Contacts of the helix formed by residues 542 - 558 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541B GLY* 1.3 74.2 - - - -
543B ALA* 1.3 57.6 + - + +
544B TRP* 3.4 11.2 + - - +
545B GLN* 2.7 74.1 + - - +
546B LYS* 2.7 12.2 + - - -
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Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ASP* 1.3 72.3 - - + +
544B TRP* 1.3 62.9 + - - +
546B LYS* 3.2 11.7 + - - +
547B PHE* 2.8 38.0 + - + -
595B TRP* 3.8 27.1 - - + -
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Residues in contact with TRP 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ASP* 3.2 11.2 + - - +
543B ALA* 1.3 79.2 - - - +
545B GLN* 1.3 69.3 + - + +
547B PHE* 3.4 3.3 + - - +
548B ALA* 3.0 45.4 + - + +
551B ARG* 4.3 4.8 + - - -
595B TRP* 3.9 33.7 - + + +
659B PRO* 6.2 1.3 - - + -
682B ASP* 3.7 14.4 - - - -
687B HIS 3.4 15.8 + - - -
688B GLY* 3.9 7.3 - - - -
689B SER* 3.5 34.0 - - - +
717B PRO* 4.5 15.7 - - + -
718B LEU* 4.3 12.1 - - + -
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Residues in contact with GLN 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B PRO* 6.4 1.3 - - - -
540B PRO 3.9 6.3 - - - +
541B GLY* 3.2 10.1 - - - -
542B ASP* 2.7 50.0 + - - +
544B TRP* 1.3 83.9 - - + +
546B LYS* 1.3 59.7 + - - +
549B ASN* 2.7 35.9 + - - +
659B PRO* 3.9 23.8 - - + +
718B LEU* 3.8 20.0 - - + +
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Residues in contact with LYS 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B LEU* 3.9 26.2 - - + +
537B ASP* 4.1 25.6 + - - +
539B MET* 3.1 47.8 + - + +
540B PRO 4.0 1.6 - - - +
541B GLY 3.3 20.3 + - - +
542B ASP 2.7 23.3 + - - +
543B ALA* 3.2 10.7 + - - +
545B GLN* 1.3 73.3 - - - +
547B PHE* 1.3 60.5 + - + +
549B ASN 3.4 0.7 + - - -
550B LEU* 3.1 22.9 + - - +
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Residues in contact with PHE 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B LEU* 3.9 27.4 - - + -
543B ALA* 2.8 33.1 + - + +
544B TRP 3.9 2.9 - - - +
545B GLN 3.3 0.2 - - - -
546B LYS* 1.3 77.7 - - + +
548B ALA* 1.3 59.9 + - - +
550B LEU* 3.1 6.8 + - + +
551B ARG* 2.9 42.0 + - - +
573B ALA* 4.1 4.7 - - + -
595B TRP* 3.4 63.3 - + + -
596B HIS* 3.8 34.5 - + - -
599B VAL* 4.1 17.2 - - + +
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Residues in contact with ALA 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B TRP* 3.0 48.2 + - + +
545B GLN 3.9 2.7 - - - +
546B LYS 3.4 0.2 - - - -
547B PHE* 1.3 76.0 - - - +
549B ASN* 1.3 62.0 + - - +
551B ARG* 3.4 18.2 + - - +
552B ALA* 3.0 15.9 + - - +
718B LEU* 2.9 35.9 - - + +
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Residues in contact with ASN 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B MET* 3.4 11.5 - - + +
497B PRO* 5.1 2.2 - - - +
500B ARG* 2.7 31.5 + - - +
539B MET* 3.6 15.7 - - + -
540B PRO* 3.3 33.5 + - - +
545B GLN* 2.7 26.9 + - - +
546B LYS 3.5 5.8 - - - +
548B ALA* 1.3 74.8 - - - +
550B LEU* 1.3 66.1 - - - +
551B ARG 3.3 0.2 + - - -
552B ALA* 3.3 4.6 + - - +
553B TYR* 3.0 24.9 + - - +
657B PHE* 5.3 0.5 - - - -
718B LEU* 3.6 20.8 - - - +
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Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B ILE* 3.3 42.4 - - + +
536B LEU* 4.3 11.4 - - + +
539B MET* 4.0 7.8 - - + -
546B LYS 3.1 11.9 + - - +
547B PHE* 3.1 10.5 + - + +
549B ASN* 1.3 80.4 - - - +
551B ARG* 1.3 61.8 - - - +
553B TYR* 3.3 7.3 - - + +
554B TYR* 3.0 55.3 + - + +
573B ALA* 3.4 33.9 - - + -
599B VAL* 4.2 9.9 - - + -
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Residues in contact with ARG 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B TRP* 4.3 6.5 + - - +
547B PHE* 2.9 25.5 + - - +
548B ALA* 3.5 37.8 - - - +
550B LEU* 1.3 73.6 - - - +
552B ALA* 1.3 66.6 + - - +
554B TYR* 3.0 6.5 + - - +
555B GLY 2.9 18.7 + - - -
595B TRP* 4.9 2.0 - - - -
598B GLY 5.0 0.2 - - - -
599B VAL* 4.4 18.9 - - + +
602B LEU* 3.2 28.3 - - + +
681B THR* 2.5 52.4 + - - +
682B ASP* 3.8 4.0 + - - +
686B TYR* 3.7 28.3 + - - +
687B HIS 3.6 16.8 + - - -
688B GLY* 3.3 22.2 - - - +
718B LEU 5.5 1.4 + - - -
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B ALA 3.0 9.5 + - - +
549B ASN* 3.9 5.2 - - - +
551B ARG* 1.3 75.3 - - - +
553B TYR* 1.3 56.7 + - - +
555B GLY 3.1 0.5 + - - -
556B TRP* 2.9 15.2 + - - +
657B PHE* 4.2 16.6 - - + -
681B THR* 3.8 6.4 + - - -
718B LEU* 3.5 7.2 - - - +
719B ALA* 3.3 31.6 - - - +
720B THR* 2.7 34.5 - - + +
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Residues in contact with TYR 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B TRP* 3.5 27.1 - + - -
486B MET 4.6 0.3 + - - -
489B THR* 2.8 38.1 + - + -
490B LEU* 3.1 34.8 - - + +
493B MET* 3.7 32.3 - - + -
523B LEU* 3.7 18.4 - - + +
535B ILE* 4.5 12.6 - - + -
539B MET* 4.7 4.0 - - + -
549B ASN 3.0 18.3 + - - +
550B LEU* 3.3 5.4 - - + +
551B ARG 3.1 0.2 - - - -
552B ALA* 1.3 75.9 - - - +
554B TYR* 1.3 68.7 + + - +
556B TRP* 3.1 10.6 + + + +
557B MET* 2.8 28.4 + - + +
657B PHE* 4.6 2.4 - + - -
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Residues in contact with TYR 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B LEU* 3.7 27.8 - - + -
535B ILE* 4.2 5.5 - - + +
550B LEU* 3.0 51.6 + - + +
551B ARG* 3.0 8.7 + - - +
553B TYR* 1.3 83.3 - + - +
555B GLY* 1.3 58.5 + - - +
557B MET* 4.1 5.2 - - - -
558B TRP* 3.0 48.1 + + + +
566B LEU* 4.0 7.6 - - + -
570B ASN* 3.0 42.4 + - - +
573B ALA* 5.5 0.2 - - - -
599B VAL* 4.1 11.7 - - + -
602B LEU* 5.0 3.1 - - + -
603B VAL* 3.9 21.5 - - + -
606B LEU* 4.0 17.4 - - + +
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Residues in contact with GLY 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B ARG 2.9 13.2 + - - -
552B ALA 3.1 2.0 + - - -
554B TYR* 1.3 79.5 - - - +
556B TRP* 1.3 56.2 + - - +
559B ALA* 3.6 4.7 + - - +
606B LEU* 4.2 17.2 - - - +
653B VAL* 4.7 0.5 - - - +
679B LEU* 4.8 0.2 - - - -
681B THR* 4.3 5.4 - - - -
720B THR* 3.4 21.2 + - - -
722B TRP* 3.3 29.4 + - - -
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Residues in contact with TRP 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B TRP* 4.3 17.6 - + - +
489B THR* 4.4 6.8 - - + +
507B LEU* 3.4 38.4 + - + +
552B ALA 2.9 12.0 + - - +
553B TYR* 3.1 13.0 + + - +
555B GLY* 1.3 78.2 - - - +
557B MET* 1.3 64.0 + - - +
559B ALA* 3.1 5.1 + - - +
560B PHE* 2.9 55.8 + + + +
628B TRP* 3.8 11.4 - + - -
639B LEU* 3.7 41.1 - - + -
641B PHE* 3.4 30.0 - + - -
653B VAL* 5.3 2.5 - - + -
655B SER* 3.6 22.7 - - - +
657B PHE* 4.2 17.5 - + + -
720B THR* 4.0 2.0 - - - +
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Residues in contact with MET 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B TRP* 3.4 35.7 - - + -
521B LEU* 3.3 51.3 - - + +
523B LEU* 3.4 31.0 - - + -
553B TYR* 2.8 19.3 + - + +
554B TYR* 3.7 8.3 - - - +
556B TRP* 1.3 77.0 - - - +
558B TRP* 1.3 87.1 + - + +
559B ALA 3.3 0.5 + - - -
560B PHE* 3.4 3.0 + - - -
564B LYS* 3.4 10.1 - - + -
565B LEU 3.5 23.6 - - - +
566B LEU* 4.7 0.7 - - + -
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Residues in contact with TRP 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B SER* 3.8 11.4 + - - -
281B PHE* 4.8 4.0 - + - -
554B TYR* 3.0 52.0 + + + +
556B TRP 3.3 0.2 - - - -
557B MET* 1.3 104.6 - - + +
559B ALA* 1.3 55.7 + - - +
564B LYS* 3.0 38.2 + - + +
566B LEU* 4.1 31.4 - - + -
603B VAL* 4.4 14.4 - - + -
606B LEU* 3.7 35.7 - - + -
607B ASN* 3.2 29.8 + - - +
610B TYR* 3.7 32.0 - + + +
616B MET* 4.0 6.1 - - - +
722B TRP* 3.9 17.6 - - + -
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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