Contacts of the helix formed by residues 592 - 607 (chain A) in PDB entry 3SXS
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 592 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A GLU* 5.5 0.9 - - - +
564A ASP* 5.5 6.1 + - - -
590A SER* 3.0 7.4 + - - +
591A SER* 1.3 92.4 - - - +
593A SER* 1.3 62.9 + - - +
594A ASP 3.3 2.5 - - - -
595A VAL* 3.1 20.7 + - + +
596A TRP 3.3 6.2 + - - -
653A PRO* 3.1 30.6 + - + +
654A GLU* 4.0 9.7 + - - +
656A ARG* 2.7 50.5 + - + +
657A PRO 3.4 17.7 - - - +
658A THR* 3.7 28.9 - - - +
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Residues in contact with SER 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ILE* 4.4 2.7 - - - -
534A HIS 5.9 0.2 - - - -
578A TRP 4.8 0.3 - - - +
579A SER* 5.8 0.2 - - - -
580A ALA* 4.1 7.4 + - - +
582A GLU* 2.7 26.2 + - - +
583A VAL* 3.7 8.5 - - - +
589A TYR* 3.4 26.0 - - - -
590A SER* 2.9 29.2 + - - -
592A LYS* 1.3 77.7 - - - +
594A ASP* 1.3 61.7 + - - +
596A TRP* 3.5 7.1 - - - +
597A ALA* 3.5 16.3 + - - +
656A ARG* 4.0 1.3 - - - +
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Residues in contact with ASP 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A MET* 3.0 20.4 - - + +
528A GLU* 6.1 0.3 - - - +
532A PHE 4.3 1.2 - - - +
533A ILE* 3.1 18.4 - - - +
534A HIS* 3.0 42.9 + - + +
537A LEU* 3.8 6.2 - - + +
590A SER 5.0 0.2 + - - -
591A SER 3.6 17.2 - - - +
593A SER* 1.3 71.9 - - - +
595A VAL* 1.4 64.4 + - - +
597A ALA* 3.5 8.1 - - - +
598A PHE* 2.8 29.1 + - - +
659A PHE* 3.4 18.3 - - - -
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A GLU* 4.6 1.8 - - - +
591A SER 4.8 0.4 - - - +
592A LYS* 3.1 25.4 + - + +
594A ASP* 1.4 76.0 + - - +
596A TRP* 1.3 67.4 + - - +
598A PHE* 3.2 4.4 + - - +
599A GLY 3.1 15.2 + - - -
648A CYS* 3.2 35.3 - - + +
656A ARG* 4.2 7.6 - - + -
657A PRO* 3.4 29.6 - - + +
658A THR* 4.4 0.7 - - - -
659A PHE* 3.7 38.6 - - + +
662A LEU* 3.9 7.2 - - + -
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Residues in contact with TRP 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LYS 4.8 1.6 + - - -
578A TRP 3.7 16.4 - - - -
579A SER 3.4 17.6 + - - -
580A ALA* 3.7 13.5 - - + -
581A PRO* 3.3 24.0 - - + -
592A LYS 3.3 7.1 + - - +
593A SER 3.5 10.5 - - - +
595A VAL* 1.3 78.2 - - - +
597A ALA* 1.3 64.1 + - - +
599A GLY 3.0 12.0 + - - -
600A ILE* 3.3 25.7 + - + +
613A TYR* 4.6 8.9 + - - -
625A VAL* 3.5 34.1 - - + -
630A ARG* 3.7 11.7 - - - -
648A CYS 3.3 15.6 + - - +
649A TRP* 3.2 58.5 + + + -
650A HIS 3.5 7.9 - - - -
656A ARG* 3.7 11.0 - - - +
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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
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534A HIS 5.7 0.2 - - - +
536A ASP* 5.9 0.2 - - - -
537A LEU* 3.4 35.9 - - + +
578A TRP* 3.4 23.3 - - + +
593A SER 3.5 5.8 + - - +
594A ASP* 3.3 13.4 + - - +
596A TRP* 1.3 78.9 - - - +
598A PHE* 1.4 56.7 + - - +
600A ILE* 3.1 9.0 + - - +
601A LEU* 2.8 27.7 + - - +
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Residues in contact with PHE 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A CYS 3.5 27.4 - - - -
520A VAL* 3.8 27.4 - - + -
521A CYS* 3.7 16.4 - - + -
537A LEU* 3.8 9.1 - - + +
594A ASP 2.8 17.8 + - - +
595A VAL 3.2 7.4 + - - +
597A ALA* 1.4 71.6 - - - +
599A GLY* 1.3 58.7 + - - +
601A LEU* 3.1 10.0 + - + +
602A MET* 2.8 62.3 + - + +
648A CYS* 4.2 3.6 - - - -
659A PHE* 3.5 20.0 - + + -
662A LEU* 3.9 28.3 - - + -
666A ILE* 4.1 14.4 - - + -
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Residues in contact with GLY 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL 3.1 6.5 + - - -
596A TRP 3.0 5.3 + - - -
598A PHE* 1.3 75.0 - - - +
600A ILE* 1.3 61.1 + - - +
602A MET* 3.3 6.5 + - - +
603A TRP 3.0 17.8 + - - -
645A MET* 3.8 12.1 - - - +
648A CYS* 3.8 17.4 - - - -
649A TRP* 3.4 27.5 - - - -
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Residues in contact with ILE 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LYS 3.8 17.3 - - - +
578A TRP* 3.5 28.7 - - + +
596A TRP* 3.3 28.5 + - + +
597A ALA 3.1 6.7 + - - +
599A GLY* 1.3 76.0 - - - +
601A LEU* 1.4 57.1 + - - +
603A TRP* 3.1 5.6 + - - +
604A GLU* 2.9 27.4 + - - +
612A PRO* 3.6 26.0 - - + -
613A TYR* 3.7 17.0 - - + +
631A LEU* 3.6 20.4 - - + -
649A TRP* 3.4 22.0 - - + +
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Residues in contact with LEU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 5.0 1.1 - - + -
517A CYS* 4.9 3.8 - - - -
520A VAL* 3.8 27.4 - - + -
537A LEU* 3.8 20.2 - - + +
538A ALA* 3.7 17.3 - - - -
539A ALA* 4.0 9.2 - - - +
542A CYS* 3.7 28.3 - - - -
578A TRP* 4.5 0.6 - - - +
597A ALA 2.8 12.5 + - - +
598A PHE* 3.4 17.0 - - + +
600A ILE* 1.4 75.9 - - - +
602A MET* 1.4 66.0 + - - +
604A GLU* 3.1 16.3 + - - +
605A VAL* 2.9 36.9 + - + +
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Residues in contact with MET 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 5.0 5.2 - - + -
517A CYS* 3.8 31.0 - - + -
598A PHE* 2.8 56.3 + - + +
599A GLY* 3.3 7.2 + - - +
601A LEU* 1.4 70.8 - - - +
603A TRP* 1.3 56.2 + - - +
605A VAL* 3.3 0.7 + - - +
606A PHE* 3.0 37.0 + - + +
641A ILE* 3.9 36.1 - - + +
644A ILE* 4.1 20.4 - - + +
645A MET* 3.9 23.6 - - + -
648A CYS* 5.3 0.2 - - - -
666A ILE* 4.9 6.3 - - + -
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Residues in contact with TRP 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 GLY 3.0 13.9 + - - +
600A ILE 3.1 7.6 + - - +
602A MET* 1.3 75.1 - - - +
604A GLU* 1.3 61.8 + - - +
606A PHE 3.4 0.5 + - - -
607A SER* 2.9 53.2 + - - -
610A LYS* 3.6 31.0 - - + -
611A MET 3.7 13.5 - - - -
612A PRO* 3.5 31.2 - - + -
613A TYR 4.9 1.1 - - - -
614A ASP* 6.2 0.9 - - - -
631A LEU* 3.6 39.3 - - + +
632A TYR* 2.8 30.6 + - + +
634A PRO* 3.5 18.2 - - + +
645A MET* 3.9 17.2 - - - -
649A TRP* 4.4 1.1 - + + -
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Residues in contact with GLU 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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498A LEU* 3.8 15.4 - - - +
501A LEU* 4.4 1.3 - - - -
538A ALA* 4.9 0.2 - - - +
539A ALA* 2.9 41.1 + - + +
540A ARG* 4.8 2.1 + - - -
578A TRP* 2.9 43.6 + - + +
600A ILE 2.9 17.8 + - - +
601A LEU* 3.3 13.7 - - - +
603A TRP* 1.3 76.7 - - - +
605A VAL* 1.4 60.9 + - - +
607A SER* 3.3 1.7 + - - -
608A LEU 3.1 3.5 + - - -
609A GLY* 2.8 32.0 + - - -
610A LYS 4.3 15.2 - - - +
612A PRO* 4.5 6.9 - - + +
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Residues in contact with VAL 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 4.1 20.9 - - + -
501A LEU* 3.8 12.4 - - + +
513A LEU* 3.4 56.5 - - + +
516A MET* 4.2 13.9 - - + -
517A CYS* 3.8 10.8 - - - -
539A ALA* 5.4 0.2 - - + -
601A LEU* 2.9 34.3 + - + +
602A MET 3.6 7.2 - - - +
604A GLU* 1.4 77.4 - - + +
606A PHE* 1.3 58.3 + - + +
608A LEU* 3.0 18.2 + - - +
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Residues in contact with PHE 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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510A PRO* 3.9 9.9 - - + -
513A LEU* 3.7 24.0 - - + -
514A LEU* 3.5 31.0 - - + -
517A CYS* 3.7 24.5 - - - -
602A MET* 3.0 29.3 + - + +
605A VAL* 1.3 77.5 - - + +
607A SER* 1.3 58.0 - - - +
608A LEU 3.3 1.6 + - - -
634A PRO* 3.7 27.3 - - + +
635A HIS 5.1 0.3 + - - -
636A LEU* 3.6 50.0 + - - +
637A ALA* 3.7 13.2 - - + +
641A ILE* 3.6 33.2 - - + -
645A MET* 4.4 2.0 - - + -
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Residues in contact with SER 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A TRP* 2.9 50.0 + - - -
604A GLU 3.9 2.9 - - - -
605A VAL 3.1 0.4 - - - -
606A PHE* 1.3 74.1 - - - +
608A LEU* 1.3 70.5 + - - +
609A GLY 3.2 0.4 - - - -
610A LYS* 3.3 44.9 - - - +
634A PRO* 3.5 13.4 - - - +
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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
------------------------------------------------------------
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