Contacts of the helix formed by residues 583 - 592 (chain A) in PDB entry 5W5G
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 ASN 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A TYR* 3.9 3.4 - - - -
581A PRO 4.1 0.2 + - - -
582A GLN* 1.3 75.4 - - - +
584A SER* 1.3 54.6 + - - +
585A LYS* 3.1 14.0 + - - +
586A ASP* 2.6 41.8 + - - +
587A PHE* 2.7 31.9 + - - +
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Residues in contact with SER 584 (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 TRP* 4.5 13.0 - - - -
535A TYR* 3.6 33.6 - - - -
583A ASN* 1.3 73.8 + - - +
585A LYS* 1.3 72.5 + - - +
587A PHE* 3.2 7.9 + - - +
588A VAL* 2.9 30.5 + - - +
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Residues in contact with LYS 585 (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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583A ASN* 3.1 10.1 + - - +
584A SER* 1.3 84.7 + - - +
586A ASP* 1.3 64.6 + - - +
588A VAL* 3.5 5.6 + - - +
589A GLN* 3.4 19.1 + - - +
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Residues in contact with ASP 586 (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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582A GLN* 3.6 26.4 - - + +
583A ASN* 2.6 41.1 + - - +
585A LYS* 1.3 74.7 - - - +
587A PHE* 1.3 65.0 + - - +
589A GLN* 3.5 19.7 + - - +
590A MET* 3.2 17.0 + - - +
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Residues in contact with PHE 587 (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 TRP* 5.1 2.9 - + - -
494A TRP* 4.4 8.5 - + - -
535A TYR* 3.3 38.4 - + + +
538A TYR* 4.0 14.6 - + - -
539A ILE* 4.2 9.9 - - + -
567A SER* 3.7 33.7 - - - -
570A GLU* 3.8 37.0 - - + -
571A ALA* 4.4 1.6 - - + -
582A GLN* 4.1 12.9 - - + +
583A ASN 2.7 21.1 + - - +
584A SER* 3.3 5.6 - - - +
586A ASP* 1.3 74.8 - - - +
588A VAL* 1.3 66.2 + - + +
590A MET* 3.2 5.2 + - - +
591A VAL* 2.9 43.5 + - + +
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Residues in contact with VAL 588 (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 TRP* 4.5 9.6 - - + -
494A TRP* 4.0 28.0 - - + +
584A SER* 2.9 21.0 + - - +
585A LYS* 3.9 5.8 - - - +
587A PHE* 1.3 77.4 - - + +
589A GLN* 1.3 65.7 + - - +
591A VAL* 3.2 9.7 + - + +
592A ARG* 3.0 47.6 + - + +
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Residues in contact with GLN 589 (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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585A LYS 3.4 10.9 + - - +
586A ASP* 3.6 23.4 - - - +
587A PHE 3.3 0.4 - - - -
588A VAL* 1.3 78.9 - - - +
590A MET* 1.3 62.9 + - - +
592A ARG* 3.2 41.3 - - + +
593A LYS* 3.7 20.3 - - + +
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Residues in contact with MET 590 (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 GLU* 4.1 17.9 - - + -
582A GLN* 3.3 34.1 - - - +
586A ASP 3.2 10.8 + - - +
587A PHE* 3.5 7.6 - - + +
589A GLN* 1.3 80.4 - - - +
591A VAL* 1.3 64.3 + - + +
593A LYS* 3.1 37.9 + - + +
594A ILE* 4.0 14.1 + - + +
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Residues in contact with VAL 591 (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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379A ARG* 5.7 0.2 + - - -
494A TRP* 4.3 17.3 - - + -
566A ALA* 3.7 24.3 - - + +
567A SER* 3.5 28.9 - - - +
570A GLU* 5.6 3.1 - - + -
587A PHE* 2.9 36.7 + - + +
588A VAL* 3.5 12.8 - - + +
590A MET* 1.3 77.8 - - + +
592A ARG* 1.3 64.7 + - - +
593A LYS 3.1 1.4 + - - -
594A ILE* 3.2 27.4 + - + +
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Residues in contact with ARG 592 (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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588A VAL* 3.0 32.8 + - + +
589A GLN* 3.2 49.9 - - + +
590A MET 3.3 0.2 + - - -
591A VAL* 1.3 78.1 - - + +
593A LYS* 1.3 62.3 + - + +
594A ILE 3.4 2.1 - - - +
627B GLY 4.0 8.3 - - - +
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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