Contacts of the helix formed by residues 542 - 560 (chain A) in PDB entry 1M7X
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 ASP 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A GLY* 1.3 74.0 - - - -
543A ALA* 1.3 56.3 + - + +
544A TRP* 3.8 9.4 + - - +
545A GLN* 2.5 64.1 + - - +
546A LYS* 3.0 4.6 + - - -
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Residues in contact with ALA 543 (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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541A GLY 4.1 0.8 + - - -
542A ASP* 1.3 68.3 - - + +
544A TRP* 1.3 66.8 + - - +
546A LYS* 2.9 21.5 + - - +
547A PHE* 3.1 25.0 + - + -
595A TRP* 3.6 27.1 - - + -
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Residues in contact with TRP 544 (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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542A ASP* 2.9 10.5 + - - +
543A ALA* 1.3 78.3 - - - +
545A GLN* 1.3 75.3 + - + +
547A PHE* 3.4 1.8 + - - +
548A ALA* 3.0 46.9 + - + +
551A ARG* 4.4 4.3 + - - +
595A TRP* 3.9 29.7 - + + -
659A PRO* 5.2 4.7 - - + -
682A ASP* 3.7 19.1 - - - -
687A HIS 3.3 24.1 + - - -
688A GLY 4.1 5.5 + - - -
689A SER* 3.8 13.5 - - - +
717A PRO* 4.2 31.2 - - + -
718A LEU* 4.2 13.9 - - + -
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Residues in contact with GLN 545 (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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497A PRO* 4.7 9.9 - - - +
540A PRO 4.0 6.5 - - - +
541A GLY* 3.8 8.3 - - - -
542A ASP* 2.5 55.4 + - - +
544A TRP* 1.3 88.6 - - + +
546A LYS* 1.3 59.8 + - - +
548A ALA* 3.8 0.7 - - - +
549A ASN* 2.8 32.3 + - - +
659A PRO* 3.7 31.3 - - + +
718A LEU* 3.9 17.4 - - + +
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Residues in contact with LYS 546 (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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536A LEU* 4.0 28.7 - - + +
537A ASP* 4.2 15.9 - - - +
539A MET* 3.0 42.4 + - + +
540A PRO* 3.6 7.9 - - - +
541A GLY 2.9 32.0 + - - +
542A ASP 3.0 4.6 + - - +
543A ALA* 2.9 16.1 + - - +
545A GLN* 1.3 77.7 - - - +
547A PHE* 1.3 64.2 + - + +
549A ASN* 3.4 3.5 + - - +
550A LEU* 3.1 17.2 + - - +
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Residues in contact with PHE 547 (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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536A LEU* 3.8 21.3 - - + -
543A ALA* 3.1 25.2 + - + -
544A TRP 4.0 3.6 - - - +
546A LYS* 1.3 75.5 - - + +
548A ALA* 1.3 55.6 + - - +
550A LEU* 3.1 6.1 + - + +
551A ARG* 2.7 55.6 + - - +
573A ALA* 3.8 22.9 - - + -
595A TRP* 3.6 48.5 - + + -
596A HIS* 3.7 28.0 - + - -
599A VAL* 3.5 22.7 - - + -
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Residues in contact with ALA 548 (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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544A TRP* 3.0 43.8 + - + +
545A GLN 3.8 3.4 - - - +
547A PHE* 1.3 73.1 - - - +
549A ASN* 1.3 61.5 + - - +
551A ARG* 3.4 24.2 - - - +
552A ALA* 2.9 24.1 + - - +
718A LEU* 3.0 28.7 - - + +
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Residues in contact with ASN 549 (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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493A MET* 3.2 21.4 - - + +
497A PRO* 4.9 2.6 - - - +
500A ARG* 3.1 35.6 + - - -
539A MET* 3.8 10.5 - - + -
540A PRO* 3.4 30.6 + - - +
545A GLN* 2.8 26.4 + - - +
546A LYS 3.5 5.4 - - - +
548A ALA* 1.3 75.5 - - - +
550A LEU* 1.3 58.8 + - - +
552A ALA* 3.2 4.9 + - - +
553A TYR* 2.8 25.5 + - - +
718A LEU* 3.2 20.4 - - - +
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Residues in contact with LEU 550 (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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535A ILE* 3.8 24.7 - - + -
536A LEU* 4.1 22.4 - - + +
539A MET* 4.0 10.0 - - + -
546A LYS 3.1 11.6 + - - +
547A PHE* 3.2 8.1 - - + +
549A ASN* 1.3 80.1 - - - +
551A ARG* 1.3 58.0 + - - +
553A TYR* 3.2 6.5 + - + +
554A TYR* 2.9 63.3 + - + +
573A ALA* 3.4 34.5 - - + -
599A VAL* 3.9 18.8 - - + -
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Residues in contact with ARG 551 (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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544A TRP* 4.4 4.9 + - - +
547A PHE* 2.7 54.6 + - - +
548A ALA* 3.4 24.5 - - - +
550A LEU* 1.3 71.0 - - - +
552A ALA* 1.3 59.8 + - - +
554A TYR* 3.2 6.4 + - - +
555A GLY 2.8 25.3 + - - -
595A TRP* 4.3 4.8 - - - +
598A GLY 4.6 1.8 - - - -
599A VAL* 4.2 22.6 - - + +
602A LEU* 3.4 24.2 - - + +
681A THR* 3.0 30.5 + - - +
682A ASP* 4.6 1.4 + - - +
686A TYR* 3.3 40.3 + - - +
687A HIS 3.6 5.7 + - - -
688A GLY* 3.4 26.7 - - - -
718A LEU 5.5 0.6 + - - -
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Residues in contact with ALA 552 (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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548A ALA 2.9 19.9 + - - +
549A ASN* 3.5 6.1 - - - +
551A ARG* 1.3 76.3 - - - +
553A TYR* 1.3 64.2 + - - +
555A GLY 3.2 0.2 + - - -
556A TRP* 3.0 9.5 + - - +
657A PHE* 3.9 17.9 - - + -
681A THR* 4.0 5.5 + - - -
718A LEU* 3.5 16.8 - - - +
719A ALA* 3.5 11.9 - - - +
720A THR* 2.7 33.1 - - + +
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Residues in contact with TYR 553 (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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485A TRP* 3.3 25.2 - + - -
486A MET 4.6 0.3 + - - -
489A THR* 2.7 39.9 + - + -
490A LEU* 3.2 31.0 - - + +
493A MET* 3.7 32.1 - - + -
507A LEU* 6.5 0.4 - - + -
523A LEU* 3.4 26.4 - - + +
535A ILE* 4.4 8.5 - - + -
539A MET* 5.0 3.1 - - + -
549A ASN 2.8 14.2 + - - +
550A LEU* 3.3 10.1 - - + +
552A ALA* 1.3 74.0 - - - +
554A TYR* 1.3 80.8 + + - +
556A TRP* 2.9 16.4 + + + +
557A MET* 2.8 22.1 + - + +
657A PHE* 4.4 1.3 - - - -
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Residues in contact with TYR 554 (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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523A LEU* 3.8 25.4 - - + -
535A ILE* 4.4 5.5 - - + +
550A LEU* 2.9 41.1 + - + +
551A ARG* 3.6 10.5 - - - +
553A TYR* 1.3 83.9 - + - +
555A GLY* 1.3 63.1 + - - +
557A MET* 3.3 6.0 + - - -
558A TRP* 3.0 40.9 + + + +
566A LEU* 4.2 9.0 - - + -
570A ASN* 3.0 41.9 + - - +
573A ALA* 5.4 0.2 - - - -
599A VAL* 3.9 20.2 - - + -
602A LEU* 4.7 3.4 - - + -
603A VAL* 4.0 22.2 - - + -
606A LEU* 3.7 17.0 - - + +
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Residues in contact with GLY 555 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A ARG 2.8 14.7 + - - -
552A ALA 3.5 4.3 - - - -
553A TYR 3.1 0.2 - - - -
554A TYR* 1.3 78.6 - - - +
556A TRP* 1.3 58.5 + - - +
559A ALA* 3.6 4.3 + - - +
606A LEU* 4.2 12.9 - - - +
679A LEU* 4.8 0.2 - - - -
681A THR* 4.2 9.2 - - - -
720A THR* 3.7 16.8 + - - -
722A TRP* 3.4 30.1 + - - -
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Residues in contact with TRP 556 (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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485A TRP* 4.3 12.2 - + - +
489A THR* 4.3 13.2 - - + +
507A LEU* 3.4 41.5 + - + +
552A ALA 3.0 11.0 + - - +
553A TYR* 2.9 16.3 + + - +
555A GLY* 1.3 74.7 - - - +
557A MET* 1.3 64.4 + - - +
559A ALA* 3.2 5.7 + - - +
560A PHE* 2.9 55.1 + + + +
628A TRP* 4.0 14.4 - + - -
639A LEU* 3.8 43.5 - - + -
641A PHE* 4.0 21.4 - + - -
653A VAL* 5.2 4.0 - - + -
655A SER* 3.5 24.2 - - - +
657A PHE* 4.2 15.9 - + + -
720A THR* 3.9 2.6 - - - +
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Residues in contact with MET 557 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A TRP* 3.7 34.3 - - + -
521A LEU* 3.4 31.3 - - + +
523A LEU* 3.8 31.6 - - + -
553A TYR* 2.8 16.0 + - + +
554A TYR* 3.6 9.6 - - - +
556A TRP* 1.3 78.1 - - - +
558A TRP* 1.3 82.3 + - + +
559A ALA 3.2 1.2 + - - -
560A PHE* 3.3 5.8 + - - -
564A LYS* 2.9 24.8 + - + -
565A LEU 3.3 31.4 - - - +
566A LEU* 4.6 1.3 - - + -
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Residues in contact with TRP 558 (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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244A SER* 3.6 13.6 + - - -
281A PHE* 4.5 5.6 - + - -
554A TYR* 3.0 37.0 + + + +
557A MET* 1.3 102.6 - - + +
559A ALA* 1.3 56.7 + - - +
564A LYS* 3.2 33.4 + - + +
566A LEU* 4.2 35.0 - - + -
603A VAL* 4.5 9.6 - - + -
606A LEU* 3.7 31.9 - - + -
607A ASN* 2.9 34.8 + - - +
610A TYR* 3.5 45.3 - + + -
616A MET* 4.1 3.6 - - - +
722A TRP* 3.8 20.5 - - + -
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Residues in contact with ALA 559 (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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555A GLY 3.6 6.6 + - - +
556A TRP 3.2 3.7 + - - +
557A MET 3.1 0.4 - - - -
558A TRP* 1.3 78.4 - - - +
560A PHE* 1.3 62.0 + - - +
616A MET* 3.3 24.2 - - + -
641A PHE* 3.4 10.0 - - + -
643A ARG* 3.0 27.2 + - - +
653A VAL* 3.7 20.9 - - + -
722A TRP* 3.6 22.2 - - + +
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Residues in contact with PHE 560 (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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482A ASN* 5.7 1.1 - - - -
485A TRP* 3.4 35.0 - + - +
507A LEU 3.8 21.5 - - - -
510A GLY* 4.1 11.7 - - - -
511A ILE* 3.3 46.2 - - + -
514A ASN* 5.6 2.0 - - - -
521A LEU* 3.8 13.5 - - + +
556A TRP* 2.9 39.4 + + - +
557A MET* 3.3 1.9 + - - +
559A ALA* 1.3 77.2 - - - +
561A PRO* 1.3 92.8 - - + +
562A GLY 3.2 0.3 + - - -
564A LYS* 2.9 21.1 + - - -
626A PHE* 4.5 4.0 - + - -
628A TRP* 4.8 0.9 - + - -
641A PHE* 4.2 9.2 - + - -
643A ARG* 3.3 4.0 + - - -
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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
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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