Contacts of the helix formed by residues 540 - 551 (chain A) in PDB entry 1MMG
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 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A THR* 1.3 75.7 - - - +
541A ASN* 1.4 55.6 + - - +
543A LEU* 3.6 8.1 - - - +
544A ILE* 2.9 32.6 + - - +
566A THR* 6.1 2.2 - - + -
581A ILE* 3.7 25.9 - - + +
582A GLN* 3.3 12.9 - - + +
583A ASP* 3.0 38.7 + - - +
584A TRP 3.9 3.5 + - - -
585A LEU* 4.3 10.6 + - - +
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Residues in contact with ASN 541 (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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539A THR* 3.0 10.3 + - - +
540A ASP* 1.4 77.5 - - - +
542A THR* 1.3 58.6 + - - +
544A ILE* 3.4 10.7 - - - +
545A THR* 2.5 49.4 + - - -
565A LYS* 5.2 7.3 + - - +
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Residues in contact with THR 542 (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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532A GLN* 2.4 45.0 - - - +
537A ASN 5.4 0.2 + - - -
538A ALA* 3.3 17.7 - - + -
539A THR* 3.1 21.2 + - - +
541A ASN* 1.3 76.8 + - - +
543A LEU* 1.3 65.9 + - - +
545A THR* 3.6 4.5 - - - -
546A LYS* 2.9 24.3 + - - +
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Residues in contact with LEU 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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528A LEU* 4.4 1.6 - - + +
529A LEU* 3.9 33.0 - - + +
532A GLN* 3.7 30.7 - - + +
539A THR 2.9 11.6 + - - +
540A ASP* 3.6 5.4 - - - +
542A THR* 1.3 82.6 - - - +
544A ILE* 1.4 63.2 + - - +
546A LYS* 3.2 3.8 + - + +
547A LEU* 3.0 37.3 + - + +
581A ILE* 3.6 31.0 - - + +
584A TRP* 3.9 21.8 - - + -
585A LEU* 4.1 11.9 - - + -
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Residues in contact with ILE 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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540A ASP 2.9 25.5 + - - +
541A ASN* 3.4 16.4 - - - +
543A LEU* 1.4 76.6 - - - +
545A THR* 1.3 60.7 + - - +
547A LEU* 3.4 7.4 + - + +
548A HIS* 2.9 49.0 + - + +
558A TYR* 4.8 0.7 - - - +
565A LYS 3.6 19.3 - - - +
566A THR* 3.8 5.8 - - + +
567A GLU* 3.3 45.1 - - - +
568A PHE* 4.0 15.7 - - + -
581A ILE* 4.1 13.5 - - + -
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Residues in contact with THR 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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541A ASN* 2.5 40.1 + - - -
542A THR* 3.6 5.1 - - - -
544A ILE* 1.3 75.1 - - - +
546A LYS* 1.4 62.2 + - - +
548A HIS* 3.4 8.7 + - - +
549A SER* 2.7 34.3 + - - -
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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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528A LEU* 4.3 18.9 - - + +
531A GLU* 4.4 19.9 + - + +
532A GLN* 4.1 22.7 - - + +
542A THR 2.9 18.1 + - - +
543A LEU* 3.6 4.9 - - + +
545A THR* 1.4 78.4 - - - +
547A LEU* 1.4 50.4 + - - +
549A SER* 3.2 6.6 + - - -
550A HIS* 2.9 70.2 + - + +
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Residues in contact with LEU 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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525A ILE* 4.1 23.1 - - + +
528A LEU* 3.9 30.5 - - + -
529A LEU* 6.0 0.2 - - + -
543A LEU* 3.0 28.2 + - + +
544A ILE* 3.5 8.5 - - + +
546A LYS* 1.4 72.4 - - - +
548A HIS* 1.3 65.9 + - - +
550A HIS 3.2 1.2 + - - -
551A PHE* 3.0 39.9 + - + +
558A TYR* 3.3 16.5 + - + +
568A PHE* 3.9 21.3 - - + -
581A ILE* 3.7 29.6 - - + -
584A TRP* 5.4 0.9 - - + -
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Residues in contact with HIS 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 ILE* 2.9 42.4 + - + +
545A THR* 3.7 8.1 - - - +
547A LEU* 1.3 76.0 - - - +
549A SER* 1.4 61.8 + - - +
552A SER* 2.8 34.8 + - - +
554A LYS* 5.0 0.7 + - - +
558A TYR* 2.7 32.1 + - - -
560A GLU* 3.6 46.3 - - + +
561A PRO* 3.7 6.1 - - + +
564A SER 5.2 3.6 + - - -
565A LYS* 5.2 4.5 + - - -
567A GLU 3.6 20.6 + - - -
568A PHE* 3.9 1.6 - - + -
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Residues in contact with SER 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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545A THR* 2.7 25.4 + - - -
546A LYS* 3.3 12.6 - - - -
548A HIS* 1.4 71.1 - - - +
550A HIS* 1.3 68.3 + - - +
554A LYS* 3.2 28.0 + - - +
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Residues in contact with HIS 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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522A PRO* 6.0 0.6 - - - +
523A PRO* 4.4 21.5 + - + +
528A LEU* 3.7 23.6 - - + +
546A LYS* 2.9 63.7 + - + +
547A LEU 4.0 0.9 - - - +
549A SER* 1.3 86.6 - - - +
551A PHE* 1.4 81.7 + - + +
554A LYS* 3.6 16.3 - - - +
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Residues in contact with PHE 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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516A LEU* 3.5 21.5 - - + -
522A PRO* 6.2 1.3 - - + -
523A PRO 3.4 26.5 - - - -
524A GLY* 3.8 11.2 - - - -
525A ILE* 4.0 9.9 - - + -
528A LEU* 3.5 28.7 - - + -
547A LEU* 3.0 31.4 + - + +
550A HIS* 1.4 88.1 - - + +
552A SER* 1.4 61.6 + - - +
553A LYS 3.1 1.6 + - - -
554A LYS* 2.8 22.1 + - - -
555A ASN* 2.9 23.8 + - + +
558A TYR* 3.3 43.8 - + + +
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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