5 36.3 - - + -
552M TRP* 4.2 39.0 - + + -
651M LYS 2.9 20.7 + - - +
652M VAL* 2.8 5.8 + - - +
654M ASN* 1.3 72.5 - - - +
656M TRP* 1.3 64.1 + - - +
658M LEU* 3.4 21.1 - - + +
659M HIS* 3.6 39.9 + + - -
1076N HIS* 6.4 0.2 - + - -
61W TYR* 5.9 5.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 656 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530M GLY* 4.0 8.5 - - - -
533M LYS* 3.9 13.5 - - + -
534M LEU* 3.2 62.5 - - + +
539M THR* 4.2 14.3 - - + +
541M ILE* 3.6 12.7 - - + +
545M GLN* 4.1 12.2 + - - +
549M MET* 3.5 35.0 - - + -
652M VAL 2.8 6.7 + - - +
653M VAL* 2.7 16.4 + - - +
655M PHE* 1.3 73.0 - - - +
657M LEU* 1.3 94.6 + - + +
658M LEU 2.8 5.3 + - - -
659M HIS* 2.9 15.1 + - - +
660M ASN* 3.0 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 657 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526M ASP* 3.6 51.1 - - + +
529M CYS* 5.3 2.7 - - + -
530M GLY* 3.9 16.6 - - - +
533M LYS* 5.9 2.9 - - + -
653M VAL* 2.7 19.0 + - + +
654M ASN* 3.6 5.8 - - - +
656M TRP* 1.3 94.0 - - + +
658M LEU* 1.3 55.7 + - - +
660M ASN* 3.7 3.4 - - - +
661M GLY* 2.9 39.9 + - - +
662M PHE* 3.8 16.4 - - + -
829N CYS* 4.2 13.2 - - + +
830N TYR 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 658 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654M ASN 2.6 16.8 + - - +
655M PHE* 3.4 22.0 - - + +
656M TRP 2.8 0.8 + - - -
657M LEU* 1.3 75.8 - - - +
659M HIS* 1.3 80.7 - - + +
661M GLY* 4.0 4.9 + - - -
829N CYS 4.6 1.5 - - - +
830N TYR* 3.4 36.9 - - + -
831N SER* 3.0 42.0 - - - +
1074N ASN* 3.8 6.7 + - - +
1076N HIS* 3.9 22.9 - - + +
1081N LEU* 4.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 659 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545M GLN* 4.1 25.8 - - + +
655M PHE* 3.6 34.7 - + - -
656M TRP* 2.9 6.6 + - - +
658M LEU* 1.3 95.0 - - + +
660M ASN* 1.3 63.4 + - - +
661M GLY 3.0 5.4 - - - -
1074N ASN* 2.7 39.5 + - + +
1076N HIS* 4.4 9.8 - + + +
1077N THR* 4.7 18.8 + - + +
1079N LYS* 6.1 6.5 - - + -
1080N LYS 4.1 3.7 - - - +
1081N LEU* 3.1 27.6 - - - +
1082N MET 4.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 660 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533M LYS* 3.8 22.6 - - - +
656M TRP* 3.0 58.8 + - + +
657M LEU* 4.1 2.8 - - - +
659M HIS* 1.3 75.7 - - - +
661M GLY* 1.3 74.8 + - - +
1082N MET* 3.4 33.2 - - - +
1083N ALA* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 661 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533M LYS* 4.7 0.2 + - - -
657M LEU* 2.9 20.3 + - - +
658M LEU 4.4 1.8 - - - -
659M HIS 3.0 6.2 - - - -
660M ASN* 1.3 97.6 + - - +
662M PHE* 1.3 66.6 + - - +
828N ALA* 6.2 0.4 - - - -
829N CYS 4.2 9.6 - - - -
1081N LEU* 4.3 19.5 - - - -
1083N ALA* 4.0 7.7 - - - +
----------------------------------------------------------
Back to top of page
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