Contacts of the helix formed by residues 589 - 610 (chain A) in PDB entry 1UZF
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 ALA 589 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.6 14.9 - - + +
239A GLU* 3.3 36.2 + - + +
240A LEU* 4.1 21.1 - - + -
528A ILE* 4.5 7.0 - - + -
588A SER* 1.3 71.9 + - - +
590A SER* 1.3 58.5 + - - +
591A ALA 3.3 2.0 - - - -
592A MET* 3.3 7.3 + - - +
593A LEU* 2.9 35.2 + - + +
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Residues in contact with SER 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 4.9 1.8 + - - -
535A GLU* 5.0 2.7 - - - -
588A SER* 3.2 16.4 + - - -
589A ALA* 1.3 77.9 - - - +
591A ALA* 1.3 57.4 + - - +
593A LEU* 3.2 10.8 + - - +
594A SER* 2.8 32.2 + - - -
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Residues in contact with ALA 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 3.2 35.9 - - - +
532A GLN* 3.5 18.8 - - + +
535A GLU* 3.7 29.7 + - + +
547A LEU* 3.9 4.2 - - - +
588A SER* 4.4 2.0 + - - -
589A ALA 3.3 0.6 - - - -
590A SER* 1.3 77.9 - - - +
592A MET* 1.3 59.1 + - - +
594A SER* 3.3 2.6 + - - -
595A TYR* 2.9 29.8 + - - +
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Residues in contact with MET 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.4 38.4 - - + -
243A LEU* 5.5 0.4 - - + -
454A LYS* 3.8 29.8 - - + +
455A ILE* 4.1 8.5 - - + -
458A ILE* 4.1 10.3 - - + -
527A PHE* 3.7 15.3 - - + +
528A ILE* 4.3 6.7 + - + +
531A PHE* 3.4 48.9 - - + +
588A SER 5.2 0.4 + - - -
589A ALA* 3.3 13.2 + - - +
591A ALA* 1.3 78.4 - - - +
593A LEU* 1.3 63.7 + - - +
595A TYR* 3.3 0.9 + - - +
596A PHE* 3.2 40.1 + - + -
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Residues in contact with LEU 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 3.9 31.4 - - + +
240A LEU* 4.4 17.9 - - + -
243A LEU* 4.4 17.6 - - + +
589A ALA* 2.9 36.0 + - + +
590A SER* 3.6 8.7 - - - +
592A MET* 1.3 74.3 - - - +
594A SER* 1.3 58.9 + - - +
596A PHE* 3.2 2.4 + - - +
597A LYS* 2.8 31.1 + - - +
600A LEU* 5.7 8.7 - - + +
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Residues in contact with SER 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU* 4.4 13.3 + - - -
547A LEU* 4.7 11.2 + - - +
590A SER 2.8 20.9 + - - -
591A ALA 3.6 4.5 - - - -
593A LEU* 1.3 73.0 - - - +
595A TYR* 1.3 64.9 + - - +
597A LYS* 3.3 20.3 + - - +
598A PRO* 4.0 2.8 - - - +
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Residues in contact with TYR 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 4.5 8.1 + - + +
423A THR* 5.7 0.5 - - - +
446A PHE* 3.6 12.8 - - - -
447A LEU* 3.8 15.5 - - + +
450A MET* 3.5 31.6 - - + +
531A PHE* 3.5 26.9 - + + -
534A HIS* 4.1 23.8 - + - -
547A LEU* 4.1 13.6 - - + +
548A HIS* 3.4 44.3 + - + +
591A ALA 2.9 14.1 + - - +
592A MET 3.4 8.7 - - - +
593A LEU 3.3 0.2 - - - -
594A SER* 1.3 79.8 + - - +
596A PHE* 1.3 95.8 + + - +
597A LYS 3.7 0.2 + - - -
598A PRO* 3.8 8.3 - - - +
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Residues in contact with PHE 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.6 24.0 - - + -
447A LEU* 3.7 11.0 - - + -
450A MET* 4.0 6.5 - - + -
451A ALA* 3.5 38.6 - - + -
454A LYS* 4.1 11.2 - - + -
455A ILE* 3.8 20.9 - - + -
531A PHE* 3.8 18.8 - + - -
592A MET* 3.2 27.0 + - + +
593A LEU 3.5 1.3 - - - +
595A TYR* 1.3 103.0 - + - +
597A LYS* 1.3 66.4 + - - +
598A PRO* 3.3 4.5 - - - -
599A LEU* 2.8 33.8 + - + +
600A LEU* 2.9 11.0 + - - +
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Residues in contact with LYS 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU 2.8 17.0 + - - +
594A SER* 3.3 15.4 + - - +
596A PHE* 1.3 70.8 - - - +
598A PRO* 1.3 72.5 - - + +
600A LEU* 3.0 18.1 + - + +
601A ASP* 2.9 54.9 + - - +
604A ARG* 4.9 9.3 - - - +
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Residues in contact with PRO 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASP* 5.1 2.5 - - - +
444A ILE* 4.1 11.2 - - + +
447A LEU* 3.6 19.3 - - + -
546A PRO* 5.8 2.9 - - + -
548A HIS* 4.3 16.8 - - + +
594A SER 4.0 2.7 - - - +
595A TYR 3.8 10.1 - - - +
596A PHE 3.3 4.7 - - - -
597A LYS* 1.3 97.2 - - + +
599A LEU* 1.3 55.3 + - - +
601A ASP* 3.5 9.6 + - + +
602A TRP* 3.0 26.5 + - - +
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Residues in contact with LEU 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 5.2 2.9 - - + -
247A LEU* 5.4 0.2 - - + -
444A ILE* 4.2 23.1 - - + +
447A LEU* 3.5 26.5 - - + +
448A MET* 4.1 26.7 - - + +
451A ALA* 3.3 33.4 - - + -
596A PHE* 2.8 25.5 + - + +
598A PRO* 1.3 73.0 - - - +
600A LEU* 1.3 58.5 + - - +
602A TRP* 3.1 6.0 + - + +
603A LEU* 2.8 58.8 + - + +
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Residues in contact with LEU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 5.2 4.3 - - + -
243A LEU* 3.8 45.0 - - + +
246A ASN* 4.2 15.0 - - + +
593A LEU* 5.7 8.5 - - + +
596A PHE 2.9 8.9 + - - +
597A LYS* 3.4 22.7 - - + +
599A LEU* 1.3 75.9 - - - +
601A ASP* 1.3 59.4 + - - +
603A LEU* 3.4 3.0 + - - +
604A ARG* 3.0 69.9 + - - +
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Residues in contact with ASP 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A LYS* 2.9 55.9 + - - +
598A PRO* 3.7 9.7 - - + +
600A LEU* 1.3 79.5 - - - +
602A TRP* 1.3 61.9 + - - +
604A ARG* 3.5 10.6 + - - +
605A THR* 3.2 26.3 + - - -
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Residues in contact with TRP 602 (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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250A TYR* 3.5 43.5 - + - -
292A PRO* 3.7 25.1 - - + -
293A PHE* 3.7 22.3 - + - -
444A ILE* 3.9 35.9 - - + -
448A MET* 4.3 4.0 - - + -
598A PRO 3.0 18.2 + - - +
599A LEU* 3.1 7.4 + - + +
601A ASP* 1.3 75.0 - - - +
603A LEU* 1.3 79.5 + - + +
605A THR* 3.3 8.0 + - - -
606A GLU* 2.9 49.4 + - + +
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Residues in contact with LEU 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 4.4 12.8 - - + -
246A ASN* 4.1 17.9 - - + +
247A LEU* 4.1 26.0 - - + +
250A TYR* 3.8 36.1 - - + -
448A MET* 4.0 9.2 - - + -
599A LEU* 2.8 48.0 + - + +
600A LEU* 3.7 3.1 - - - +
602A TRP* 1.3 87.2 - - + +
604A ARG* 1.3 60.8 + - - +
606A GLU* 3.7 1.3 - - - +
607A ASN* 2.8 37.3 + - - -
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Residues in contact with ARG 604 (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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242A PRO* 4.0 24.7 - - - +
246A ASN* 3.9 26.1 - - - +
597A LYS* 4.9 5.5 - - - +
600A LEU* 3.0 47.6 + - + +
601A ASP* 3.9 13.5 + - - +
602A TRP 3.3 0.2 - - - -
603A LEU* 1.3 75.2 - - - +
605A THR* 1.3 58.8 + - - +
607A ASN* 4.1 1.1 - - - +
608A GLU* 2.8 35.0 + - - +
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Residues in contact with THR 605 (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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601A ASP 3.2 13.3 + - - -
602A TRP* 3.6 10.0 - - - -
603A LEU 3.3 0.4 - - - -
604A ARG* 1.3 79.2 - - - +
606A GLU* 1.3 62.7 + - - +
608A GLU* 3.4 12.3 + - - +
609A LEU* 3.0 33.1 + - + +
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Residues in contact with GLU 606 (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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250A TYR* 3.7 35.1 - - + -
602A TRP* 2.9 45.4 + - + +
603A LEU* 3.7 3.8 - - - +
605A THR* 1.3 78.2 - - - +
607A ASN* 1.3 64.2 + - - +
609A LEU* 3.4 14.6 - - - +
610A HIS* 2.9 60.8 + - + -
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Residues in contact with ASN 607 (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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246A ASN* 3.0 51.0 + - - +
249A ALA* 4.2 6.4 - - - +
250A TYR* 3.6 26.3 + - - +
603A LEU* 2.8 23.1 + - - +
604A ARG 4.1 2.2 - - - +
606A GLU* 1.3 74.9 - - - +
608A GLU* 1.3 57.5 - - - +
610A HIS* 3.3 1.7 + - - -
611A GLY 3.0 22.3 + - - -
612A GLU* 3.0 40.4 + - + +
614A LEU* 4.9 3.8 - - + -
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Residues in contact with GLU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ARG* 2.8 21.7 + - - +
605A THR* 3.6 12.1 - - - +
607A ASN* 1.3 77.1 - - - +
609A LEU* 1.3 59.5 + - - +
611A GLY* 3.0 19.3 + - - -
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Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A THR* 3.0 26.1 + - + +
606A GLU* 3.4 23.6 - - - +
608A GLU* 1.3 79.2 - - - +
610A HIS* 1.3 85.5 + - + +
611A GLY 3.2 1.2 + - - -
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Residues in contact with HIS 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TYR* 6.1 0.2 - + - -
253A ARG* 3.6 29.7 + - + +
606A GLU* 2.9 55.0 + - + +
607A ASN* 3.9 3.1 - - - +
608A GLU 3.1 0.8 - - - -
609A LEU* 1.3 94.8 + - + +
611A GLY* 1.3 63.0 + - - +
612A GLU* 3.5 21.6 + - + +
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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