Contacts of the helix formed by residues 535 - 553 (chain B) in PDB entry 6GYS
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 HIS 535 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520B LEU* 3.4 24.0 - - + -
521B TRP* 3.3 46.8 + + + -
524B VAL* 2.7 34.9 + - + -
525B GLN 3.3 25.6 - - - -
526B LEU* 3.7 6.7 - - + -
534B TYR* 1.3 75.6 - - - +
536B PRO* 1.3 74.5 - - + +
537B VAL* 3.1 25.4 + - + +
538B PHE* 3.2 27.7 - - + +
539B LYS* 3.3 5.7 + - - +
590B PHE* 3.5 10.4 - - - -
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Residues in contact with PRO 536 (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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520B LEU* 4.7 5.6 - - + -
524B VAL* 3.8 16.6 - - + -
525B GLN 5.1 0.7 - - - +
535B HIS* 1.3 93.8 - - + +
537B VAL* 1.3 58.4 + - - +
539B LYS* 3.7 3.8 - - + +
540B ILE* 2.9 36.4 + - + +
590B PHE* 3.8 22.7 - - + -
593B ILE* 3.7 50.5 - - + -
594B VAL* 3.9 7.4 - - + +
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Residues in contact with VAL 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 6.2 0.2 - - + -
475B ILE* 5.8 1.1 - - + -
476B PHE* 4.0 25.8 - - + -
517B LEU* 3.7 41.1 - - + -
520B LEU* 4.1 3.6 - - + -
521B TRP* 3.7 30.3 - - + +
535B HIS* 3.1 26.8 + - + +
536B PRO* 1.3 72.6 - - - +
538B PHE* 1.3 71.3 + - + +
540B ILE* 3.4 1.7 + - - +
541B LEU* 3.0 30.5 + - + +
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Residues in contact with PHE 538 (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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1B MET* 3.1 53.4 - - + +
57B TYR* 4.4 20.9 - + + -
61B LEU* 4.3 17.9 - - + -
476B PHE* 5.2 1.3 - + - -
521B TRP* 4.2 17.9 - + - -
526B LEU* 3.6 23.3 - - + -
533B PHE* 3.2 30.5 - - + -
534B TYR* 3.7 3.8 - + + -
535B HIS* 3.2 22.4 - - + +
537B VAL* 1.3 77.4 - - + +
539B LYS* 1.3 52.0 - - + +
541B LEU* 2.8 12.2 + - + +
542B GLN* 2.8 37.4 + - + +
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B HIS 3.3 10.4 + - - +
536B PRO* 3.3 4.5 + - + +
538B PHE* 1.3 77.9 - - - +
540B ILE* 1.3 61.5 + - - +
542B GLN* 4.1 9.6 - - + +
543B ASN* 2.7 56.7 + - - +
546B LYS* 5.8 2.2 - - - +
590B PHE* 4.5 18.4 - - + -
591B ARG* 5.9 9.0 - - - -
594B VAL* 3.8 24.1 - - + +
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Residues in contact with ILE 540 (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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513B ARG* 3.6 19.3 - - - +
517B LEU* 3.7 29.4 - - + -
520B LEU* 3.9 13.2 - - + -
536B PRO* 2.9 22.7 + - + +
537B VAL 3.6 4.0 - - - +
539B LYS* 1.3 74.9 - - - +
541B LEU* 1.3 65.9 + - + +
543B ASN* 3.0 5.8 + - - +
544B ASP* 2.9 47.6 + - - +
594B VAL* 3.9 26.9 - - + +
597B PHE* 3.7 24.2 - - + -
598B GLN* 5.1 6.6 + - + +
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Residues in contact with LEU 541 (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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61B LEU* 5.6 4.5 - - + -
64B PHE* 3.2 33.4 - - + -
65B TRP* 6.2 0.2 - - + -
68B TYR* 4.1 29.0 - - + +
472B PHE* 4.2 25.4 - - + -
513B ARG* 4.5 3.6 - - - +
514B LEU* 6.0 4.0 - - + -
517B LEU* 4.2 15.7 - - + -
537B VAL* 3.0 32.1 + - + +
538B PHE* 2.8 8.7 + - + +
540B ILE* 1.3 78.1 - - + +
542B GLN* 1.3 61.1 + - - +
543B ASN 3.3 0.7 + - - -
544B ASP* 3.1 26.0 + - - +
545B ILE* 3.7 10.7 + - - +
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Residues in contact with GLN 542 (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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1B MET* 3.1 39.7 + - - +
2B PHE* 5.3 7.4 - - + -
64B PHE* 3.2 35.9 - - - -
538B PHE* 2.8 21.9 + - + +
539B LYS* 4.2 12.1 - - + +
541B LEU* 1.3 77.3 - - - +
543B ASN* 1.3 64.9 + - - +
545B ILE* 4.5 3.8 + - - +
546B LYS* 3.4 30.3 + - - +
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Residues in contact with ASN 543 (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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539B LYS* 2.7 54.5 + - - +
540B ILE 3.0 3.8 + - - +
542B GLN* 1.3 78.7 - - - +
544B ASP* 1.3 61.9 + - - +
545B ILE 3.3 2.2 - - - -
546B LYS* 3.1 32.1 + - + +
547B ILE* 2.8 34.6 + - + +
594B VAL* 5.2 5.7 - - - +
598B GLN* 5.1 9.6 - - - +
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Residues in contact with ASP 544 (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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68B TYR* 4.1 15.3 - - + -
513B ARG* 3.2 27.2 + - - -
540B ILE* 2.9 38.1 + - - +
541B LEU* 3.1 21.9 + - - +
543B ASN* 1.3 76.7 - - - +
545B ILE* 1.3 58.9 + - - +
547B ILE* 3.3 18.9 + - - +
548B ILE* 3.0 37.1 + - + +
598B GLN* 4.2 4.5 + - - -
603B ILE* 4.4 10.7 - - + +
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Residues in contact with ILE 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.6 35.4 - - + -
67B ASN* 4.5 7.4 - - + +
68B TYR* 3.6 46.9 - - + +
71B TRP* 3.9 19.1 - - + +
72B ILE* 5.6 0.9 - - + -
541B LEU 3.7 3.8 + - - +
542B GLN 4.6 4.5 - - - +
543B ASN 3.3 0.2 - - - -
544B ASP* 1.3 75.2 - - - +
546B LYS* 1.3 59.1 + - + +
548B ILE* 4.2 4.9 - - - +
549B GLU* 2.8 55.7 + - + +
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Residues in contact with LYS 546 (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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539B LYS* 5.8 2.4 - - - +
542B GLN* 3.4 21.9 - - - +
543B ASN* 3.1 30.4 + - + +
545B ILE* 1.3 76.7 - - + +
547B ILE* 1.3 59.8 + - - +
549B GLU* 4.1 7.0 - - - +
550B LEU* 2.9 32.1 + - - +
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Residues in contact with ILE 547 (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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543B ASN* 2.8 21.0 + - + +
544B ASP* 3.3 11.9 - - - +
546B LYS* 1.3 75.4 - - - +
548B ILE* 1.3 64.4 + - + +
550B LEU* 3.2 8.6 + - - +
551B LYS* 2.9 40.5 + - + +
598B GLN* 3.9 25.4 - - - +
602B ASN* 5.1 3.4 - - - +
603B ILE* 3.7 35.0 - - + -
604B SER* 4.3 10.8 - - - +
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Residues in contact with ILE 548 (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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71B TRP* 4.9 9.6 - - + +
72B ILE* 3.7 28.9 - - + -
76B GLY* 4.2 21.8 - - - -
80B THR* 6.4 1.1 - - + -
544B ASP* 3.0 19.2 + - + +
545B ILE* 4.2 4.0 - - - +
547B ILE* 1.3 87.3 - - + +
549B GLU* 1.3 54.0 + - + +
551B LYS* 3.3 11.7 - - + +
552B ASN* 2.6 49.1 + - - +
603B ILE* 3.8 25.1 - - + +
606B ILE* 5.4 5.6 - - + -
607B LEU* 5.8 9.4 - - + -
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Residues in contact with GLU 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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71B TRP* 2.9 58.1 + - + -
545B ILE* 2.8 32.0 + - - +
546B LYS* 4.2 6.5 - - - +
548B ILE* 1.3 75.0 - - + +
550B LEU* 1.3 52.9 + - - +
552B ASN* 3.3 7.1 - - - +
553B ASP* 2.5 36.1 + - - +
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Residues in contact with LEU 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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546B LYS 2.9 19.9 + - - +
547B ILE* 3.4 8.1 - - - +
549B GLU* 1.3 75.5 - - - +
551B LYS* 1.3 59.6 + - - +
553B ASP* 3.0 35.3 - - + +
556B PHE* 4.2 26.8 - - + -
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Residues in contact with LYS 551 (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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80B THR* 5.3 6.7 - - + +
82B GLN* 3.4 24.4 - - - +
547B ILE* 2.9 28.1 + - + +
548B ILE* 3.3 17.2 - - + +
550B LEU* 1.3 77.7 - - - +
552B ASN* 1.3 59.5 + - - +
553B ASP 3.7 1.6 - - - +
554B GLU* 2.6 30.3 - - - +
604B SER* 3.0 29.7 + - - -
607B LEU* 3.1 31.1 - - + +
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Residues in contact with ASN 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TRP* 3.7 28.5 - - + -
75B ILE* 4.3 7.5 - - - +
80B THR* 2.9 37.3 + - - +
306B PRO* 5.2 4.0 - - + -
307B ARG* 3.3 33.0 + - - +
548B ILE* 2.6 41.5 + - - +
549B GLU* 3.1 6.7 + - - +
551B LYS* 1.3 72.5 - - - +
553B ASP* 1.3 61.0 + - - +
554B GLU* 2.9 11.3 + - - +
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Residues in contact with ASP 553 (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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549B GLU 2.5 20.0 + - - +
550B LEU* 3.0 32.2 - - + +
551B LYS 3.2 3.3 - - - +
552B ASN* 1.3 70.5 - - - +
554B GLU* 1.3 57.9 + - - +
555B MET* 3.2 36.9 + - - +
556B PHE* 4.3 13.9 + - - +
267C PHE 5.7 0.7 - - - +
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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