Contacts of the helix formed by residues 583 - 593 (chain A) in PDB entry 5JQY
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 TYR 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A PRO 4.6 0.2 - - - -
581A THR* 3.1 30.6 + - - +
582A GLY* 1.3 78.7 - - - +
584A THR* 1.3 62.9 + - - +
585A GLU 3.3 3.4 - - - -
586A LEU* 3.4 10.6 + - + -
587A VAL* 3.2 25.0 + - - +
656A GLU* 3.4 40.4 - - + -
689A MET* 3.8 12.3 - - + -
742A VAL* 3.4 27.4 - - + -
743A TRP* 2.9 30.0 + - - +
745A PRO* 3.7 11.9 - - + +
752A ARG* 3.1 32.8 + - - -
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Residues in contact with THR 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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578A PRO* 3.9 22.4 - - + +
579A LYS* 4.0 18.6 - - + +
582A GLY* 3.1 11.7 + - - -
583A TYR* 1.3 74.9 - - - +
585A GLU* 1.3 70.4 + - - +
587A VAL* 3.9 6.8 - - - +
588A LYS* 2.9 41.2 + - - +
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Residues in contact with GLU 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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582A GLY 5.0 0.2 + - - -
583A TYR 3.3 0.6 - - - -
584A THR* 1.3 80.1 + - - +
586A LEU* 1.3 65.4 + - - +
588A LYS* 3.4 34.6 + - - +
589A SER* 3.0 23.7 + - - -
592A ARG* 5.5 3.3 + - - -
653A LYS* 5.4 8.2 + - - +
654A PHE* 3.8 15.6 - - + -
656A GLU* 5.7 2.0 - - - +
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Residues in contact with LEU 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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583A TYR* 3.4 10.2 + - + +
585A GLU* 1.3 80.4 - - - +
587A VAL* 1.3 62.6 + - - +
589A SER* 3.2 2.1 + - - -
590A LEU* 3.0 52.1 + - + +
651A LEU* 4.6 9.9 - - + -
654A PHE* 3.6 41.3 - - + -
656A GLU* 4.2 18.1 + - + +
657A THR* 4.4 2.9 - - + -
689A MET* 3.8 17.0 - - + -
740A VAL* 4.1 9.0 - - + -
742A VAL* 3.6 31.0 - - + -
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Residues in contact with VAL 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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578A PRO* 4.1 32.3 - - + -
581A THR* 5.3 0.2 - - - +
583A TYR 3.2 16.7 + - - +
584A THR* 3.9 4.9 - - - +
585A GLU 3.3 0.2 - - - -
586A LEU* 1.3 75.3 - - - +
588A LYS* 1.3 64.9 + - + +
590A LEU* 3.2 8.4 + - - +
591A GLU* 3.0 47.4 + - - +
689A MET* 3.8 26.0 - - + -
716A VAL* 4.1 12.1 - - + -
718A ILE* 4.3 7.6 - - + -
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Residues in contact with LYS 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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584A THR* 2.9 27.5 + - - +
585A GLU* 3.4 33.2 + - - +
587A VAL* 1.3 78.0 - - + +
589A SER* 1.3 56.2 + - - +
591A GLU* 4.0 4.2 - - - +
592A ARG* 2.8 75.7 + - - +
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Residues in contact with SER 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 GLU 3.0 18.1 + - - -
586A LEU* 3.6 4.9 - - - -
587A VAL 3.2 0.2 - - - -
588A LYS* 1.3 74.3 - - - +
590A LEU* 1.3 67.1 - - - +
592A ARG* 4.6 3.8 - - - +
593A ASN* 2.9 36.9 + - - +
650A LEU* 3.3 31.9 - - - +
654A PHE* 3.7 21.1 - - - -
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Residues in contact with LEU 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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586A LEU* 3.0 44.7 + - + +
587A VAL* 3.7 3.8 - - - +
589A SER* 1.3 76.7 - - - +
591A GLU* 1.3 58.1 + - - +
593A ASN 3.7 0.5 - - - -
594A TRP* 3.1 31.4 + - - +
597A ILE* 3.9 22.6 - - + +
650A LEU* 5.1 4.5 - - + -
651A LEU* 4.5 7.6 - - + -
689A MET* 4.1 19.3 - - + -
691A LEU* 3.6 14.6 - - + +
716A VAL* 4.1 19.7 - - + -
738A PHE* 4.3 8.1 - - + -
740A VAL* 4.2 26.0 - - + -
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Residues in contact with GLU 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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578A PRO* 5.8 0.5 - - - +
587A VAL* 3.0 31.2 + - - +
588A LYS* 4.0 4.6 - - - +
590A LEU* 1.3 74.7 - - - +
592A ARG* 1.3 65.6 + - + +
594A TRP* 3.1 22.5 - - - -
691A LEU* 4.5 1.3 - - - -
714A GLY 3.4 22.0 - - - +
715A LYS* 3.2 30.1 + - - +
716A VAL* 2.9 41.0 + - + +
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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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585A GLU* 5.5 2.6 + - - -
588A LYS* 2.8 65.1 + - - +
589A SER* 4.9 2.2 - - - +
591A GLU* 1.3 79.4 - - + +
593A ASN* 1.3 69.1 + - - +
594A TRP* 3.5 1.1 + - - -
595A LYS* 4.7 11.4 + - - -
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Residues in contact with ASN 593 (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 SER* 2.9 41.8 + - - +
590A LEU 3.7 2.0 - - - -
592A ARG* 1.3 84.7 - - - +
594A TRP* 1.3 63.9 + - - +
595A LYS 3.2 4.4 + - - -
596A LEU* 3.3 40.7 + - + +
597A ILE* 3.5 6.0 + - - +
650A LEU* 3.7 22.2 - - + +
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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