Contacts of the helix formed by residues 533 - 547 (chain B) in PDB entry 3T6A
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 GLU 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526B PRO* 4.7 5.4 - - - +
528B GLU 4.9 1.0 - - - +
529B ASN* 3.8 16.1 - - + +
530B LYS* 3.1 51.2 + - + +
531B PRO 3.1 2.9 + - - -
532B LEU* 1.3 74.7 - - - +
534B THR* 1.3 66.9 + - - +
535B ALA* 3.2 2.0 - - + +
536B LEU* 3.0 27.8 + - + +
537B LEU* 3.0 21.7 + - - +
786B LEU* 4.6 1.2 + - - +
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Residues in contact with THR 534 (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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532B LEU 3.1 7.3 + - - -
533B GLU* 1.3 74.1 - - - +
535B ALA* 1.3 59.4 + - + +
537B LEU* 3.9 6.3 - - - +
538B LYS* 3.0 29.1 + - - +
616B CYS* 5.7 0.2 - - - -
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Residues in contact with ALA 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B GLU* 3.2 1.7 - - + +
534B THR* 1.3 80.9 + - + +
536B LEU* 1.3 61.1 + - + +
538B LYS* 3.5 9.6 - - + +
539B ARG* 2.9 30.0 + - - +
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Residues in contact with LEU 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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524B PHE 4.8 5.8 - - - +
525B LEU* 4.3 13.9 - - + -
526B PRO* 4.3 18.2 - - + -
529B ASN* 3.8 34.8 - - + +
533B GLU* 3.0 28.9 + - + +
535B ALA* 1.3 76.8 - - + +
537B LEU* 1.3 67.3 + - - +
539B ARG* 3.1 9.1 + - + +
540B ALA* 3.0 23.2 + - - +
782B PHE* 6.2 0.9 - - + -
786B LEU* 3.6 29.3 - - + +
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Residues in contact with LEU 537 (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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532B LEU* 3.5 54.7 - - + +
533B GLU 3.0 14.9 + - - +
534B THR* 4.0 6.1 - - - +
536B LEU* 1.3 75.7 - - - +
538B LYS* 1.3 63.3 + - - +
540B ALA* 3.5 5.0 + - + +
541B LYS* 3.0 24.4 + - - +
611B VAL* 4.8 16.4 - - + -
615B GLY* 6.4 0.9 - - - -
616B CYS* 3.7 18.0 - - + +
786B LEU* 4.0 24.0 - - + +
787B LEU* 5.5 2.5 - - + -
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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
----------------------------------------------------------
534B THR* 3.0 21.8 + - - +
535B ALA* 3.5 10.3 - - + +
536B LEU 3.1 0.2 - - - -
537B LEU* 1.3 76.6 - - - +
539B ARG* 1.3 63.0 + - - +
541B LYS* 3.3 5.2 + - + +
542B GLU* 3.0 47.6 + - + +
616B CYS* 4.1 13.2 - - - -
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Residues in contact with ARG 539 (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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535B ALA 2.9 17.8 + - - +
536B LEU* 3.5 9.9 - - + +
538B LYS* 1.3 78.4 - - - +
540B ALA* 1.3 63.3 + - - +
542B GLU* 3.2 43.5 + - - +
543B LEU* 3.2 27.9 + - + +
546B ASN* 4.9 7.1 - - - +
773B GLU* 2.6 46.0 + - - +
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Residues in contact with ALA 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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536B LEU 3.0 15.0 + - - +
537B LEU* 3.9 5.2 - - + +
539B ARG* 1.3 77.5 - - - +
541B LYS* 1.3 64.0 + - - +
543B LEU* 2.9 18.5 + - - +
544B PHE* 3.1 21.0 + - + -
777B ILE* 3.1 32.7 - - + +
782B PHE* 6.0 0.7 - - + -
786B LEU* 4.3 14.1 - - + -
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Residues in contact with LYS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LEU 3.0 14.0 + - - +
538B LYS* 3.3 9.9 - - + +
540B ALA* 1.3 75.4 - - - +
542B GLU* 1.3 59.0 + - + +
544B PHE* 3.2 10.9 + - + +
545B THR* 2.9 47.1 + - - +
612B ASP* 3.2 29.2 + - - +
616B CYS* 3.5 37.2 + - + +
617B THR* 5.2 0.4 - - - -
626B THR* 2.7 35.1 + - - +
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Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B LYS* 3.0 43.7 + - + +
539B ARG* 3.3 37.3 + - - +
540B ALA 3.2 0.2 - - - -
541B LYS* 1.3 76.3 - - + +
543B LEU* 1.3 53.0 + - - +
545B THR* 3.2 6.5 + - - -
546B ASN* 2.8 49.7 + - - +
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Residues in contact with LEU 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 ARG* 3.2 34.0 + - + +
540B ALA* 2.9 12.6 + - - +
542B GLU* 1.3 78.5 - - - +
544B PHE* 1.3 65.8 + - + +
545B THR 3.3 0.3 + - - -
546B ASN* 3.4 6.9 + - + +
547B ASN* 2.8 42.7 + - - +
771B ASP* 4.9 9.2 - - - +
773B GLU* 3.8 39.3 - - + +
774B MET* 3.8 19.4 - - + +
777B ILE* 4.5 17.7 - - + -
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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
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540B ALA* 3.1 14.9 + - + -
541B LYS* 3.9 9.9 - - + +
543B LEU* 1.3 77.5 - - + +
545B THR* 1.3 53.4 + - - +
547B ASN 3.6 1.7 - - - +
552B ILE* 3.5 32.2 - - + +
609B ILE* 6.3 3.6 - - + -
612B ASP* 4.4 20.0 - - + +
629B LYS* 2.7 34.5 - - + -
774B MET* 3.9 19.3 - - - -
777B ILE* 3.7 45.8 - - + -
778B CYS* 5.4 5.4 - - - -
783B GLN* 6.4 0.2 - - - -
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Residues in contact with THR 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B LYS* 2.9 40.0 + - - +
542B GLU* 3.5 8.3 - - - -
544B PHE* 1.3 79.9 - - - +
546B ASN* 1.3 69.5 + - - +
547B ASN 3.2 1.8 + - - -
629B LYS* 3.8 16.6 + - - +
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Residues in contact with ASN 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ARG* 4.9 7.1 - - - +
542B GLU* 2.8 35.6 + - - +
543B LEU* 3.4 5.9 + - + +
545B THR* 1.3 82.5 - - - +
547B ASN* 1.3 65.2 + - - +
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Residues in contact with ASN 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 LEU* 2.8 37.5 + - - +
544B PHE 3.6 1.6 + - - +
545B THR 3.2 0.8 - - - -
546B ASN* 1.3 87.2 - - - +
548B ASP* 1.3 65.4 + - - +
551B VAL* 4.3 16.1 - - + +
552B ILE* 3.7 10.6 - - + +
629B LYS* 3.0 27.5 + - - -
771B ASP* 5.8 1.1 + - - +
774B MET* 3.0 27.9 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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