Contacts of the helix formed by residues 584 - 589 (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 TRP 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A SER* 3.1 20.5 + - - -
466A PHE* 3.2 42.4 - + + +
469A LEU* 3.9 29.8 - - + -
525A ILE* 4.5 8.7 - - + -
529A LEU* 3.9 18.4 - - + +
540A ASP* 3.9 1.2 + - - -
543A LEU* 3.9 14.1 - - + -
547A LEU* 5.6 0.9 - - + -
568A PHE* 3.8 30.1 - + - -
579A TYR* 4.1 9.9 - - + -
580A GLU 2.9 26.9 + - - -
581A ILE* 3.2 29.8 + - + +
582A GLN 3.3 9.2 - - - -
583A ASP* 1.3 76.0 - - - +
585A LEU* 1.4 54.0 + - - +
587A LYS* 3.2 8.1 + - + +
588A ASN* 2.7 36.4 + - - +
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Residues in contact with LEU 585 (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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529A LEU* 4.3 3.1 - - + -
532A GLN* 3.4 42.2 - - + +
533A SER* 4.1 7.2 - - - +
538A ALA* 3.5 14.4 - - + +
539A THR* 3.3 46.0 - - - +
540A ASP* 3.9 7.3 + - - +
543A LEU* 4.1 17.5 - - + -
583A ASP 3.2 1.4 - - - -
584A TRP* 1.4 75.8 - - - +
586A GLU* 1.3 56.1 + - - +
588A ASN* 3.2 6.9 + - - +
589A LYS* 3.0 51.6 + - - +
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Residues in contact with GLU 586 (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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416A SER* 5.7 4.5 - - - -
420A ALA* 6.0 2.1 - - - +
423A LYS* 5.9 1.1 + - - -
583A ASP* 3.1 30.9 + - + +
585A LEU* 1.3 73.8 - - - +
587A LYS* 1.3 58.4 + - + +
589A LYS* 3.1 4.3 + - - -
590A ASP* 2.6 33.4 + - - -
591A PRO* 3.2 30.9 - - + +
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Residues in contact with LYS 587 (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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465A SER* 2.9 23.5 + - - -
466A PHE* 3.7 31.9 - - + -
467A GLU* 2.9 33.8 + - - +
582A GLN 4.2 2.2 - - - -
583A ASP* 2.9 32.7 + - + +
584A TRP* 3.4 11.9 - - + +
586A GLU* 1.3 81.5 - - + +
588A ASN* 1.3 60.5 + - - +
589A LYS 3.4 0.2 + - - -
590A ASP* 3.5 7.4 + - - +
630A VAL* 3.3 22.5 - - - +
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Residues in contact with ASN 588 (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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466A PHE* 4.4 4.3 - - + -
529A LEU* 3.7 22.4 - - + +
530A ASP* 2.8 25.1 + - - +
533A SER* 2.9 24.5 + - - +
584A TRP 2.7 20.4 + - - +
585A LEU 3.6 5.4 - - - +
586A GLU 3.1 0.2 - - - -
587A LYS* 1.3 73.5 - - - +
589A LYS* 1.3 60.0 + - - +
620A ARG* 4.1 0.2 + - - -
629A THR* 3.4 14.8 - - - +
630A VAL* 3.0 28.5 + - - +
631A ALA* 2.9 36.6 + - - +
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Residues in contact with LYS 589 (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 4.7 0.6 + - - -
533A SER* 2.9 39.7 + - - +
534A VAL 5.2 0.2 - - - -
535A PHE 3.7 18.8 + - - -
536A PRO* 4.7 9.0 + - - +
538A ALA 5.3 1.2 + - - -
585A LEU* 3.0 41.7 + - - +
586A GLU* 3.9 4.0 - - - +
588A ASN* 1.3 80.3 - - - +
590A ASP* 1.3 68.5 + - - +
591A PRO* 3.2 15.7 - - + +
620A ARG* 2.9 23.5 + - - +
629A THR* 5.8 1.8 - - + +
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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