Contacts of the helix formed by residues 594 - 602 (chain A) in PDB entry 1RQG
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 ALA 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A ALA* 2.9 36.5 - - + +
587A LYS* 3.6 20.2 - - + -
590A PHE* 3.4 15.9 + - + -
591A GLY 3.6 9.4 + - - +
593A GLU* 1.3 79.0 - - - +
595A GLU* 1.3 61.2 + - - +
597A VAL* 3.2 21.7 + - - +
598A LEU* 3.3 14.5 + - + +
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Residues in contact with GLU 595 (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 LYS* 3.1 31.8 + - - +
591A GLY 5.2 0.2 + - - -
592A ASP 6.3 0.4 - - - -
593A GLU* 3.1 1.5 - - - +
594A ALA* 1.3 81.0 - - - +
596A VAL* 1.3 61.9 + - + +
597A VAL 3.1 5.1 + - - -
598A LEU* 4.5 10.1 - - - +
599A ARG* 2.9 74.6 + - - +
606A LYS* 4.9 5.7 - - - +
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Residues in contact with VAL 596 (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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592A ASP 5.5 1.1 - - - +
593A GLU* 2.9 19.0 + - + +
595A GLU* 1.3 78.7 - - + +
597A VAL* 1.3 64.8 + - - +
599A ARG* 5.2 9.4 - - - +
600A ARG* 3.5 25.1 + - + +
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Residues in contact with VAL 597 (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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558A LEU* 3.9 43.3 - - + +
590A PHE* 4.4 15.5 - - + -
593A GLU* 3.2 22.9 - - + +
594A ALA* 3.3 11.9 - - - +
595A GLU 3.1 1.4 + - - -
596A VAL* 1.3 79.1 - - - +
598A LEU* 1.3 63.2 + - + +
599A ARG 3.0 1.3 - - - +
600A ARG* 2.5 49.4 + - - +
601A VAL* 2.8 12.2 + - + +
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Residues in contact with LEU 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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558A LEU* 4.5 6.5 - - + -
582A VAL* 4.0 21.8 - - + -
583A ILE* 3.6 44.9 - - + +
586A ALA* 3.5 25.4 - - + -
587A LYS* 5.0 3.4 - - + -
594A ALA 3.5 17.9 - - - +
595A GLU* 4.5 14.6 - - - +
597A VAL* 1.3 82.0 - - - +
599A ARG* 1.3 57.2 + - + +
601A VAL* 4.6 2.0 - - - +
602A TYR* 2.8 53.1 + - + +
605A ILE* 5.5 3.6 - - + -
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Residues in contact with ARG 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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595A GLU* 2.9 59.1 + - - +
596A VAL* 5.3 7.7 - - - +
597A VAL 3.0 1.2 - - - +
598A LEU* 1.3 78.2 - - + +
600A ARG* 1.3 61.0 + - - +
601A VAL 3.3 0.2 - - - -
602A TYR 3.1 11.8 - - - +
603A LYS* 2.9 26.6 - - - +
605A ILE* 5.0 11.7 - - + +
606A LYS* 3.9 28.8 - - + +
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Residues in contact with ARG 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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558A LEU 5.6 0.2 + - - -
562A ALA* 4.4 9.6 - - - +
563A LYS* 3.3 66.4 - - - +
566A PRO* 3.2 27.7 - - + +
596A VAL* 3.5 22.9 + - + +
597A VAL* 2.5 41.5 + - - +
599A ARG* 1.3 75.8 - - - +
601A VAL* 1.3 57.3 + - - +
602A TYR 4.9 0.2 - - - -
603A LYS* 5.0 1.3 + - - -
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Residues in contact with VAL 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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558A LEU* 4.1 17.0 - - + -
562A ALA* 3.8 28.7 - - + -
566A PRO* 4.1 9.8 - - + +
567A GLU* 4.9 2.8 - - - +
569A ALA* 4.1 7.4 - - + -
570A ARG* 3.2 52.4 - - + +
573A LEU* 3.9 14.6 - - + -
597A VAL 2.8 11.6 + - - +
598A LEU* 4.0 2.5 - - - +
600A ARG* 1.3 83.4 - - - +
602A TYR* 1.3 70.8 + - + +
603A LYS* 3.0 7.8 + - - +
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Residues in contact with TYR 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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570A ARG* 3.8 15.9 - - + +
573A LEU* 3.5 18.6 - - + +
574A ASP* 4.0 12.6 + - + -
579A ARG* 3.2 68.4 - - + +
582A VAL* 3.3 34.2 - - + +
583A ILE* 5.5 2.2 - - + -
598A LEU* 2.8 53.7 + - + +
599A ARG* 3.1 10.8 - - - +
601A VAL* 1.3 77.2 - - + +
603A LYS* 1.3 68.0 + - - +
604A ASP* 3.0 9.7 + - - +
605A ILE* 4.1 12.0 + - + -
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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