Contacts of the helix formed by residues 530 - 546 (chain O) in PDB entry 5MQF
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 TRP 530 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525O GLN 4.7 5.5 + - - +
527O LYS* 2.9 18.3 + - - +
528O ARG 2.9 0.2 + - - -
529O HIS* 1.3 77.3 - - - +
531O LYS* 1.3 56.6 + - - +
533O TYR* 3.2 9.2 + - - +
534O ILE* 2.9 25.8 + - - +
571O THR* 6.5 1.8 - - - -
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Residues in contact with LYS 531 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527O LYS 3.9 1.3 + - - +
528O ARG* 2.7 17.6 + - - +
530O TRP* 1.3 73.9 - - - +
532O ARG* 1.3 56.4 + - - +
534O ILE* 3.3 9.5 + - - +
535O TYR* 2.9 25.1 + - - +
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Residues in contact with ARG 532 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491O TYR* 5.3 12.6 - - + -
521O VAL* 3.7 21.8 - - + +
522O PRO* 5.3 0.7 - - + -
523O PRO* 4.6 2.5 - - + -
528O ARG 3.0 5.5 + - - +
529O HIS* 3.0 20.3 + - + +
531O LYS* 1.3 74.9 - - - +
533O TYR* 1.3 58.7 + - - +
535O TYR* 3.1 10.7 + - + +
536O LEU* 2.9 27.0 + - - +
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Residues in contact with TYR 533 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529O HIS 2.4 28.6 + - - +
530O TRP* 3.5 9.9 - - - +
532O ARG* 1.3 69.0 - - - +
534O ILE* 1.3 57.2 + - - +
536O LEU* 3.4 7.3 + - - +
537O TRP* 2.9 29.3 + - - +
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Residues in contact with ILE 534 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530O TRP 2.9 14.0 + - - +
531O LYS* 3.6 12.1 - - - +
532O ARG 3.3 0.2 - - - -
533O TYR* 1.3 76.3 - - - +
535O TYR* 1.3 58.0 + - - +
537O TRP* 4.0 6.0 - - - +
538O ILE* 2.9 29.6 + - - +
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Residues in contact with TYR 535 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491O TYR* 5.3 10.3 - - + -
531O LYS 2.9 13.9 + - - +
532O ARG* 3.1 13.4 + - - +
534O ILE* 1.3 76.3 - - - +
536O LEU* 1.3 60.1 + - - +
538O ILE* 3.8 4.8 - - - +
539O ASN* 2.9 29.1 + - - +
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Residues in contact with LEU 536 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514O TYR* 5.4 2.0 - - - +
517O ALA 5.5 1.1 - - - +
518O ILE* 4.1 33.4 - - + +
532O ARG 2.9 14.7 + - - +
533O TYR* 3.8 7.0 - - - +
535O TYR* 1.3 74.1 - - - +
537O TRP* 1.3 60.6 + - - +
539O ASN* 3.8 5.6 - - - +
540O TYR* 2.9 31.0 + - - +
560O ALA* 6.5 0.2 - - + -
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Residues in contact with TRP 537 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533O TYR 2.9 18.5 + - - +
534O ILE* 4.0 7.2 - - - +
536O LEU* 1.3 77.5 - - - +
538O ILE* 1.3 57.7 + - - +
540O TYR* 3.9 3.7 - - - +
541O ALA* 2.9 30.1 + - - +
557O VAL* 5.6 9.9 - - + +
561O SER* 5.9 4.3 - - - -
575O MET* 5.8 8.7 - - + -
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Residues in contact with ILE 538 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534O ILE 2.9 19.7 + - - +
535O TYR* 3.9 6.1 - - - +
537O TRP* 1.3 77.0 - - - +
539O ASN* 1.3 59.9 + - - +
541O ALA* 3.8 5.0 - - - +
542O LEU* 2.9 30.8 + - - +
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Residues in contact with ASN 539 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514O TYR* 3.9 24.4 - - + +
517O ALA* 6.3 2.5 - - + -
535O TYR 2.9 18.9 + - - +
536O LEU* 3.9 6.1 - - - +
538O ILE* 1.3 77.7 - - - +
540O TYR* 1.3 57.2 + - - +
542O LEU* 4.2 2.8 - - - +
543O TYR* 2.9 31.7 + - - +
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Residues in contact with TYR 540 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514O TYR* 4.3 9.1 - - + +
536O LEU 2.9 18.4 + - - +
537O TRP* 4.3 2.2 - - - +
539O ASN* 1.3 76.5 - - - +
541O ALA* 1.3 57.7 + - - +
543O TYR* 4.5 4.3 - - - -
544O GLU* 2.9 34.3 + - - +
553O ARG 5.3 1.6 - - - +
557O VAL* 3.9 27.6 - - + +
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Residues in contact with ALA 541 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537O TRP 2.9 22.6 + - - +
538O ILE* 3.8 6.7 - - - +
539O ASN 3.3 0.2 - - - -
540O TYR* 1.3 77.5 - - - +
542O LEU* 1.3 51.1 + - - +
544O GLU* 4.8 1.6 - - - -
545O GLU* 2.7 39.7 + - - +
557O VAL* 5.4 1.5 - - + +
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Residues in contact with LEU 542 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538O ILE 2.9 18.1 + - - +
539O ASN* 4.2 3.6 - - - +
541O ALA* 1.3 75.9 - - - +
543O TYR* 1.3 60.2 + - - +
545O GLU* 3.7 2.2 - - - -
546O LEU* 2.9 30.1 + - - +
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Residues in contact with TYR 543 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507O ALA* 4.5 13.3 - - - +
510O VAL* 3.7 41.9 - - + +
511O ARG* 4.3 6.3 - - + +
514O TYR* 4.8 1.1 - - + -
539O ASN 2.9 21.0 + - - +
540O TYR* 4.4 3.8 - - - +
542O LEU* 1.3 78.6 - - - +
544O GLU* 1.3 61.1 + - - +
546O LEU* 3.5 16.3 + - - +
547O GLU 4.5 1.6 + - - -
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Residues in contact with GLU 544 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540O TYR* 2.9 22.4 + - + +
541O ALA* 4.5 1.3 - - - +
543O TYR* 1.3 79.4 - - - +
545O GLU* 1.3 59.3 + - - +
546O LEU 3.5 0.5 + - - -
547O GLU 4.4 0.7 + - - -
548O ALA* 3.7 11.1 + - - +
551O PRO* 3.4 29.8 - - + +
553O ARG* 3.6 37.5 - - + -
554O THR* 4.3 4.7 - - - +
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Residues in contact with GLU 545 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541O ALA 2.7 23.2 + - - +
542O LEU* 3.7 2.7 - - - +
544O GLU* 1.3 74.4 - - - +
546O LEU* 1.3 63.5 + - - +
548O ALA 2.8 22.5 - - - +
549O LYS* 5.2 1.1 - - - +
550O ASP 5.5 4.0 - - - +
551O PRO* 5.1 2.5 - - - -
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Residues in contact with LEU 546 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507O ALA* 5.6 4.7 - - + -
510O VAL* 6.1 2.2 - - + -
542O LEU 2.9 19.2 + - - +
543O TYR* 3.5 12.8 - - - +
544O GLU 3.3 1.4 - - - -
545O GLU* 1.3 81.4 - - - +
547O GLU* 1.3 63.1 + - + +
548O ALA 4.5 0.2 - - - +
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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