Contacts of the helix formed by residues 536 - 553 (chain A) in PDB entry 1SNX
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 SER 536 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ILE* 3.9 7.2 - - - +
528A GLU* 3.7 13.0 + - - -
534A ARG* 3.7 7.7 + - - +
535A TYR* 1.3 79.7 - - - +
537A SER* 1.3 59.1 + - - +
538A LYS* 2.4 32.3 + - - +
539A SER* 2.6 15.1 + - - -
599A PRO* 5.2 4.5 - - - +
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Residues in contact with SER 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A GLU* 4.0 35.5 + - - +
478A VAL 5.2 0.6 + - - -
479A ILE* 3.1 31.3 - - - +
536A SER* 1.3 76.7 - - - +
538A LYS* 1.3 57.2 + - - +
539A SER* 3.1 9.1 + - - -
540A ASP* 3.4 15.7 - - - +
541A VAL* 3.2 23.7 + - - +
605A PHE* 3.4 5.6 - - - -
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Residues in contact with LYS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 2.4 29.1 + - - +
537A SER* 1.3 73.4 - - - +
539A SER* 1.3 63.0 + - - +
540A ASP 3.0 1.5 + - - -
541A VAL* 3.3 25.3 + - + +
542A TRP 3.7 1.7 + - - -
599A PRO* 4.4 17.3 - - + +
600A GLU* 4.4 10.5 + - - +
602A ARG* 2.6 56.1 + - + +
603A PRO* 2.7 25.2 + - - +
604A ALA* 4.1 12.0 - - - +
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Residues in contact with SER 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ILE* 4.1 3.3 - - - +
525A ALA* 5.2 0.2 - - - -
526A SER* 3.4 28.5 + - - -
528A GLU* 4.3 4.9 - - - -
529A VAL* 4.4 2.0 - - - +
535A TYR* 3.3 30.6 - - - +
536A SER* 2.6 34.1 + - - -
537A SER 3.2 5.7 + - - +
538A LYS* 1.3 82.2 - - - +
540A ASP* 1.3 62.2 + - - +
542A TRP* 3.6 10.9 - - - +
543A SER* 3.7 7.8 + - - -
602A ARG* 4.1 2.5 - - - +
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Residues in contact with ASP 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A MET* 5.5 1.5 - - - +
478A VAL 5.1 0.5 - - - +
479A ILE* 3.6 11.9 - - - +
480A HIS* 2.5 46.6 + - - +
481A ARG* 4.4 2.4 - - - -
482A ASP 4.3 4.2 + - - -
483A LEU* 4.5 12.5 + - + -
535A TYR* 4.9 4.2 - - - -
537A SER* 3.4 12.3 - - - +
539A SER* 1.3 84.0 + - - +
541A VAL* 1.3 54.3 + - - +
542A TRP 2.3 8.2 + - - -
543A SER* 2.3 39.1 + - - -
544A PHE* 2.6 10.9 + - - -
605A PHE* 4.3 12.0 - - + -
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A GLU* 4.9 0.9 - - - +
537A SER 3.3 16.2 - - - +
538A LYS* 3.3 20.9 - - + +
540A ASP* 1.3 75.5 - - - +
542A TRP* 1.3 58.1 + - - +
544A PHE* 3.4 3.5 - - - +
545A GLY 3.3 5.0 + - - -
594A CYS* 3.2 41.3 - - - +
602A ARG* 4.3 15.9 - - + -
603A PRO* 4.3 19.5 - - + +
605A PHE* 3.5 34.9 - - + +
608A LEU* 4.5 11.0 - - + -
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Residues in contact with TRP 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LYS 4.8 1.6 + - - -
524A TRP 4.0 0.2 - - - -
525A ALA 3.3 23.0 + - - -
526A SER* 3.8 8.7 - - - -
527A PRO* 3.3 31.9 - - + -
530A PHE* 5.7 0.7 - + - -
538A LYS 3.7 1.8 + - - -
539A SER 3.6 11.4 - - - +
540A ASP 2.3 11.3 + - - -
541A VAL* 1.3 68.2 - - - +
543A SER* 1.3 54.3 + - - +
544A PHE 2.8 3.8 - - - -
545A GLY* 2.4 26.0 + - - -
546A VAL* 3.0 27.6 + - + +
559A TYR* 4.6 6.8 + - - -
571A ILE* 3.7 20.8 - - + +
576A ARG* 2.7 32.8 - - - -
594A CYS 3.3 26.9 + - - +
595A TRP* 3.2 28.1 - + + -
596A LYS 2.9 26.2 - - - -
602A ARG* 3.9 11.2 - - - +
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Residues in contact with SER 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ASP* 5.9 1.0 - - - -
483A LEU* 3.2 34.1 - - - +
524A TRP* 2.4 42.5 + - - +
525A ALA* 4.0 2.8 + - - -
535A TYR* 6.1 1.0 - - - -
539A SER 3.7 9.7 + - - -
540A ASP* 2.3 27.2 + - - -
542A TRP* 1.3 73.4 - - - +
544A PHE* 1.3 59.5 + - - -
546A VAL 4.0 1.1 - - - +
547A LEU* 3.1 17.8 + - - +
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Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A CYS* 3.7 9.9 - - - -
466A VAL* 3.4 30.7 - - + -
467A CYS* 3.7 37.7 - - + -
483A LEU* 3.3 29.5 - - + +
540A ASP 2.6 11.8 + - - +
541A VAL 3.4 11.0 - - - +
543A SER* 1.3 73.0 - - - +
545A GLY* 1.3 58.6 + - - +
547A LEU* 3.7 6.7 - - + +
548A MET* 3.0 44.8 + - + +
594A CYS* 4.2 11.0 - - - -
605A PHE* 3.7 18.4 - + + -
608A LEU* 4.2 16.4 - - + -
612A LEU* 4.5 7.9 - - + -
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Residues in contact with GLY 545 (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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541A VAL 3.3 2.2 + - - -
542A TRP 2.4 20.1 + - - -
544A PHE* 1.3 70.0 - - - +
546A VAL* 1.3 66.3 + - - -
547A LEU 3.0 0.9 - - - -
548A MET* 2.7 10.1 + - - +
549A TRP* 2.7 21.0 + - - +
591A MET* 5.0 1.3 - - - -
594A CYS* 3.8 18.2 - - - -
595A TRP* 3.6 20.6 - - - -
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LYS 3.6 19.7 - - - +
524A TRP* 3.2 31.2 - - + +
542A TRP* 3.0 32.3 + - + +
543A SER 4.1 1.1 - - - +
545A GLY* 1.3 72.3 - - - +
547A LEU* 1.3 67.3 + - - +
549A TRP* 2.8 22.9 - - - +
550A GLU* 3.0 7.6 + - - +
558A PRO* 3.3 34.8 - - + -
559A TYR* 4.0 14.1 - - + +
577A LEU* 4.7 0.2 - - - -
595A TRP* 3.4 6.7 - - + +
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 4.0 13.0 - - + -
466A VAL* 4.2 14.8 - - + -
483A LEU* 3.3 35.4 - - + -
484A ALA* 3.7 5.8 - - - -
485A ALA* 3.4 19.3 - - + +
488A CYS* 3.7 16.6 - - - -
524A TRP* 3.8 0.6 - - - +
543A SER 3.1 15.4 + - - +
544A PHE* 3.7 6.5 - - + +
545A GLY 3.0 0.2 - - - -
546A VAL* 1.3 77.4 - - - +
548A MET* 1.3 58.7 + - + +
550A GLU* 2.4 49.1 + - - +
551A VAL* 2.9 27.5 + - + +
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Residues in contact with MET 548 (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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460A LEU* 5.3 0.9 - - + -
463A CYS* 4.1 20.2 - - + -
544A PHE* 3.0 38.3 + - + +
545A GLY* 2.7 14.3 + - - +
547A LEU* 1.3 80.6 - - + +
549A TRP* 1.3 70.4 + - - +
551A VAL* 2.8 15.7 + - - +
552A PHE* 3.0 25.1 + - + -
587A VAL* 4.1 17.3 - - + -
590A ILE* 4.6 19.5 - - + -
591A MET* 4.1 24.2 - - + -
594A CYS* 4.8 11.4 - - - -
612A LEU* 4.6 14.6 - - + -
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Residues in contact with TRP 549 (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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545A GLY 2.7 12.2 + - - +
546A VAL* 2.8 17.9 - - - +
547A LEU 2.8 0.2 + - - -
548A MET* 1.3 77.0 - - - +
550A GLU* 1.3 67.7 + - + -
552A PHE* 2.7 12.3 + - - +
553A SER* 2.9 32.5 + - - -
556A LYS* 2.6 37.7 - - + -
557A ILE 3.8 6.7 - - - -
558A PRO* 3.3 33.2 - - + -
577A LEU* 3.2 43.0 - - + +
578A TYR* 3.4 43.4 + + - -
580A PRO* 3.7 13.3 - - + +
591A MET* 3.4 32.2 - - + +
595A TRP* 4.4 0.4 - - + -
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Residues in contact with GLU 550 (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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444A SER* 5.3 1.4 + - - -
447A LEU* 4.2 4.0 - - + -
485A ALA* 3.4 32.2 + - + +
524A TRP* 2.6 44.5 + - - -
546A VAL 3.2 7.9 - - - +
547A LEU* 2.4 30.7 + - - +
549A TRP* 1.3 81.4 - - + +
551A VAL* 1.3 68.4 + - - +
552A PHE 2.9 0.9 + - - -
553A SER* 3.0 15.3 + - - -
555A GLY* 3.0 24.5 + - - +
556A LYS 3.8 14.3 + - - +
557A ILE* 5.0 1.6 - - - +
558A PRO* 4.1 3.8 - - + +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.7 27.8 - - + -
447A LEU* 3.7 12.9 - - + +
459A LEU* 3.4 47.9 - - + +
462A MET* 5.0 7.0 - - + -
463A CYS* 3.6 17.7 - - - +
466A VAL* 5.8 0.4 - - + -
547A LEU* 2.9 19.5 + - + +
548A MET* 2.8 14.5 + - - +
550A GLU* 1.3 76.8 - - - +
552A PHE* 1.3 78.1 + - + +
554A GLU* 3.2 10.6 + - - -
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Residues in contact with PHE 552 (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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456A ALA* 5.6 5.4 - - + -
459A LEU* 4.0 16.4 - - + -
460A LEU* 4.1 18.2 - - + -
463A CYS* 3.7 16.2 - - - -
548A MET* 3.4 20.6 - - + -
549A TRP* 2.7 12.4 + - - +
551A VAL* 1.3 90.7 - - + +
553A SER* 1.3 52.5 + - - +
554A GLU* 2.5 18.8 + - - +
580A PRO* 3.7 17.2 - - + +
581A ARG* 5.9 0.3 - - - +
582A LEU* 3.3 35.2 - - + +
583A ALA* 3.2 30.1 - - + +
584A SER* 4.3 0.7 - - - -
587A VAL* 3.7 36.1 - - + -
591A MET* 5.6 1.1 - - - -
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Residues in contact with SER 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A TRP* 2.9 52.3 + - - -
550A GLU* 3.0 3.0 + - - -
552A PHE* 1.3 69.0 - - - +
554A GLU* 1.3 54.5 + - - +
555A GLY 2.5 19.3 + - - -
556A LYS* 2.9 32.8 + - - +
578A TYR* 5.0 2.7 - - - -
580A PRO* 3.7 21.9 - - - +
581A ARG* 6.5 0.9 - - - -
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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
------------------------------------------------------------
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