Contacts of the helix formed by residues 541 - 552 (chain A) in PDB entry 3MOS
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 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A GLY 3.1 22.4 + - - +
491A GLN* 3.6 7.8 - - - +
492A ALA* 2.9 38.2 + - + +
534A PRO 5.2 1.0 + - - +
536A THR 4.8 1.8 + - - -
539A PRO 4.0 1.0 + - - -
540A LEU* 1.3 72.3 - - - +
542A ARG* 1.3 60.9 + - - +
543A LYS* 3.7 7.3 + - - +
544A LEU* 2.9 34.8 + - - +
545A ILE* 3.0 29.2 + - + +
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Residues in contact with ARG 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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540A LEU* 3.0 12.5 + - - +
541A ASP* 1.3 69.5 + - - +
543A LYS* 1.3 59.5 + - - +
545A ILE* 3.1 8.5 + - - +
546A LEU* 2.8 66.1 + - + +
575A ALA* 2.9 44.8 + - + +
576A VAL* 5.2 1.3 - - + -
577A VAL 5.7 1.0 + - - -
579A GLU* 2.9 33.9 + - - +
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Residues in contact with LYS 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 ASP* 3.3 6.0 - - - +
542A ARG* 1.3 81.6 - - - +
544A LEU* 1.3 63.2 + - - +
546A LEU* 3.8 6.1 - - - +
547A ASP* 3.0 43.2 + - - +
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Residues in contact with LEU 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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491A GLN* 5.8 0.4 - - + -
492A ALA* 3.5 35.2 - - + +
493A LYS 4.2 0.4 - - - +
494A VAL* 4.0 24.9 - - + +
532A LEU* 4.1 6.5 - - + -
541A ASP* 2.9 30.5 + - + +
543A LYS* 1.3 73.6 - - - +
545A ILE* 1.3 60.4 + - - +
547A ASP* 4.5 11.4 - - + +
548A SER* 2.3 47.1 + - - +
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Residues in contact with ILE 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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492A ALA* 5.8 0.4 - - + -
504A THR* 5.0 1.5 - - + +
506A ILE* 3.9 28.5 - - + -
532A LEU* 4.0 24.7 - - + -
534A PRO* 5.7 1.3 - - + -
540A LEU* 3.8 35.0 - - + -
541A ASP* 3.0 24.3 + - + +
542A ARG* 3.1 6.5 + - - +
544A LEU* 1.3 77.6 - - - +
546A LEU* 1.3 60.0 + - - +
548A SER* 3.6 2.3 - - - -
549A ALA* 2.9 25.8 + - - +
556A ILE* 3.6 26.9 - - + +
572A VAL* 4.3 9.2 - - + -
575A ALA* 5.9 0.9 - - + -
576A VAL* 4.1 13.9 - - + -
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Residues in contact with LEU 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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542A ARG* 2.8 66.8 + - + +
543A LYS* 3.8 5.8 - - - +
545A ILE* 1.3 69.6 - - - +
547A ASP* 1.3 60.9 + - - +
549A ALA* 3.1 4.1 + - - +
550A ARG* 2.9 59.4 + - - +
576A VAL* 3.8 30.1 - - + -
579A GLU* 4.2 11.7 - - + +
582A ILE* 4.1 22.9 - - + -
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Residues in contact with ASP 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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530A ARG* 4.9 0.8 + - - -
543A LYS* 3.0 41.7 + - - +
544A LEU* 4.0 13.1 - - + +
546A LEU* 1.3 74.8 - - - +
548A SER* 1.3 63.3 + - - +
550A ARG* 3.2 24.2 + - - +
551A ALA* 3.2 22.0 + - - +
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Residues in contact with SER 548 (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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494A VAL* 4.1 3.8 - - - +
504A THR* 3.0 34.9 + - - -
530A ARG* 3.8 22.8 + - - +
532A LEU* 3.5 12.5 - - - +
544A LEU* 2.3 37.5 + - - +
545A ILE 3.6 3.8 - - - -
547A ASP* 1.3 77.5 - - - +
549A ALA* 1.3 60.4 + - - +
551A ALA* 3.2 5.4 + - - +
552A THR* 3.1 17.3 + - - +
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Residues in contact with ALA 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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504A THR* 3.7 2.6 + - - -
545A ILE 2.9 13.4 + - - +
546A LEU* 3.1 9.8 + - - +
548A SER* 1.3 76.5 - - - +
550A ARG* 1.3 53.5 + - - +
552A THR* 3.0 19.6 + - - -
554A GLY* 2.6 34.3 + - - +
556A ILE* 3.7 29.6 - - + -
582A ILE* 3.9 17.7 - - + -
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Residues in contact with ARG 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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546A LEU* 2.9 41.6 + - - +
547A ASP* 3.2 31.0 + - - +
549A ALA* 1.3 77.0 - - - +
551A ALA* 1.3 59.9 + - - +
552A THR 3.6 0.3 + - - -
553A LYS* 4.0 6.6 + - - -
554A GLY* 4.4 5.1 + - - +
579A GLU* 3.8 20.6 + - - +
580A PRO 5.9 0.8 + - - -
582A ILE* 4.4 14.0 - - + +
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Residues in contact with ALA 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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499A LYS* 4.9 9.2 - - - +
501A ASP* 3.9 7.4 + - - +
530A ARG* 3.5 37.3 + - - +
547A ASP 3.2 10.6 + - - +
548A SER 3.6 4.5 - - - +
549A ALA 3.2 0.6 - - - -
550A ARG* 1.3 78.3 - - - +
552A THR* 1.3 57.2 + - - +
553A LYS* 3.5 3.5 + - - +
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Residues in contact with THR 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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501A ASP* 3.3 40.6 - - + -
502A GLN 2.9 19.1 - - - +
503A VAL 3.6 12.3 - - - -
504A THR* 2.8 40.5 + - - +
530A ARG* 3.8 11.0 - - + +
548A SER 3.1 7.4 + - - +
549A ALA* 3.0 5.7 + - - -
551A ALA* 1.3 76.3 - - - +
553A LYS* 1.3 67.4 + - - +
554A GLY 3.3 0.2 - - - -
555A ARG* 3.2 13.2 + - - +
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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