Contacts of the helix formed by residues 654 - 671 (chain E) in PDB entry 1XMI
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 654 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577E TYR* 4.2 4.5 + - - -
652E GLN 3.8 2.4 + - - -
653E PHE* 1.3 77.9 - - - +
655E ALA* 1.3 63.8 + - - +
656E GLU* 3.4 16.6 - - - +
657E ARG* 3.2 25.2 + - - +
658E ARG* 3.1 21.1 + - - +
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Residues in contact with ALA 655 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653E PHE 3.9 0.4 + - - -
654E SER* 1.3 71.6 - - - +
656E GLU* 1.3 58.1 + - - +
658E ARG* 3.4 18.0 + - - +
659E ASN* 2.9 45.5 + - - +
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Residues in contact with GLU 656 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553E ARG* 5.1 11.1 + - - +
577E TYR* 3.2 29.0 + - + -
654E SER* 3.4 18.2 - - - +
655E ALA* 1.3 78.5 - - - +
657E ARG* 1.3 55.9 + - - +
659E ASN* 3.8 6.0 - - - +
660E SER* 2.9 28.1 + - - -
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Residues in contact with ARG 657 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573E SER* 5.6 2.2 + - - -
576E GLY* 3.1 37.8 + - - +
577E TYR* 3.7 40.0 - - + -
648E ASP* 3.9 19.6 + - - -
653E PHE* 3.3 54.0 - - + +
654E SER* 3.2 25.1 + - - +
656E GLU* 1.3 75.6 - - - +
658E ARG* 1.3 59.4 + - - +
660E SER* 3.3 3.1 + - - -
661E ILE* 3.1 29.4 + - + +
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Residues in contact with ARG 658 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650E PHE* 3.6 44.9 + - + -
651E ASP* 4.5 10.3 + - - +
653E PHE* 2.8 43.7 + - + +
654E SER 3.1 13.1 + - - +
655E ALA* 3.9 11.9 - - - +
657E ARG* 1.3 76.2 - - - +
659E ASN* 1.3 61.1 + - - +
661E ILE* 3.4 10.4 + - - +
662E LEU* 3.0 34.4 + - + +
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Residues in contact with ASN 659 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B PHE* 3.4 46.7 - - + +
655E ALA* 2.9 31.9 + - - +
656E GLU* 4.0 5.7 - - - +
658E ARG* 1.3 78.7 - - - +
660E SER* 1.3 58.5 + - - +
662E LEU* 3.9 11.5 - - - +
663E THR* 2.9 35.8 + - - +
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Residues in contact with SER 660 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550E GLY* 3.3 11.0 - - - +
551E GLY 3.1 21.8 + - - -
577E TYR* 2.9 34.7 + - - +
656E GLU 2.9 20.3 + - - -
657E ARG 3.4 6.5 - - - -
658E ARG 3.2 0.2 - - - -
659E ASN* 1.3 74.1 - - - +
661E ILE* 1.3 59.0 + - - +
663E THR* 2.5 21.5 + - - -
664E GLU* 3.0 18.5 + - - +
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Residues in contact with ILE 661 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ATP 4.7 15.0 - - - +
576E GLY 3.8 15.3 - - - +
577E TYR 4.0 10.3 - - - -
578E LEU 3.5 19.1 - - - +
579E ASP* 3.8 20.2 - - + +
580E VAL 5.5 0.2 - - - +
650E PHE* 4.5 9.9 - - + -
653E PHE* 3.9 26.9 - - + -
657E ARG 3.1 20.8 + - - +
658E ARG* 3.7 6.5 - - - +
660E SER* 1.3 75.4 - - - +
662E LEU* 1.3 60.9 + - + +
664E GLU* 3.3 4.0 + - - +
665E THR* 2.9 33.1 + - - +
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Residues in contact with LEU 662 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B THR* 4.9 7.9 - - + -
469B MET* 3.7 29.2 - - + -
490B PHE* 4.6 3.6 - - + -
492B SER* 3.7 25.8 - - - +
493B GLN* 5.6 4.3 - - + +
494B PHE* 3.9 20.6 - - + +
572B ASP* 6.0 0.4 - - - +
658E ARG* 3.0 23.1 + - + +
659E ASN* 3.9 14.8 - - - +
660E SER 3.3 0.2 - - - -
661E ILE* 1.3 80.1 - - + +
663E THR* 1.3 57.6 + - - +
665E THR* 3.2 6.4 + - - +
666E LEU* 2.8 33.1 + - - +
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Residues in contact with THR 663 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B PHE* 3.2 31.6 - - + -
496B TRP* 3.9 27.4 - - + -
549E SER* 4.6 16.6 - - - -
551E GLY 5.3 0.2 + - - -
659E ASN 2.9 20.6 + - - +
660E SER* 2.5 25.7 + - - -
662E LEU* 1.3 73.6 - - - +
664E GLU* 1.3 57.5 + - - +
666E LEU* 3.3 8.4 + - - +
667E ARG* 2.8 34.0 + - - +
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Residues in contact with GLU 664 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549E SER* 3.9 9.0 + - - -
551E GLY* 3.3 22.6 + - - -
555E ARG* 2.7 33.8 + - - -
577E TYR 3.9 8.7 - - - +
578E LEU* 4.0 11.2 - - + +
579E ASP* 3.3 20.4 - - - +
582E THR* 4.3 0.9 - - - +
660E SER 3.0 16.5 + - - +
661E ILE 3.5 8.1 - - - +
663E THR* 1.3 76.1 + - - +
665E THR* 1.3 63.8 + - - +
667E ARG* 2.7 35.9 + - - +
668E ARG* 3.2 27.4 + - - +
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Residues in contact with THR 665 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B MET* 4.1 13.2 - - - +
472B MET* 3.9 22.2 - - + -
474B GLU* 3.3 28.8 + - + +
490B PHE* 3.9 22.2 - - + -
579E ASP* 3.5 7.6 - - - +
661E ILE* 2.9 17.7 + - - +
662E LEU* 3.2 12.2 + - - +
664E GLU* 1.3 76.4 - - - +
666E LEU* 1.3 61.4 + - - +
668E ARG* 3.3 10.0 + - - +
669E PHE* 3.3 19.6 - - + +
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Residues in contact with LEU 666 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B PHE* 3.2 45.1 - - + +
491B CYS* 4.6 0.4 - - - -
492B SER* 3.8 25.8 - - - +
494B PHE* 4.0 7.9 - - + +
496B TRP* 3.7 41.5 - - + +
557B SER* 5.8 2.9 - - - +
560B ARG* 5.4 6.5 - - - +
662E LEU 2.8 20.9 + - - +
663E THR* 3.6 9.0 - - - +
665E THR* 1.3 73.9 - - - +
667E ARG* 1.3 59.1 + - - +
669E PHE* 3.2 3.8 + - - +
670E SER* 2.8 37.2 + - - +
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Residues in contact with ARG 667 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B TRP* 4.1 15.7 - - + -
525E GLN* 3.9 15.7 + - - +
528E GLU* 6.5 1.1 - - - -
529E ASP* 5.0 6.1 - - - -
552E GLN* 6.1 0.4 - - - -
555E ARG* 3.8 22.6 - - - +
582E THR* 3.1 32.1 + - - +
663E THR 2.8 20.3 + - - +
664E GLU* 2.7 43.2 + - - +
665E THR 3.3 0.2 - - - -
666E LEU* 1.3 72.7 - - - +
668E ARG* 1.3 71.5 + - - +
670E SER* 4.0 4.7 - - - -
671E LEU* 2.8 43.8 + - - +
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Residues in contact with ARG 668 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B GLU* 3.9 9.2 - - - -
525E GLN* 4.7 4.0 + - - -
579E ASP* 3.2 24.9 - - - -
581E LEU* 3.7 25.0 - - - +
582E THR* 3.2 25.2 + - - +
585E GLU* 2.8 44.4 + - - -
664E GLU 3.2 12.9 + - - +
665E THR 3.4 7.4 - - - +
666E LEU 3.2 0.2 - - - -
667E ARG* 1.3 91.1 - - - +
669E PHE* 1.3 70.1 + - + +
670E SER 3.4 0.8 + - - -
671E LEU* 4.2 12.1 - - - +
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Residues in contact with PHE 669 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B MET* 3.3 55.6 - - + -
474B GLU* 4.7 5.6 - - - -
488B ILE* 3.8 46.3 - - + +
489B SER* 4.7 2.3 + - - -
490B PHE* 4.5 15.9 + - + +
564B LYS* 2.8 33.3 + - - +
581E LEU* 5.2 3.1 - - + -
665E THR* 3.3 27.8 + - + +
666E LEU* 3.2 5.7 + - - +
668E ARG* 1.3 91.5 - - + +
670E SER* 1.3 60.3 + - - +
671E LEU* 5.4 0.9 - - - -
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Residues in contact with SER 670 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B PHE 6.2 0.2 - - - -
496B TRP* 3.6 18.8 - - - -
508B ALA* 2.7 25.9 - - - +
509B GLY* 4.1 4.5 - - - +
510B VAL* 4.6 6.5 + - - +
560B ARG* 4.4 20.8 - - - -
564B LYS* 4.9 6.7 - - - +
666E LEU* 2.8 20.1 + - - -
668E ARG 3.4 1.0 - - - -
669E PHE* 1.3 79.8 - - - +
671E LEU* 1.3 82.5 + - - +
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Residues in contact with LEU 671 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B TRP* 4.5 3.7 - - - -
498B MET* 4.3 15.5 - - - +
508B ALA* 3.4 25.7 - - - +
509B GLY* 4.1 18.4 - - - +
593D LYS* 5.6 11.2 - - + +
528E GLU* 5.6 11.4 - - + -
667E ARG* 2.8 31.0 + - - +
668E ARG* 4.2 15.9 - - - +
669E PHE 5.4 0.7 - - - -
670E SER* 1.3 90.7 + - - +
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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