Contacts of the helix formed by residues 582 - 603 (chain A) in PDB entry 5E3H
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 ILE 582 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533A ARG 5.8 0.4 - - - +
536A LYS* 4.7 5.4 - - + +
537A ALA* 4.3 27.4 - - + +
540A LEU* 3.8 21.1 - - + -
581A GLU* 1.3 79.3 - - + +
583A GLU* 1.3 82.7 + - + +
584A GLN 3.3 0.2 - - - -
585A ASP* 3.5 15.2 + - + +
586A LEU* 3.5 23.8 + - + +
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Residues in contact with GLU 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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540A LEU* 4.7 8.8 - - + +
544A HIS* 4.6 14.9 + - + +
574A VAL* 3.1 43.8 - - + +
575A ARG* 5.4 0.3 - - - -
581A GLU 3.1 9.6 + - - +
582A ILE* 1.3 90.7 - - + +
584A GLN* 1.3 59.1 + - - +
585A ASP 3.2 0.7 - - - -
586A LEU* 3.5 7.5 + - - +
587A THR* 3.0 31.9 + - - +
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Residues in contact with GLN 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A GLU* 3.3 16.3 + - - +
582A ILE 3.3 0.2 - - - -
583A GLU* 1.3 80.9 - - - +
585A ASP* 1.3 58.8 + - - +
587A THR* 3.2 23.2 - - + +
588A GLN* 3.3 12.0 + - - +
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Residues in contact with ASP 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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485A LEU* 3.9 22.3 - - - +
581A GLU 4.1 1.5 + - - +
582A ILE* 3.5 17.3 + - + +
583A GLU 3.2 0.4 - - - -
584A GLN* 1.3 78.5 - - - +
586A LEU* 1.3 64.9 + - + +
588A GLN* 3.1 20.7 + - - +
589A ARG* 3.3 7.4 + - - +
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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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482A THR* 4.8 15.9 - - + +
485A LEU* 3.4 33.2 - - + -
537A ALA 5.7 0.2 - - - +
540A LEU* 4.0 24.9 - - + +
541A TYR* 4.3 13.0 - - + +
544A HIS* 4.1 28.7 - - + +
548A TYR* 4.5 6.8 + - + +
571A PHE* 4.7 2.6 - - - -
582A ILE* 3.5 18.4 + - + +
583A GLU* 3.5 7.0 + - - +
585A ASP* 1.3 73.2 - - - +
587A THR* 1.3 65.5 + - - +
588A GLN 3.1 1.8 - - - -
589A ARG* 3.2 18.7 + - + +
590A PHE* 3.2 11.6 + - - +
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Residues in contact with THR 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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571A PHE* 3.9 32.7 - - - +
574A VAL* 5.9 3.1 - - - -
583A GLU 3.0 17.9 + - - +
584A GLN* 3.2 27.4 - - + +
586A LEU* 1.3 75.3 - - - +
588A GLN* 1.3 58.2 + - - +
590A PHE* 3.7 3.5 - - - +
591A GLU* 2.9 41.6 + - + +
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Residues in contact with GLN 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 GLN 3.4 11.9 - - - +
585A ASP* 3.1 19.6 + - - +
587A THR* 1.3 81.0 - - - +
589A ARG* 1.3 57.3 + - - +
591A GLU* 3.9 5.5 - - - +
592A GLU* 3.0 29.3 + - - +
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Residues in contact with ARG 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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478A LEU* 4.3 18.6 - - + +
481A ASP* 5.5 8.1 - - + +
548A TYR* 5.8 0.2 - - - +
585A ASP 3.3 6.3 + - - +
586A LEU* 3.2 14.5 + - + +
588A GLN* 1.3 80.3 - - - +
590A PHE* 1.3 62.4 + - - +
592A GLU* 3.6 15.1 - - - +
593A LYS* 3.6 10.2 + - - +
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Residues in contact with PHE 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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478A LEU* 4.1 12.7 - - + +
548A TYR* 3.6 19.7 - + - +
564A LEU* 4.1 11.7 - - + -
567A LEU* 3.6 36.3 - - + -
568A LYS* 4.7 8.3 - - + -
571A PHE* 3.3 41.7 - + + -
586A LEU 3.2 4.8 + - - +
587A THR* 3.7 8.7 - - - +
588A GLN 3.2 0.4 - - - -
589A ARG* 1.3 76.2 - - - +
591A GLU* 1.3 70.9 + - + +
592A GLU 3.1 1.7 + - - -
593A LYS* 3.2 3.6 + - - +
594A LEU* 2.8 65.6 + - + +
597A LEU* 4.8 7.8 - - + +
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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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587A THR* 2.9 35.9 + - + +
588A GLN* 3.9 6.5 - - - +
590A PHE* 1.3 81.5 - - + +
592A GLU* 1.3 61.7 + - - +
594A LEU* 3.3 37.7 + - - +
595A GLN* 4.2 4.3 + - - +
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Residues in contact with GLU 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 GLN 3.0 18.2 + - - +
589A ARG* 3.6 9.6 - - - +
590A PHE 3.1 0.4 - - - -
591A GLU* 1.3 79.8 - - - +
593A LYS* 1.3 59.8 + - - +
595A GLN* 4.2 9.7 + - - +
596A GLU* 5.0 0.7 + - - +
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Residues in contact with LYS 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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474A ILE* 5.0 7.4 - - + -
478A LEU* 4.5 17.0 - - + -
589A ARG 3.6 8.2 + - - +
590A PHE 3.2 5.8 + - - +
592A GLU* 1.3 77.2 - - + +
594A LEU* 1.3 61.0 + - - +
595A GLN 3.3 1.1 - - - -
596A GLU* 3.0 18.3 + - - +
597A LEU* 2.9 41.8 + - + +
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Residues in contact with LEU 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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564A LEU* 3.8 28.9 - - + -
568A LYS* 6.3 1.8 - - + -
590A PHE* 2.8 39.4 + - + +
591A GLU* 3.3 32.5 - - - +
592A GLU 3.3 0.6 - - - -
593A LYS* 1.3 77.3 - - - +
595A GLN* 1.3 58.9 + - - +
597A LEU* 3.1 6.4 + - - -
598A GLU* 2.8 42.7 + - + +
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Residues in contact with GLN 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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591A GLU 4.2 3.7 + - - +
592A GLU 4.6 8.1 - - - +
593A LYS 3.3 0.4 - - - -
594A LEU* 1.3 80.2 - - - +
596A GLU* 1.3 65.7 + - - +
598A GLU* 3.5 17.3 - - + +
599A SER* 3.8 7.9 + - - -
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Residues in contact with GLU 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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474A ILE* 5.3 10.3 - - - +
592A GLU 5.0 0.4 + - - +
593A LYS* 3.0 20.5 + - - +
595A GLN* 1.3 84.0 + - - +
597A LEU* 1.3 66.4 + - + +
598A GLU 3.1 0.2 - - - -
599A SER* 3.1 17.1 + - - -
600A VAL* 3.3 19.9 + - + +
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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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470A LYS 5.3 0.7 - - - +
471A PHE* 4.3 24.0 - - + +
474A ILE* 3.7 26.2 - - + -
475A ILE* 3.7 27.4 - - + -
478A LEU* 5.5 3.1 - - + -
564A LEU* 3.8 28.0 - - + +
567A LEU* 5.8 0.4 - - + -
590A PHE* 4.8 12.8 - - + -
593A LYS* 2.9 31.8 + - + +
594A LEU* 3.7 7.6 - - - +
596A GLU* 1.3 75.7 - - + +
598A GLU* 1.3 63.6 + - - +
600A VAL* 3.9 11.3 - - + +
601A SER* 3.3 23.4 + - - -
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Residues in contact with GLU 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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564A LEU* 3.5 21.1 - - - +
594A LEU* 2.8 25.4 + - + +
595A GLN* 3.5 12.8 - - - +
596A GLU 3.1 0.2 - - - -
597A LEU* 1.3 78.4 - - - +
599A SER* 1.3 60.3 + - - +
601A SER* 3.8 5.0 + - - -
602A ARG* 3.6 17.0 + - - +
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Residues in contact with SER 599 (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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595A GLN* 3.8 9.9 + - - -
596A GLU* 3.1 10.6 + - - -
598A GLU* 1.3 77.3 - - - +
600A VAL* 1.3 59.4 + - - +
601A SER 3.1 2.0 - - - -
602A ARG* 2.9 24.5 + - - +
603A ASP* 3.2 11.8 + - - +
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Residues in contact with VAL 600 (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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470A LYS* 4.1 25.1 - - + +
471A PHE* 4.2 12.6 - - + +
560A MET* 3.7 26.3 - - - +
596A GLU* 3.3 23.3 + - + +
597A LEU* 3.5 16.8 + - + +
599A SER* 1.3 76.7 - - - +
601A SER* 1.3 61.1 + - - +
602A ARG 3.4 0.3 + - - -
603A ASP* 3.4 20.2 + - - +
606A ASN* 3.8 15.5 + - - +
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Residues in contact with SER 601 (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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471A PHE* 5.4 0.9 - - - -
560A MET* 4.5 14.2 - - - +
561A LYS* 3.2 41.7 + - - +
564A LEU* 4.3 12.0 - - - +
597A LEU 3.3 14.7 + - - -
598A GLU* 3.8 6.5 - - - -
599A SER 3.1 0.2 - - - -
600A VAL* 1.3 79.1 - - - +
602A ARG* 1.3 62.3 + - - +
603A ASP 3.3 3.7 + - - +
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Residues in contact with ARG 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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598A GLU 3.6 10.0 + - - +
599A SER* 2.9 15.0 + - - +
601A SER* 1.3 77.4 - - - +
603A ASP* 1.3 63.3 + - - +
604A PRO* 3.2 13.0 - - - +
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Residues in contact with ASP 603 (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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599A SER 3.2 9.2 + - - +
600A VAL* 3.7 8.8 - - - +
601A SER 3.3 4.3 - - - +
602A ARG* 1.3 75.3 - - - +
604A PRO* 1.3 69.8 - - - +
605A SER* 2.9 26.2 + - - -
606A ASN* 3.4 39.2 + - - +
607A GLU* 4.4 2.9 + - - +
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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