Contacts of the helix formed by residues 593 - 601 (chain A) in PDB entry 2R5N
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 593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A ARG* 4.4 6.6 + - - +
591A LYS 3.9 0.8 + - - -
592A GLN* 1.3 79.0 - - - +
594A ALA* 1.3 65.9 + - - +
595A ALA* 4.0 12.5 - - - +
596A TYR* 3.0 24.8 + - - +
597A ARG* 3.1 20.4 + - - +
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Residues in contact with ALA 594 (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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593A ASP* 1.3 74.8 - - - +
595A ALA* 1.3 57.2 + - - +
597A ARG* 3.3 26.6 + - - +
598A GLU* 2.9 32.6 + - - +
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Residues in contact with ALA 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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593A ASP* 3.3 13.5 + - - +
594A ALA* 1.3 78.6 - - - +
596A TYR* 1.3 60.7 + - - +
598A GLU* 3.7 6.9 - - - +
599A SER* 3.0 23.8 + - - -
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Residues in contact with TYR 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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535A ASN* 4.0 14.1 + - - +
538A ARG* 3.3 61.7 - - + +
540A GLY 2.7 30.3 + - - -
541A TYR* 3.3 18.9 - - - +
589A PHE* 4.1 7.6 - + - -
592A GLN* 3.6 22.4 - - + -
593A ASP* 3.0 16.9 + - - +
595A ALA* 1.3 77.2 - - - +
597A ARG* 1.3 62.4 + - - +
599A SER* 2.6 29.7 + - - -
600A VAL* 3.2 23.7 + - + +
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Residues in contact with ARG 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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589A PHE* 3.4 55.5 - - + +
590A ASP* 3.6 16.9 + - - +
592A GLN* 2.8 21.3 + - + +
593A ASP* 3.1 8.0 + - - +
594A ALA* 3.5 34.1 - - - +
596A TYR* 1.3 74.4 - - - +
598A GLU* 1.3 58.4 + - - +
600A VAL* 3.2 1.9 + - - +
601A LEU* 2.8 34.5 + - - +
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Residues in contact with GLU 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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594A ALA 2.9 19.0 + - - +
595A ALA* 3.7 7.0 - - - +
597A ARG* 1.3 76.9 - - - +
599A SER* 1.3 61.8 + - - +
601A LEU 4.0 3.4 - - - +
602A PRO* 3.1 42.1 - - - +
603A LYS* 2.9 48.4 + - - +
604A ALA* 5.0 1.0 + - - +
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Residues in contact with SER 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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542A VAL* 4.3 3.1 - - - +
579A ARG* 2.8 31.2 + - - -
595A ALA 3.0 13.8 + - - -
596A TYR* 2.6 35.3 + - - -
598A GLU* 1.3 78.2 - - - +
600A VAL* 1.3 53.6 + - - +
602A PRO* 4.2 1.0 - - - +
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Residues in contact with VAL 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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540A GLY 4.0 0.9 - - - +
541A TYR* 4.2 11.7 - - - +
542A VAL* 4.1 7.2 - - + +
553A ILE* 4.3 0.3 - - - +
579A ARG* 3.0 20.3 + - - +
581A VAL* 3.6 46.0 - - + +
589A PHE* 3.8 17.5 - - + -
596A TYR* 3.2 48.8 + - + +
597A ARG 3.8 4.7 - - - +
599A SER* 1.3 81.4 - - - +
601A LEU* 1.3 60.3 + - + +
602A PRO* 3.3 3.9 - - - +
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Residues in contact with LEU 601 (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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553A ILE* 4.1 11.9 - - + -
555A ILE* 3.7 33.7 - - + -
581A VAL* 4.1 12.3 - - + -
583A MET* 4.2 5.8 - - + -
589A PHE* 4.0 15.9 - - + -
597A ARG 2.8 16.9 + - - +
598A GLU* 3.5 6.3 - - - +
600A VAL* 1.3 87.7 - - + +
602A PRO* 1.3 69.5 - - - +
603A LYS* 3.4 2.3 + - - -
608A ARG* 3.2 29.8 + - - +
622A TYR* 3.8 28.5 - - + -
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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