Contacts of the helix formed by residues 611 - 619 (chain A) in PDB entry 5UO5
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 ILE 611 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ARG* 4.1 21.5 - - - +
559A PHE* 5.2 0.2 - - + -
562A LEU* 6.2 0.4 - - + -
564A LEU* 3.5 31.9 - - + -
603A TYR* 2.9 40.4 + - + +
604A CYS* 4.4 0.4 - - - +
609A TYR* 3.9 19.3 - - + +
610A ASN* 1.3 71.0 - - - +
612A LEU* 1.3 67.7 + - - +
613A GLU 3.2 2.9 - - - -
614A GLU* 3.1 16.7 + - - +
615A VAL* 3.0 30.5 + - + +
638A ILE* 3.7 28.5 - - + -
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Residues in contact with LEU 612 (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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604A CYS* 3.6 38.1 - - + +
606A ASN* 5.8 2.7 - - - +
610A ASN* 3.5 7.9 - - - +
611A ILE* 1.3 79.1 - - - +
613A GLU* 1.3 58.2 + - - +
615A VAL* 3.4 1.6 + - - +
616A ALA* 2.9 32.2 + - - +
630A TRP* 4.1 10.4 - - + -
631A LYS* 3.7 53.2 - - + +
634A ALA* 3.9 9.4 - - + +
635A LEU* 3.9 15.5 - - + +
638A ILE* 4.1 4.7 - - + -
692B ILE* 4.2 19.7 - - + -
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Residues in contact with GLU 613 (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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610A ASN* 4.8 6.5 + - - +
611A ILE 3.2 1.2 - - - -
612A LEU* 1.3 79.9 - - - +
614A GLU* 1.3 56.4 + - - +
616A ALA* 3.2 2.8 + - - +
617A LYS* 2.9 59.6 + - + +
623A MET* 3.5 28.0 - - + +
630A TRP* 4.3 6.5 - - + -
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Residues in contact with GLU 614 (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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521A ARG* 4.8 11.3 + - - -
562A LEU* 3.7 30.8 - - + +
611A ILE* 3.1 18.3 + - + +
613A GLU* 1.3 79.3 - - - +
615A VAL* 1.3 62.6 + - + +
617A LYS* 3.4 10.7 + - + +
618A LYS* 3.2 32.5 + - + +
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Residues in contact with VAL 615 (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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558A TRP* 4.4 10.3 - - + -
559A PHE* 4.4 6.3 - - + -
562A LEU* 4.0 23.1 - - + -
611A ILE* 3.0 28.2 + - + +
612A LEU 3.8 3.6 - - - +
614A GLU* 1.3 76.0 - - + +
616A ALA* 1.3 62.8 + - - +
618A LYS* 3.2 8.0 + - - +
619A MET* 3.0 41.8 + - + +
634A ALA* 4.2 7.4 - - + +
637A GLU* 5.1 1.3 - - + -
638A ILE* 3.6 37.9 - - + -
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Residues in contact with ALA 616 (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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612A LEU 2.9 19.5 + - - +
613A GLU 3.6 3.8 - - - +
615A VAL* 1.3 76.8 - - - +
617A LYS* 1.3 59.3 - - - +
619A MET* 3.2 2.9 + - - +
620A ASN 3.1 4.2 + - - -
621A LEU* 3.0 46.6 + - + -
623A MET* 3.7 10.8 - - + -
630A TRP* 3.4 29.2 - - + -
634A ALA* 4.3 5.3 - - + +
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Residues in contact with LYS 617 (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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613A GLU* 2.9 51.3 + - + +
614A GLU* 3.7 10.5 - - + +
616A ALA* 1.3 76.8 - - - +
618A LYS* 1.3 58.2 + - + +
620A ASN* 3.1 24.5 + - - +
621A LEU 5.0 0.9 - - - +
623A MET* 3.7 17.7 - - - -
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Residues in contact with LYS 618 (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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558A TRP* 3.5 73.3 + - + +
561A ASP* 4.7 11.7 + - - +
562A LEU* 3.9 18.8 - - + +
614A GLU* 3.2 20.7 + - + +
615A VAL 3.2 2.7 + - - +
617A LYS* 1.3 73.7 - - + +
619A MET* 1.3 58.7 + - - +
620A ASN* 3.1 14.7 + - - +
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Residues in contact with MET 619 (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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556A PHE* 4.2 16.4 - - + -
558A TRP* 3.7 19.7 - - + -
615A VAL* 3.0 34.3 + - - +
616A ALA 3.2 6.0 + - - +
618A LYS* 1.3 74.6 - - - +
620A ASN* 1.3 70.2 + - - +
621A LEU* 3.3 30.6 + - + +
633A GLN* 4.4 10.8 - - + +
634A ALA* 4.1 11.0 - - - -
637A GLU* 3.5 37.9 - - + +
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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