Contacts of the helix formed by residues 582 - 598 (chain A) in PDB entry 5J3V
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 582 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A HIS* 5.3 10.2 + - - +
539A LEU* 5.7 4.0 - - - +
542A TYR* 5.1 3.8 + - - -
572A LYS* 5.8 4.4 - - - +
576A LEU* 3.6 27.2 - - + +
580A ASP* 3.0 23.4 - - - +
581A LYS* 1.3 78.3 - - - +
583A LEU* 1.3 61.1 + - - +
584A PHE 3.3 1.3 - - - -
585A PRO* 3.3 16.9 - - - +
586A LEU* 4.0 7.8 + - - +
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Residues in contact with LEU 583 (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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573A TRP* 5.2 2.2 - - + +
576A LEU* 3.8 22.6 - - + +
577A LYS 3.4 22.2 - - - +
578A ASP* 4.0 10.5 - - - -
580A ASP 3.6 12.6 - - - +
581A LYS 3.1 0.8 - - - -
582A ASP* 1.3 78.2 - - - +
584A PHE* 1.3 66.6 + - + +
585A PRO 3.4 0.2 - - - -
586A LEU* 3.2 14.8 + - + -
587A LEU* 3.0 46.9 + - + +
611A ARG* 3.5 29.4 - - - +
615A LEU* 4.6 12.3 - - + -
640A PHE* 4.0 15.9 - - + -
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Residues in contact with PHE 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LYS* 3.5 26.2 - - + -
583A LEU* 1.3 81.2 - - + +
585A PRO* 1.3 69.4 - - + +
588A GLU* 3.2 28.1 + - - +
637A ASP* 3.7 13.7 - - - -
639A ASP* 3.6 24.9 - - + -
640A PHE* 3.6 64.8 - + - -
643A VAL* 4.0 27.0 - - + +
20C LEU* 4.1 12.8 - - + -
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Residues in contact with PRO 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 3.6 27.6 - - + +
542A TYR* 3.5 30.2 - - + +
581A LYS 3.9 3.6 - - - +
582A ASP* 3.3 22.9 - - - +
584A PHE* 1.3 94.3 - - + +
586A LEU* 1.3 60.3 + - - +
588A GLU* 3.6 2.1 + - - +
589A CYS* 3.2 22.5 + - - +
20C LEU* 3.7 18.6 - - + -
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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
----------------------------------------------------------
542A TYR* 3.4 34.7 - - + +
569A LEU* 4.0 28.0 - - + +
572A LYS* 3.9 11.7 - - + +
573A TRP* 3.8 34.8 - - + +
576A LEU* 4.4 9.9 - - + -
582A ASP 4.0 10.0 + - - +
583A LEU* 3.2 16.5 + - + +
585A PRO* 1.3 82.0 - - - +
587A LEU* 1.3 67.7 + - + +
589A CYS* 3.1 5.5 + - - +
590A LEU* 2.9 32.7 + - + +
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Residues in contact with LEU 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A TRP* 3.4 37.5 - - + -
583A LEU* 3.0 30.5 + - + +
586A LEU* 1.3 81.9 - - + +
588A GLU* 1.3 60.6 + - - +
590A LEU* 3.7 8.5 - - + +
591A SER* 2.8 29.3 + - - -
611A ARG* 6.3 1.1 - - + +
612A CYS* 5.1 2.0 - - - -
615A LEU* 4.1 25.8 - - + -
643A VAL* 3.4 29.2 - - + -
644A ALA* 4.7 5.6 - - - -
647A LEU* 3.8 24.2 - - + +
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Residues in contact with GLU 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PHE 3.2 19.2 + - - +
585A PRO 3.8 4.7 - - - +
586A LEU 3.3 0.2 - - - -
587A LEU* 1.3 78.3 - - - +
589A CYS* 1.3 61.0 + - - +
591A SER* 3.5 14.8 - - - -
592A SER* 3.6 12.0 + - - -
642A ILE* 5.8 0.3 - - - +
643A VAL* 4.1 19.6 - - + +
646A ASP* 3.4 23.6 - - - +
17C ARG* 3.3 31.0 + - - +
18C LYS* 4.3 17.7 + - - +
20C LEU* 3.9 22.7 - - + +
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Residues in contact with CYS 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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542A TYR* 3.6 42.0 - - + +
545A ILE* 3.7 28.5 - - - -
546A GLY* 3.9 7.8 - - - -
569A LEU* 4.6 11.4 - - + -
585A PRO 3.2 14.0 + - - +
586A LEU 3.1 10.0 + - - +
588A GLU* 1.3 75.0 - - - +
590A LEU* 1.3 65.0 + - - +
592A SER* 3.1 6.4 + - - -
593A VAL* 3.1 28.6 + - - +
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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
----------------------------------------------------------
566A MET* 4.2 18.4 - - + -
569A LEU* 3.7 37.0 - - + +
573A TRP* 3.7 35.0 - - + -
586A LEU* 2.9 25.8 + - + +
587A LEU* 3.4 13.9 + - + +
589A CYS* 1.3 73.6 - - - +
591A SER* 1.3 57.0 + - - +
593A VAL* 3.8 4.4 - - + +
594A ALA* 2.8 37.6 + - - +
601A PHE* 4.6 10.3 - - + -
608A VAL* 5.2 6.7 - - + -
647A LEU* 3.7 12.3 - - + -
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Residues in contact with SER 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU 2.8 19.0 + - - -
588A GLU* 3.5 9.9 - - - -
589A CYS 3.1 0.2 - - - -
590A LEU* 1.3 77.1 - - - +
592A SER* 1.3 57.0 + - - +
594A ALA* 4.8 0.7 - - - -
595A THR* 2.7 31.7 + - - -
646A ASP* 3.1 23.0 + - - -
647A LEU* 3.6 13.9 - - - +
650A GLY* 4.0 4.1 - - - -
17C ARG* 2.9 35.7 + - - -
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Residues in contact with SER 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLY* 3.3 23.8 + - - -
549A ALA* 3.4 11.4 - - - +
550A ASP* 3.2 28.8 + - - +
588A GLU 3.6 6.8 + - - -
589A CYS 3.1 8.8 + - - -
591A SER* 1.3 75.6 - - - +
593A VAL* 1.3 65.6 + - - +
595A THR* 3.6 4.8 + - - -
596A ALA* 3.2 17.3 + - - +
17C ARG* 2.8 23.9 + - - +
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Residues in contact with VAL 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ILE* 4.4 11.4 - - + +
549A ALA* 4.0 14.1 - - + -
556A LEU* 5.0 1.1 - - + -
565A LEU* 4.4 13.9 - - + -
566A MET* 4.0 17.3 - - - -
569A LEU* 4.4 10.1 - - + -
589A CYS* 3.1 31.7 + - - +
590A LEU* 3.3 8.5 + - + +
592A SER* 1.3 76.1 - - - +
594A ALA* 1.3 57.0 + - - +
596A ALA* 3.1 1.4 + - - +
597A LEU* 2.8 59.5 + - + +
601A PHE* 4.6 2.7 - - + -
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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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590A LEU 2.8 21.1 + - - +
591A SER 4.3 2.7 - - - +
593A VAL* 1.3 73.1 - - - +
595A THR* 1.3 61.7 + - - +
598A GLN* 3.2 23.0 + - - +
601A PHE* 3.9 39.2 - - + +
647A LEU* 4.7 5.6 - - + -
650A GLY 3.9 10.3 - - - +
651A LEU* 4.0 13.6 - - + +
654A GLY* 3.8 6.1 - - - -
655A LEU* 6.1 0.3 - - - +
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Residues in contact with THR 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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550A ASP* 5.7 2.2 - - - -
591A SER 2.7 22.3 + - - -
592A SER* 3.9 5.6 - - - -
593A VAL 3.2 0.6 - - - -
594A ALA* 1.3 77.6 - - - +
596A ALA* 1.3 62.4 + - - +
598A GLN* 3.3 20.3 + - - +
650A GLY* 3.4 21.7 + - - -
653A GLU* 3.7 37.1 + - + +
654A GLY* 4.2 4.1 - - - -
17C ARG* 4.8 5.0 + - - -
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Residues in contact with ALA 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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549A ALA* 3.6 26.7 - - + +
553A GLY* 3.3 24.5 - - - +
554A HIS* 3.5 23.4 - - - +
556A LEU* 4.5 6.7 - - + -
557A ASN* 4.4 1.4 - - - +
592A SER 3.2 16.6 + - - +
593A VAL* 3.1 4.4 + - - +
595A THR* 1.3 75.9 - - - +
597A LEU* 1.3 65.9 + - - +
598A GLN* 3.1 8.6 + - - +
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Residues in contact with LEU 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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556A LEU* 3.4 44.0 - - + +
557A ASN* 3.2 16.1 - - - -
561A TYR* 5.9 0.2 - - + -
562A ILE* 3.7 35.4 - - + -
565A LEU* 5.5 3.1 - - + -
566A MET* 4.0 12.6 - - + -
593A VAL* 2.8 40.1 + - + +
596A ALA* 1.3 74.1 - - - +
598A GLN* 1.3 61.2 + - - +
599A SER 3.1 1.2 + - - -
600A GLY 2.9 21.3 + - - +
601A PHE* 3.9 29.6 - - + +
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Residues in contact with GLN 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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554A HIS* 3.6 29.7 - - - +
557A ASN* 4.7 7.0 + - - +
594A ALA 3.2 14.5 + - - +
595A THR 3.3 17.9 + - - +
596A ALA* 3.1 5.7 - - - +
597A LEU* 1.3 75.8 - - - +
599A SER* 1.3 68.3 + - - +
601A PHE* 3.1 18.7 + - - +
653A GLU 5.4 1.1 - - - +
654A GLY* 3.3 26.3 - - - +
655A LEU* 3.4 10.4 - - - +
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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
------------------------------------------------------------
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