Contacts of the helix formed by residues 608 - 617 (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 608 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A GLU* 3.6 14.4 - - - +
599A ALA 4.6 3.0 - - - +
602A LEU* 3.4 21.5 + - + -
603A LYS* 3.3 37.2 - - - +
606A GLY 3.8 0.2 - - - -
607A ILE* 1.3 76.5 - - - +
609A ARG* 1.3 72.2 + - + +
610A ASP* 3.2 17.4 + - - +
611A ALA* 3.1 22.9 + - - +
612A ILE* 3.0 28.1 + - - +
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Residues in contact with ARG 609 (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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513A HIS 4.8 2.4 + - - -
514A GLU* 2.8 60.4 + - - +
517A ALA* 3.4 23.3 - - - +
518A ALA* 3.2 21.2 - - - +
521A LEU* 4.3 10.5 - - + -
608A ASP* 1.3 75.0 - - + +
610A ASP* 1.3 69.4 + - - +
612A ILE* 3.2 2.6 + - - -
613A ALA* 2.8 32.2 + - - +
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Residues in contact with ASP 610 (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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521A LEU* 3.2 24.4 - - - +
603A LYS* 4.5 14.6 - - + -
608A ASP* 3.2 14.7 + - - +
609A ARG* 1.3 82.3 - - - +
611A ALA* 1.3 56.9 + - - +
613A ALA* 3.7 4.2 - - - +
614A GLN* 2.6 40.2 + - - +
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Residues in contact with ALA 611 (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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587A LEU* 3.8 5.5 - - + +
606A GLY* 3.3 41.1 - - - +
607A ILE* 3.8 1.1 - - - +
608A ASP* 3.1 19.7 + - - +
610A ASP* 1.3 74.8 - - - +
612A ILE* 1.3 57.7 + - - +
614A GLN* 4.0 4.7 - - - +
615A ALA* 2.9 31.2 + - - +
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Residues in contact with ILE 612 (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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505A VAL* 4.0 27.4 - - + -
511A THR 4.5 0.2 - - - +
514A GLU* 3.7 30.5 - - + +
515A ALA* 3.9 5.8 - - - +
518A ALA* 3.8 14.1 - - + -
529A ILE* 5.1 1.3 - - + -
557A LEU* 4.0 7.7 - - + +
559A VAL* 4.0 28.0 - - + -
587A LEU* 4.1 9.2 - - + -
607A ILE 3.7 7.4 - - - +
608A ASP 3.0 31.7 + - - +
609A ARG 3.5 4.9 - - - +
611A ALA* 1.3 75.9 - - - +
613A ALA* 1.3 58.2 + - - +
615A ALA* 3.4 2.6 + - - +
616A VAL* 3.0 31.8 + - + +
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Residues in contact with ALA 613 (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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518A ALA* 4.3 6.1 - - + +
521A LEU* 4.6 11.4 - - + -
522A LEU* 4.2 23.0 - - + +
609A ARG 2.8 17.9 + - - +
610A ASP* 3.2 7.6 + - - +
612A ILE* 1.3 73.1 - - - +
614A GLN* 1.3 65.8 + - - +
616A VAL* 3.1 13.3 + - - +
617A ARG* 3.2 39.5 + - - +
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Residues in contact with GLN 614 (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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610A ASP 2.6 23.3 + - - +
611A ALA* 4.0 4.9 - - - +
613A ALA* 1.3 73.1 - - - +
615A ALA* 1.3 57.9 + - - +
617A ARG* 3.5 32.8 + - - +
618A GLY* 3.8 4.5 + - - -
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Residues in contact with ALA 615 (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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557A LEU* 4.2 13.8 - - + +
585A THR* 5.1 7.4 - - + +
587A LEU* 4.0 22.9 - - + -
611A ALA 2.9 20.7 + - - +
612A ILE 3.7 3.6 - - - +
614A GLN* 1.3 73.7 - - - +
616A VAL* 1.3 65.7 + - - +
618A GLY* 3.1 19.1 + - - +
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Residues in contact with VAL 616 (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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502A GLN* 5.0 2.9 - - + -
503A VAL* 3.5 36.0 - - + +
505A VAL* 4.2 5.6 - - + -
522A LEU* 3.8 15.3 - - + -
527A ILE* 4.0 14.8 - - + -
529A ILE* 3.8 21.3 - - + -
557A LEU* 3.9 16.4 - - + -
612A ILE* 3.0 23.0 + - + +
613A ALA 3.1 5.6 + - - +
615A ALA* 1.3 70.3 - - - +
617A ARG* 1.3 62.1 + - - +
618A GLY 2.8 21.1 + - - +
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Residues in contact with ARG 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 4.8 8.9 + - - +
522A LEU* 4.0 12.5 - - + +
525A GLU* 2.8 39.4 + - - +
527A ILE* 4.6 9.6 - - + -
610A ASP 5.0 0.2 + - - -
613A ALA* 3.4 26.8 - - - +
614A GLN* 3.5 38.4 + - - +
615A ALA 3.4 0.2 - - - -
616A VAL* 1.3 77.1 - - - +
618A GLY* 1.3 56.6 + - - +
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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