Contacts of the helix formed by residues 609 - 618 (chain B) in PDB entry 6HBU
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 THR 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423B ILE* 5.3 0.3 - - - +
588B GLY* 4.4 10.7 - - - -
589B GLN 3.6 10.8 + - - -
590B ASN* 3.7 11.6 + - - +
591B PHE* 4.2 3.1 - - - -
607B THR 4.2 4.9 - - - +
608B CYS* 1.3 81.5 - - + +
610B GLY* 1.3 68.2 + - - +
611B GLU* 3.4 18.4 + - + +
612B GLU* 3.4 42.0 + - + +
613B TYR* 3.7 7.8 + - - +
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Residues in contact with GLY 610 (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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586B PHE* 3.2 30.3 - - - +
587B LEU 5.3 0.2 - - - -
589B GLN 2.9 16.5 + - - +
591B PHE* 4.0 13.0 - - - -
609B THR* 1.3 75.4 + - - +
611B GLU* 1.3 63.6 + - - +
613B TYR* 3.3 14.9 + - - +
614B LEU* 3.4 15.9 - - - +
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Residues in contact with GLU 611 (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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586B PHE 3.8 5.8 + - - +
587B LEU* 4.9 12.1 - - + +
588B GLY* 5.1 11.4 + - - -
609B THR* 3.2 16.7 - - + +
610B GLY* 1.3 76.1 - - - +
612B GLU* 1.3 64.1 + - + +
614B LEU* 3.3 2.9 + - - +
615B VAL* 3.2 28.1 + - - +
621B LEU* 4.0 36.8 - - + +
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Residues in contact with GLU 612 (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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606B ALA 4.8 2.1 - - - +
607B THR* 4.0 13.5 - - + +
608B CYS* 3.2 29.8 + - - +
609B THR* 3.4 26.2 + - + +
610B GLY 3.3 0.4 - - - -
611B GLU* 1.3 76.4 - - + +
613B TYR* 1.3 62.1 + - - +
615B VAL* 4.1 8.0 - - - +
616B LYS* 3.4 20.4 + - - +
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Residues in contact with TYR 613 (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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423B ILE* 3.7 33.4 - - + +
424B GLN* 5.6 1.9 + - - -
427B ALA* 3.3 18.4 - - + +
554B LEU* 5.2 4.7 - - - +
582B GLN* 3.7 24.6 + - - -
586B PHE* 4.1 29.6 - + + -
607B THR* 5.3 9.4 - - + -
609B THR 3.7 5.9 + - - +
610B GLY* 3.3 14.5 + - - +
611B GLU 3.2 0.6 - - - -
612B GLU* 1.3 79.7 - - - +
614B LEU* 1.3 61.6 + - + +
616B LYS* 3.4 33.1 + - - +
617B GLN* 3.0 43.8 + - + +
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Residues in contact with LEU 614 (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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582B GLN* 3.9 8.5 - - + +
583B HIS* 3.5 37.7 - - + +
586B PHE* 3.6 26.7 - - + +
587B LEU* 5.0 1.8 - - + -
610B GLY 3.4 14.1 - - - +
611B GLU 3.3 8.3 + - - +
613B TYR* 1.3 87.4 - - + +
615B VAL* 1.3 60.8 + - - +
617B GLN* 3.7 4.7 - - - +
618B GLY 2.9 7.8 + - - -
619B ILE* 2.8 56.8 + - + +
621B LEU* 3.7 22.7 - - + -
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Residues in contact with VAL 615 (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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611B GLU 3.2 17.3 + - - +
612B GLU* 4.1 8.1 - - - +
613B TYR 3.4 0.2 - - - -
614B LEU* 1.3 75.7 - - - +
616B LYS* 1.3 63.0 + - - +
618B GLY* 3.4 10.7 + - - -
619B ILE 4.9 2.7 - - - +
621B LEU* 4.2 20.6 - - + -
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Residues in contact with LYS 616 (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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557B ASN* 4.5 16.4 + - - +
559B THR* 5.1 5.5 + - - +
607B THR* 4.8 16.8 - - + -
612B GLU 3.4 11.3 + - - +
613B TYR* 3.4 31.6 + - - +
614B LEU 3.3 0.4 - - - -
615B VAL* 1.3 80.5 - - - +
617B GLN* 1.3 80.1 + - - +
618B GLY 3.6 0.2 + - - -
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Residues in contact with GLN 617 (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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553B GLY* 3.2 25.9 + - - -
554B LEU* 6.1 0.6 - - - +
557B ASN* 4.9 14.2 + - - +
558B LEU* 5.4 9.2 - - - +
559B THR* 4.7 9.5 - - - +
578B PHE* 5.3 0.2 - - - -
582B GLN* 4.1 17.8 + - - +
613B TYR* 3.0 43.0 + - + +
614B LEU 4.0 0.9 - - - +
615B VAL 3.3 0.2 - - - -
616B LYS* 1.3 103.5 + - - +
618B GLY* 1.3 60.3 + - - +
619B ILE* 3.9 22.3 - - + +
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Residues in contact with GLY 618 (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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559B THR* 5.3 8.1 - - - -
575B ARG* 5.3 6.6 + - - -
614B LEU 2.9 7.5 + - - -
615B VAL* 3.4 8.4 + - - -
616B LYS 3.3 3.6 - - - -
617B GLN* 1.3 80.1 - - - +
619B ILE* 1.3 59.5 + - - +
620B ASP* 4.3 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
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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