Contacts of the helix formed by residues 536 - 553 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ILE* 4.3 7.8 - - - +
528B GLU* 4.6 4.2 + - - -
534B ARG* 4.0 6.9 + - - -
535B TYR* 1.3 78.1 - - - +
537B SER* 1.3 58.9 + - - +
538B LYS* 2.4 32.6 + - - +
539B SER* 2.5 23.9 + - - -
599B PRO* 5.1 7.8 - - - +
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Residues in contact with SER 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B GLU* 3.7 34.7 + - - +
478B VAL 5.1 3.6 - - - -
479B ILE* 3.6 23.5 - - - +
536B SER* 1.3 71.9 - - - +
538B LYS* 1.3 61.2 + - - +
539B SER* 2.9 10.8 + - - -
540B ASP* 3.4 15.0 + - - +
541B VAL* 3.0 24.7 + - - +
605B PHE* 3.5 7.2 - - - -
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Residues in contact with LYS 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B GLU* 5.7 0.7 - - - +
536B SER* 2.4 26.7 + - - +
537B SER* 1.3 73.7 - - - +
539B SER* 1.3 66.1 - - - +
540B ASP 3.0 2.0 - - - -
541B VAL* 3.0 26.1 + - + +
542B TRP 3.2 4.3 + - - -
599B PRO* 4.5 17.7 - - + +
600B GLU* 4.5 8.6 + - - +
602B ARG* 2.6 55.3 + - + +
603B PRO* 3.0 29.5 + - - +
604B ALA* 3.7 13.9 - - - +
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Residues in contact with SER 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ILE* 4.5 0.5 - - - +
526B SER* 3.6 19.8 + - - -
528B GLU* 4.0 9.4 - - - -
529B VAL* 4.3 1.1 - - - +
535B TYR* 3.4 29.4 - - - +
536B SER* 2.5 35.5 + - - -
537B SER* 2.9 9.4 + - - -
538B LYS* 1.3 80.5 - - - +
540B ASP* 1.3 68.1 + - - +
542B TRP* 3.4 8.1 + - - +
543B SER* 3.2 18.9 + - - -
602B ARG* 4.4 0.9 - - - +
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Residues in contact with ASP 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B MET* 5.3 3.2 - - - +
478B VAL 4.9 1.0 - - - +
479B ILE* 4.2 5.7 - - - +
480B HIS* 2.7 42.5 + - - +
481B ARG* 4.2 3.5 - - - -
482B ASP 4.1 4.3 + - - -
483B LEU* 4.6 9.4 + - + -
535B TYR* 5.2 3.1 - - - -
537B SER* 3.4 20.7 + - - +
538B LYS 3.0 0.2 - - - -
539B SER* 1.3 79.0 + - - +
541B VAL* 1.3 51.2 + - - +
542B TRP 2.3 8.6 + - - -
543B SER* 2.2 41.2 + - - -
544B PHE* 2.3 16.0 + - - -
605B PHE* 4.3 10.5 - - + -
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Residues in contact with VAL 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B GLU* 4.6 1.8 - - - +
537B SER 3.0 17.5 - - - +
538B LYS* 3.2 22.2 - - + +
540B ASP* 1.3 78.6 - - - +
542B TRP* 1.3 53.9 + - - +
544B PHE* 3.0 5.4 - - - +
545B GLY 2.9 19.6 + - - -
594B CYS* 3.3 33.3 - - - +
602B ARG* 4.5 8.5 - - + -
603B PRO* 3.9 25.6 - - + +
605B PHE* 3.1 32.0 - - + +
608B LEU* 4.2 12.1 - - + -
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Residues in contact with TRP 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LYS 4.8 1.2 + - - -
524B TRP 4.7 0.2 - - - -
525B ALA 4.1 16.5 + - - -
526B SER* 3.9 13.9 - - - -
527B PRO* 3.1 36.3 - - + -
530B PHE* 5.5 0.2 - + - -
538B LYS 3.2 5.3 + - - +
539B SER 3.5 10.3 - - - +
540B ASP 2.3 10.5 + - - -
541B VAL* 1.3 69.4 - - - +
543B SER* 1.3 55.2 + - - +
544B PHE 2.6 6.4 + - - -
545B GLY* 2.5 22.2 + - - +
546B VAL* 3.0 30.6 + - + +
559B TYR* 4.4 5.5 + - - -
571B ILE* 3.7 22.8 - - + +
576B ARG* 3.5 26.2 - - - -
594B CYS* 3.2 28.0 + - - +
595B TRP* 3.3 44.6 - + + +
596B LYS 3.6 13.7 - - - -
602B ARG* 4.1 4.0 - - - +
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Residues in contact with SER 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ASP* 5.4 2.2 - - - -
483B LEU* 2.9 40.8 - - - +
524B TRP* 2.4 38.0 + - - +
525B ALA* 4.3 2.4 - - - -
535B TYR* 6.0 2.4 - - - -
539B SER 3.2 12.6 + - - -
540B ASP* 2.2 31.7 + - - -
542B TRP* 1.3 71.3 - - - +
544B PHE* 1.3 56.0 + - - -
547B LEU* 3.6 13.3 + - - +
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Residues in contact with PHE 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B CYS* 3.7 26.9 - - + -
466B VAL* 4.2 12.8 - - + -
467B CYS* 3.9 21.1 - - + -
483B LEU* 3.3 25.8 - - + -
540B ASP 2.3 20.1 + - - +
541B VAL* 3.0 19.5 - - - +
542B TRP 2.6 0.6 + - - -
543B SER* 1.3 71.2 - - - +
545B GLY* 1.3 58.5 + - - -
547B LEU* 4.5 5.2 - - + -
548B MET* 3.0 53.8 + - + +
590B ILE* 5.9 1.3 - - + -
594B CYS* 4.1 11.0 - - - -
605B PHE* 3.8 17.3 - + + -
608B LEU* 4.3 18.4 - - + -
612B LEU* 4.4 7.6 - - + -
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Residues in contact with GLY 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B VAL 2.9 5.9 + - - -
542B TRP 2.5 13.7 + - - -
544B PHE* 1.3 70.4 - - - +
546B VAL* 1.3 64.6 + - - -
548B MET* 2.8 12.0 - - - +
549B TRP* 2.7 20.6 + - - +
591B MET* 4.8 3.5 - - - +
594B CYS* 3.7 25.4 - - - -
595B TRP* 3.7 14.6 - - - -
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Residues in contact with VAL 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LYS 3.9 10.8 - - - +
524B TRP* 3.1 35.2 - - + +
542B TRP* 3.0 37.8 + - + +
545B GLY* 1.3 72.7 - - - +
547B LEU* 1.3 68.4 + - - +
549B TRP* 2.6 26.5 + - - +
550B GLU* 3.0 2.6 + - - +
558B PRO* 3.6 30.5 - - + -
559B TYR* 3.8 18.2 - - + +
577B LEU* 4.7 0.7 - - + -
595B TRP* 3.4 8.5 - - + +
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Residues in contact with LEU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 4.2 8.5 - - + -
463B CYS* 6.2 0.2 - - - -
466B VAL* 4.4 9.6 - - + -
483B LEU* 3.6 18.8 - - + -
484B ALA* 3.2 32.3 - - - +
485B ALA* 3.0 24.5 - - + +
488B CYS* 3.7 14.1 - - - -
524B TRP* 3.4 4.4 - - - +
543B SER 3.6 14.8 + - - +
544B PHE* 4.2 5.8 - - + +
545B GLY 3.3 0.4 - - - -
546B VAL* 1.3 75.9 - - - +
548B MET* 1.3 60.9 + - - +
550B GLU* 2.4 49.3 + - - +
551B VAL* 3.1 19.1 + - + -
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Residues in contact with MET 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B CYS* 4.0 27.1 - - + -
544B PHE* 3.0 35.2 + - + +
545B GLY* 2.8 17.0 + - - +
547B LEU* 1.3 85.6 - - - +
549B TRP* 1.3 63.4 + - - +
551B VAL* 2.6 24.6 + - - +
552B PHE* 3.2 27.6 + - + -
587B VAL* 4.1 11.7 - - + +
590B ILE* 5.1 11.0 - - + -
591B MET* 3.3 37.5 - - + +
594B CYS* 5.2 0.7 - - - -
612B LEU* 5.0 12.8 - - + -
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Residues in contact with TRP 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B GLY 2.7 7.7 + - - +
546B VAL* 2.6 24.4 + - - +
548B MET* 1.3 68.6 - - - +
550B GLU* 1.3 80.4 + - + -
551B VAL 2.6 2.6 + - - -
552B PHE* 2.7 16.7 + - - +
553B SER* 2.8 35.0 + - - -
556B LYS* 2.4 33.4 - - + -
557B ILE 3.0 14.4 - - - -
558B PRO* 3.0 34.1 - - + -
577B LEU* 3.4 35.7 - - + +
578B TYR* 3.6 38.5 + + - -
580B PRO* 3.9 10.2 - - + +
591B MET* 3.4 33.1 - - + +
595B TRP* 4.3 0.7 - - + -
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Residues in contact with GLU 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B SER* 5.5 0.9 + - - -
447B LEU* 3.5 5.8 - - + +
485B ALA* 3.0 37.8 + - + +
524B TRP* 2.5 48.2 + - - +
546B VAL 3.6 6.3 - - - +
547B LEU* 2.4 20.7 + - - +
549B TRP* 1.3 91.7 - - + +
551B VAL* 1.3 58.7 + - - +
553B SER* 4.3 3.8 - - - -
554B GLU 3.3 1.0 + - - -
555B GLY* 2.7 34.3 + - - +
556B LYS 4.3 8.6 + - - +
557B ILE* 4.8 4.9 - - - +
558B PRO* 4.3 6.4 - - + +
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Residues in contact with VAL 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 4.0 26.5 - - + -
447B LEU* 3.8 9.6 - - + +
459B LEU* 3.1 51.2 - - + +
462B MET* 4.7 6.5 - - + -
463B CYS* 3.7 25.4 - - - -
466B VAL* 6.4 0.9 - - + -
547B LEU* 3.1 15.6 + - + -
548B MET* 2.6 14.9 + - - +
549B TRP 2.6 4.2 + - - -
550B GLU* 1.3 71.2 - - - +
552B PHE* 1.3 57.1 + - + +
554B GLU* 2.7 30.0 + - - -
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Residues in contact with PHE 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B ALA* 5.1 8.3 - - + -
459B LEU* 4.1 22.9 - - + -
460B LEU* 4.5 17.3 - - + -
463B CYS* 4.3 17.3 - - - -
548B MET* 3.6 28.5 - - + -
549B TRP* 2.7 10.2 + - - +
551B VAL* 1.3 74.9 - - + +
553B SER* 1.3 52.3 + - - +
554B GLU* 2.5 29.7 + - - +
580B PRO* 3.8 23.0 - - + +
581B ARG* 5.5 2.1 - - - +
582B LEU* 3.3 42.5 + - + +
583B ALA* 3.5 10.1 - - + +
584B SER* 5.3 0.4 - - - -
587B VAL* 3.5 36.6 - - + -
591B MET* 5.5 1.1 - - - -
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Residues in contact with SER 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B TRP* 2.8 70.0 + - - -
550B GLU* 3.4 1.8 - - - -
552B PHE* 1.3 69.5 - - - +
554B GLU* 1.3 52.6 + - - +
555B GLY 2.4 21.6 + - - -
556B LYS* 2.9 32.1 + - - +
578B TYR* 4.5 2.9 + - - -
580B PRO* 3.5 11.9 - - - +
581B ARG* 6.5 0.2 - - - -
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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