Contacts of the helix formed by residues 582 - 598 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B HIS* 5.3 7.5 + - - -
539B LEU* 5.6 4.7 - - - +
542B TYR* 5.2 3.1 - - - -
572B LYS* 6.3 0.9 - - - +
576B LEU* 3.4 28.3 - - + +
580B ASP* 3.1 22.0 + - - +
581B LYS* 1.3 80.5 - - - +
583B LEU* 1.3 58.3 + - - +
584B PHE 3.3 1.3 - - - -
585B PRO* 3.2 20.5 - - + +
586B LEU* 3.9 7.3 + - - +
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Residues in contact with LEU 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B TRP 5.1 0.2 - - - +
576B LEU* 3.7 29.2 - - + -
577B LYS 3.3 22.2 - - - +
578B ASP* 4.0 9.4 - - - +
580B ASP 3.4 14.1 + - - +
581B LYS 3.1 0.4 - - - -
582B ASP* 1.3 79.2 - - - +
584B PHE* 1.3 61.2 + - + +
586B LEU* 4.4 5.6 - - + -
587B LEU* 2.8 58.7 + - + +
611B ARG* 3.6 25.1 - - - +
615B LEU* 4.5 13.5 - - + -
640B PHE* 4.1 16.2 - - + -
643B VAL* 4.8 0.7 - - + -
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Residues in contact with PHE 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LYS* 3.3 32.5 - - + -
583B LEU* 1.3 78.7 - - + +
585B PRO* 1.3 69.7 - - + +
588B GLU* 3.2 26.3 + - - +
637B ASP* 4.1 7.4 - - - -
639B ASP* 3.5 26.2 - - + -
640B PHE* 3.5 63.7 - + - -
643B VAL* 3.7 29.9 - - + +
20D LEU* 3.6 14.7 - - + +
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Residues in contact with PRO 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B LEU* 3.6 38.4 - - + +
542B TYR* 3.5 31.2 - - + +
581B LYS 4.1 2.0 - - - +
582B ASP* 3.2 25.4 - - - +
584B PHE* 1.3 96.5 - - + +
586B LEU* 1.3 58.3 + - - +
588B GLU* 4.1 2.4 - - - +
589B CYS* 3.2 23.9 + - - +
20D LEU* 3.7 14.8 - - + -
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B TYR* 3.6 34.9 - - + +
569B LEU* 4.0 26.5 - - + +
572B LYS* 3.8 11.0 - - + +
573B TRP* 3.6 37.7 - - + +
576B LEU* 4.2 9.4 - - + -
582B ASP 3.9 10.1 + - - +
583B LEU* 3.2 8.4 + - + +
585B PRO* 1.3 81.8 - - - +
587B LEU* 1.3 73.2 + - + +
589B CYS* 3.2 5.0 + - - +
590B LEU* 2.8 33.0 + - + +
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B TRP* 3.7 35.7 - - + -
583B LEU* 2.8 50.4 + - + +
586B LEU* 1.3 74.6 - - + +
588B GLU* 1.3 60.8 + - - +
589B CYS 3.1 1.3 - - - -
590B LEU* 3.8 7.1 - - - +
591B SER* 3.1 28.1 + - - -
611B ARG* 6.1 0.4 - - - -
612B CYS* 4.6 5.4 - - - -
615B LEU* 4.1 25.8 - - + -
643B VAL* 3.4 24.7 - - + +
644B ALA* 4.7 4.5 - - - -
647B LEU* 3.7 22.0 - - + +
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Residues in contact with GLU 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B TYR* 5.5 2.4 - - - +
543B ASP* 5.9 2.8 - - - -
546B GLY* 6.0 0.9 - - - -
584B PHE 3.2 21.2 + - - +
585B PRO 4.1 3.0 - - - +
587B LEU* 1.3 77.4 - - - +
589B CYS* 1.3 62.7 + - - +
591B SER* 2.7 20.2 + - - +
592B SER* 3.8 5.0 + - - -
643B VAL* 4.2 9.5 - - + +
646B ASP* 6.1 3.1 - - + +
17D ARG* 2.9 33.6 + - + +
18D LYS 4.8 10.1 - - - +
19D GLN* 5.8 0.2 - - - -
20D LEU* 3.9 28.4 + - + +
23D LYS* 4.5 18.9 - - - +
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Residues in contact with CYS 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B TYR* 3.6 42.0 - - + +
545B ILE* 3.9 24.0 - - - -
546B GLY* 4.0 8.3 - - - -
569B LEU* 4.6 10.3 - - - -
585B PRO 3.2 20.4 + - - +
586B LEU 3.2 5.6 + - - +
587B LEU 3.1 0.4 - - - -
588B GLU* 1.3 80.7 + - - +
590B LEU* 1.3 64.1 + - - +
591B SER 3.2 0.4 - - - -
592B SER* 3.3 6.2 + - - -
593B VAL* 3.2 22.7 + - - +
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Residues in contact with LEU 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B MET* 4.5 6.5 - - + -
569B LEU* 3.9 32.8 - - + +
570B ILE* 5.5 4.0 - - + -
573B TRP* 3.5 37.7 - - + -
586B LEU* 2.8 30.7 + - + +
587B LEU* 3.4 8.0 + - - +
589B CYS* 1.3 74.9 - - - +
591B SER* 1.3 61.0 + - - +
593B VAL* 3.7 6.0 - - + +
594B ALA* 2.8 33.1 + - - +
601B PHE* 4.2 21.5 - - + -
608B VAL* 4.8 8.7 - - + -
647B LEU* 3.8 12.1 - - + +
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Residues in contact with SER 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LEU 3.1 12.7 + - - -
588B GLU* 2.7 27.4 + - - -
590B LEU* 1.3 77.0 - - - +
592B SER* 1.3 58.1 + - - +
594B ALA* 4.0 1.5 - - - +
595B THR* 2.9 29.3 + - - -
646B ASP* 3.8 24.9 - - - +
647B LEU* 3.6 15.2 - - - +
650B GLY* 3.9 6.8 - - - -
17D ARG* 3.1 24.2 + - - -
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Residues in contact with SER 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B GLY* 3.4 24.5 + - - -
549B ALA* 3.3 11.3 - - - +
550B ASP* 3.1 27.1 + - - +
588B GLU* 3.8 3.5 + - - -
589B CYS 3.3 9.1 + - - -
590B LEU 3.2 0.4 - - - -
591B SER* 1.3 77.6 + - - +
593B VAL* 1.3 62.5 + - - +
595B THR* 3.5 5.1 + - - -
596B ALA* 3.2 16.5 + - - +
17D ARG* 2.6 30.9 + - - +
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Residues in contact with VAL 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B ILE* 4.2 25.4 - - + +
549B ALA* 3.9 13.7 - - + -
556B LEU* 5.1 1.6 - - + -
565B LEU* 4.3 14.8 - - + -
566B MET* 4.2 14.4 - - - -
569B LEU* 4.3 14.4 - - + -
589B CYS* 3.2 15.4 + - - +
590B LEU* 3.7 11.9 - - + +
592B SER* 1.3 75.3 - - - +
594B ALA* 1.3 56.0 + - - +
596B ALA* 3.1 2.9 + - - +
597B LEU* 2.8 58.2 + - + +
601B PHE* 5.0 1.1 - - + -
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Residues in contact with ALA 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B LEU 2.8 21.1 + - - +
591B SER* 4.0 5.4 - - - +
593B VAL* 1.3 74.2 - - - +
595B THR* 1.3 61.6 + - - +
597B LEU* 4.2 0.9 - - - +
598B GLN* 3.4 20.1 + - - +
601B PHE* 4.1 25.1 - - + +
647B LEU* 4.7 1.6 - - + -
650B GLY 4.0 8.1 - - - +
651B LEU* 3.7 31.3 - - + -
654B GLY* 3.8 8.3 - - - -
655B LEU* 4.9 1.0 + - - +
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Residues in contact with THR 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B ASP* 5.6 2.9 - - - +
591B SER 2.9 21.2 + - - -
592B SER* 3.8 6.1 - - - -
593B VAL 3.2 0.6 - - - -
594B ALA* 1.3 77.8 - - - +
596B ALA* 1.3 58.0 + - - +
598B GLN* 3.2 27.5 + - - +
650B GLY* 3.2 22.6 + - - -
653B GLU* 3.6 38.5 + - + +
654B GLY* 3.9 5.5 - - - +
17D ARG* 5.6 0.9 + - - -
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Residues in contact with ALA 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B ALA* 3.5 31.9 - - + +
553B GLY* 3.2 33.8 - - - +
554B HIS* 3.4 14.7 - - - -
556B LEU* 4.4 9.2 - - + -
557B ASN* 4.1 3.6 + - - +
592B SER 3.2 12.8 + - - +
593B VAL 3.1 4.3 + - - +
595B THR* 1.3 74.3 - - - +
597B LEU* 1.3 63.0 + - - +
598B GLN* 3.1 8.0 + - - +
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Residues in contact with LEU 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B LEU* 3.5 42.0 - - + +
557B ASN* 3.1 16.4 - - - -
561B TYR* 6.0 0.2 - - + -
562B ILE* 3.8 24.9 - - + -
565B LEU* 5.5 3.4 - - + -
566B MET* 3.7 26.2 - - + -
593B VAL* 2.8 39.9 + - + +
594B ALA 3.7 0.4 + - - +
596B ALA* 1.3 70.6 - - - +
598B GLN* 1.3 57.4 + - - +
599B SER 3.0 0.7 + - - -
600B GLY 2.7 30.9 + - - +
601B PHE* 4.1 24.7 - - + +
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Residues in contact with GLN 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B GLY 5.4 0.2 - - - -
554B HIS* 4.0 26.9 - - + +
557B ASN* 4.1 9.9 - - - +
594B ALA 3.4 9.7 + - - +
595B THR* 3.2 20.2 + - - +
596B ALA 3.1 12.1 + - - +
597B LEU* 1.3 76.4 - - - +
599B SER* 1.3 64.6 + - - +
600B GLY 3.5 0.5 + - - -
601B PHE* 3.7 6.8 + - - +
653B GLU 4.5 3.6 + - - +
654B GLY* 3.0 33.5 - - - +
655B LEU* 3.3 21.3 - - - +
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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
------------------------------------------------------------
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