Contacts of the helix formed by residues 597 - 605 (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 LYS 597 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A GLY* 4.2 0.2 - - - -
423A GLU* 3.6 15.9 - - - +
596A GLY* 1.3 73.8 - - - +
598A PRO* 1.4 75.2 - - + +
599A ALA* 4.3 6.3 - - + +
600A GLU* 2.9 39.6 + - + +
601A LEU* 2.8 20.8 + - - +
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Residues in contact with PRO 598 (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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419A VAL 4.5 0.9 - - - +
420A SER* 3.2 33.9 - - - +
421A ILE 4.2 3.6 - - - +
422A GLY* 4.0 12.8 - - - +
423A GLU* 3.9 15.5 - - - +
474A ARG* 4.9 7.4 - - - +
475A PRO* 5.1 7.0 - - + -
596A GLY 3.7 0.4 - - - -
597A LYS* 1.4 86.7 - - + +
599A ALA* 1.3 57.5 + - - +
601A LEU* 3.3 1.7 + - - +
602A LEU* 3.0 36.4 + - + +
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Residues in contact with ALA 599 (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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597A LYS* 3.2 4.2 - - + +
598A PRO* 1.3 80.1 - - - +
600A GLU* 1.3 64.8 + - + +
602A LEU* 3.4 12.5 + - + +
603A LYS* 3.2 22.9 + - - +
608A ASP* 4.6 2.9 - - - +
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Residues in contact with GLU 600 (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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596A GLY* 3.9 7.0 - - - -
597A LYS* 2.9 50.8 + - + +
599A ALA* 1.3 77.1 - - + +
601A LEU* 1.4 61.5 + - + +
603A LYS* 3.4 10.5 + - - +
604A MET* 2.9 28.6 + - - +
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Residues in contact with LEU 601 (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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419A VAL* 3.4 35.8 - - + +
422A GLY* 3.5 20.2 - - - +
429A MET* 3.6 6.1 - - + -
593A PRO* 5.6 0.2 - - + -
594A ARG* 3.3 44.6 - - - +
595A SER 4.1 0.2 - - - -
596A GLY* 3.7 21.8 - - - +
597A LYS 2.8 15.3 + - - +
598A PRO 3.8 2.7 - - - +
600A GLU* 1.4 75.7 - - + +
602A LEU* 1.3 68.5 + - - +
604A MET* 4.3 4.7 - - + +
605A PHE* 3.0 40.2 + - + +
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Residues in contact with LEU 602 (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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419A VAL* 3.9 13.9 - - + -
420A SER* 4.2 5.8 - - - -
475A PRO* 6.1 0.2 - - + -
510A VAL* 3.6 35.2 - - + -
511A THR* 4.9 0.4 - - + -
514A GLU* 4.2 17.7 - - + +
561A ASP* 3.9 10.8 - - - +
598A PRO* 3.0 28.4 + - + +
599A ALA* 3.8 8.7 - - + +
600A GLU 3.4 0.2 - - - -
601A LEU* 1.3 77.8 - - - +
603A LYS* 1.3 55.8 + - - +
606A GLY 3.2 5.7 + - - -
607A ILE* 3.0 60.7 + - + +
608A ASP* 3.4 17.1 + - + -
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Residues in contact with LYS 603 (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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599A ALA 3.2 11.5 + - - +
600A GLU* 3.6 10.8 - - - +
601A LEU 3.1 0.6 - - - -
602A LEU* 1.3 72.4 - - - +
604A MET* 1.3 66.2 + - - +
605A PHE 3.0 2.4 + - - -
606A GLY* 3.1 11.8 + - - -
608A ASP* 3.3 31.4 - - - +
610A ASP* 4.5 14.6 - - + -
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Residues in contact with MET 604 (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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591A ARG* 4.3 19.9 + - - +
594A ARG* 3.7 32.8 - - - +
600A GLU 2.9 20.5 + - - +
601A LEU* 3.3 7.6 + - + +
603A LYS* 1.3 74.6 - - - +
605A PHE* 1.3 92.8 + - + +
606A GLY* 3.6 0.9 + - - -
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Residues in contact with PHE 605 (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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419A VAL* 4.4 5.6 - - + -
588A ALA 3.5 18.2 - - - +
589A VAL* 3.9 32.2 - - + -
590A ASN* 4.4 5.5 + - - -
591A ARG* 3.7 47.6 - - + +
592A VAL 4.3 1.3 - - - -
593A PRO* 3.5 37.7 - - + -
594A ARG* 4.1 9.2 - - + -
601A LEU* 3.0 37.1 + - + +
602A LEU 3.8 0.9 - - - +
604A MET* 1.3 106.7 - - + +
606A GLY* 1.3 63.6 + - - +
607A ILE* 3.4 8.8 + - + +
622A EDO 4.4 7.2 + - - -
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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