Contacts of the helix formed by residues 581 - 597 (chain A) in PDB entry 3QHE
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 LYS 581 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A GLU* 3.1 36.9 + - - +
539A ASP* 3.1 24.1 + - - -
579A VAL* 3.5 5.4 - - - +
580A LYS* 1.3 81.8 - - + +
582A GLU* 1.3 65.8 + - - +
583A SER* 3.9 17.2 + - - +
584A THR* 3.1 10.6 + - - +
585A LEU* 3.1 19.6 + - - +
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Residues in contact with GLU 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LYS 3.9 2.0 + - - -
581A LYS* 1.3 71.3 - - - +
583A SER* 1.3 57.2 + - - +
585A LEU* 3.2 8.4 + - - +
586A LYS* 2.9 31.1 + - + +
622A TYR* 3.0 37.8 + - - +
624A SER* 3.5 13.7 + - - -
625A GLN* 4.5 4.7 + - - -
626A THR* 3.0 38.5 + - - +
628A THR* 3.9 8.3 + - - -
630A ALA* 5.9 0.5 - - - +
631A ILE* 4.2 16.1 - - + +
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Residues in contact with SER 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLN* 3.6 20.2 - - - +
581A LYS* 3.9 22.3 + - - +
582A GLU* 1.3 79.5 - - - +
584A THR* 1.3 65.7 + - - +
586A LYS* 3.5 20.2 - - - +
587A SER* 3.6 4.7 + - - -
387B TYR* 5.7 5.2 - - - -
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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
----------------------------------------------------------
538A GLU* 2.8 52.2 + - - +
541A GLN* 3.8 14.6 - - + +
542A GLN* 4.0 14.5 - - - +
579A VAL* 3.3 28.9 - - + -
581A LYS* 3.1 8.4 + - - +
583A SER* 1.3 77.3 + - - +
585A LEU* 1.3 67.1 + - - +
586A LYS 3.4 0.2 + - - -
587A SER* 3.4 4.0 + - - -
588A VAL* 3.0 30.7 + - + +
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Residues in contact with LEU 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ALA* 3.8 29.8 - - + +
579A VAL* 3.6 11.8 - - + +
581A LYS 3.1 12.0 + - - +
582A GLU* 3.5 9.6 - - - +
584A THR* 1.3 78.1 - - - +
586A LYS* 1.3 56.4 + - - +
588A VAL* 3.7 3.3 - - + +
589A LEU* 2.8 58.2 + - + +
615A PHE* 3.9 17.9 - - + -
619A THR* 5.7 0.2 - - + -
622A TYR* 4.6 15.3 - - + +
631A ILE* 4.2 26.2 - - + -
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Residues in contact with LYS 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLU* 2.9 18.5 + - + +
583A SER* 3.5 12.8 - - - +
585A LEU* 1.3 76.0 - - - +
587A SER* 1.3 59.1 + - - +
589A LEU* 3.8 3.1 - - - +
590A SER* 3.0 30.0 + - - +
628A THR* 5.7 5.9 + - - +
630A ALA* 4.1 30.6 - - + +
631A ILE* 3.8 14.8 - - + +
634A SER* 4.4 3.0 + - - +
383B TYR* 4.2 17.5 - - - +
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Residues in contact with SER 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLN* 3.1 41.7 + - - +
545A ALA* 3.6 15.1 - - - +
546A SER* 3.9 13.2 - - - -
549A ARG* 4.7 9.9 - - - +
583A SER 3.6 1.9 + - - -
584A THR 3.4 9.2 + - - -
586A LYS* 1.3 76.8 - - - +
588A VAL* 1.3 67.3 + - - +
590A SER* 3.6 8.2 - - - -
591A ALA* 3.1 20.4 + - - +
383B TYR* 5.2 0.7 - - - -
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Residues in contact with VAL 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A LEU* 5.3 0.2 - - + -
541A GLN 4.8 2.0 - - - +
545A ALA* 3.6 18.1 - - + +
572A LEU* 3.3 38.1 - - + +
575A CYS* 3.8 22.4 - - + -
576A ALA* 3.7 23.6 - - + +
579A VAL* 4.8 2.2 - - + -
584A THR* 3.0 32.5 + - + +
585A LEU* 3.7 6.3 - - - +
587A SER* 1.3 77.3 + - - +
589A LEU* 1.3 61.0 + - + +
591A ALA* 3.4 3.6 + - - +
592A LEU* 3.1 21.6 + - + +
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Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ALA* 4.1 10.3 - - + -
585A LEU* 2.8 46.7 + - + +
586A LYS 3.8 2.2 - - - +
588A VAL* 1.3 71.0 - - - +
590A SER* 1.3 60.9 + - - +
592A LEU* 4.2 4.7 - - + -
593A TRP* 2.8 30.7 + - - +
615A PHE* 3.9 23.6 - - + -
616A LEU* 5.0 1.3 - - + -
619A THR* 4.5 4.9 - - + -
631A ILE* 4.0 26.0 - - + +
634A SER* 3.6 17.4 + - - -
635A GLY* 4.1 17.0 - - - +
638A ILE* 3.4 23.1 - - + +
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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
----------------------------------------------------------
549A ARG* 3.8 17.2 - - - +
586A LYS* 3.0 15.5 + - - +
587A SER* 3.3 8.9 + - - -
589A LEU* 1.3 76.0 - - - +
591A ALA* 1.3 62.0 + - - +
593A TRP* 3.3 6.7 - - - +
594A ASN* 3.2 26.5 + - - +
634A SER* 3.7 10.3 + - - -
382B GLY* 5.3 0.3 - - - -
383B TYR* 2.3 47.2 + - - +
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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
----------------------------------------------------------
545A ALA 3.6 11.0 - - - +
548A LEU* 4.1 4.9 - - + -
549A ARG* 3.6 32.5 - - - +
552A SER* 3.8 1.0 + - - -
572A LEU* 3.8 20.6 - - + -
587A SER 3.1 8.6 + - - +
588A VAL 3.7 4.0 - - - +
589A LEU 3.2 0.2 - - - -
590A SER* 1.3 75.8 - - - +
592A LEU* 1.3 61.1 + - - +
594A ASN* 3.3 3.5 + - - +
595A LEU* 2.9 34.7 + - + +
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Residues in contact with LEU 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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569A VAL* 3.8 21.3 - - + +
572A LEU* 3.8 27.3 - - + +
573A MET* 3.5 36.1 - - + +
576A ALA* 5.2 0.4 - - + -
588A VAL 3.1 13.3 + - - +
589A LEU* 3.3 9.8 + - + +
591A ALA* 1.3 75.1 - - - +
593A TRP* 1.3 56.2 + - - +
595A LEU* 4.4 4.7 - - + +
596A SER* 2.7 38.6 + - - -
606A ILE* 4.1 20.2 - - + -
616A LEU* 5.1 0.7 - - + -
638A ILE* 3.6 32.5 - - + -
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Residues in contact with TRP 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 LEU 2.8 13.4 + - - +
590A SER* 3.3 11.2 - - - +
592A LEU* 1.3 75.6 - - - +
594A ASN* 1.3 62.9 + - - +
596A SER* 3.1 13.6 + - - -
633A GLU* 3.9 15.7 - - + -
634A SER* 3.4 32.1 - - - +
637A GLY* 3.5 26.0 + - - -
638A ILE* 3.5 12.3 - - + +
640A ARG* 5.4 3.9 - - - +
641A ASN* 3.2 9.3 + - - -
675A THR* 3.6 26.9 - - + -
679A ASN* 4.0 17.6 + - - -
380B TYR 3.6 18.3 + - - -
381B GLU* 3.8 6.0 + - - -
382B GLY* 3.3 32.8 - - - +
383B TYR* 4.2 18.2 - + - -
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Residues in contact with ASN 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ARG* 2.8 33.3 + - - +
552A SER* 3.2 25.4 + - - +
553A TRP* 3.5 9.9 - - - +
590A SER 3.2 6.5 + - - +
591A ALA 3.7 1.8 - - - +
593A TRP* 1.3 76.0 - - - +
595A LEU* 1.3 63.0 + - - +
597A ALA 3.3 10.7 + - - -
598A HIS* 3.3 16.2 - - - -
381B GLU* 3.4 18.7 - - + +
382B GLY* 2.7 31.5 + - - -
383B TYR 3.0 25.7 + - - -
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Residues in contact with LEU 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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548A LEU* 5.3 4.0 - - + +
552A SER* 3.7 13.2 - - - +
563A LEU* 3.9 27.4 - - + -
564A ARG 5.2 0.2 - - - +
568A SER* 4.0 14.1 - - - -
569A VAL* 4.1 20.0 - - + -
572A LEU* 3.4 32.5 - - + -
591A ALA* 2.9 22.4 + - + +
592A LEU* 4.0 5.4 - - + +
594A ASN* 1.3 73.5 - - - +
596A SER* 1.3 62.1 + - - +
598A HIS* 3.1 35.2 + - + +
602A ASN* 2.9 30.1 + - - +
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Residues in contact with SER 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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592A LEU 2.7 24.0 + - - -
593A TRP 3.1 2.6 + - - -
594A ASN 3.3 0.2 - - - -
595A LEU* 1.3 72.6 - - - +
597A ALA* 1.3 57.3 - - - +
598A HIS 3.6 0.2 + - - -
599A CYS 4.0 2.1 - - - +
602A ASN* 4.6 4.5 - - - -
603A LYS* 3.1 30.7 - - - +
606A ILE* 3.5 28.6 - - - +
638A ILE* 3.8 13.4 - - - -
641A ASN* 3.0 34.2 + - - +
642A VAL* 4.4 4.9 - - - -
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Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ASN 3.3 12.2 + - - +
595A LEU 3.1 1.0 - - - -
596A SER* 1.3 81.1 + - - +
598A HIS* 1.3 62.7 + - - +
599A CYS* 3.5 1.2 + - - -
603A LYS* 4.6 8.3 + - - +
641A ASN* 3.6 20.2 - - - +
379B SER 5.4 0.9 - - - -
380B TYR* 3.9 14.6 - - - +
381B GLU* 3.8 19.3 - - + +
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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