Contacts of the helix formed by residues 613 - 622 (chain C) in PDB entry 3UEO
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 ASN 613 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563C PHE* 4.0 16.3 - - + -
571C ILE* 3.7 28.3 - - + -
595C VAL* 3.8 4.9 - - + +
596C VAL 3.5 5.3 + - - -
597C PRO* 4.6 0.2 - - - +
598C LEU* 4.2 19.8 - - - +
612C THR* 1.3 74.3 - - - +
614C THR* 1.3 67.6 + - - +
616C LEU* 3.3 10.5 - - + +
617C VAL* 2.7 50.2 + - + +
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Residues in contact with THR 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C LEU* 3.7 9.6 - - - +
612C THR* 3.0 11.3 + - - -
613C ASN* 1.3 87.4 + - - +
615C TRP* 1.3 61.1 + - - +
617C VAL* 4.9 0.4 - - - -
618C THR* 2.5 41.7 + - - +
633C LEU* 3.7 23.3 - - + +
634C PHE* 4.5 3.8 - - + -
659C ALA* 4.1 19.8 - - - +
660C GLU* 4.4 3.4 - - - +
663C SER* 2.7 30.2 + - - +
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Residues in contact with TRP 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C PHE* 4.4 7.9 - + - -
558C PHE* 4.4 8.1 - + - -
593C TYR* 4.0 29.6 - + - -
611C VAL* 3.4 33.4 - - + -
612C THR* 3.0 13.2 + - - +
614C THR* 1.3 79.0 - - - +
616C LEU* 1.3 90.4 + - + +
618C THR* 3.2 1.9 + - - -
619C CYS* 2.8 44.6 + - - +
625C LEU* 3.7 31.0 - - + -
626C PHE 2.8 24.9 + - - -
628C PRO* 4.1 7.8 - - + +
634C PHE* 3.5 59.8 - + + +
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Residues in contact with LEU 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C PHE* 3.5 33.4 - - + -
558C PHE* 4.1 11.7 - - + -
571C ILE* 3.7 30.7 - - + -
574C ILE* 3.8 20.4 - - + -
575C ILE* 3.9 8.1 - - + -
595C VAL* 4.7 10.1 - - + -
612C THR 3.0 8.5 + - - +
613C ASN* 3.3 12.1 - - + +
615C TRP* 1.3 100.2 - - + +
617C VAL* 1.3 66.7 + - + +
619C CYS* 3.1 10.4 + - - +
620C ILE* 3.1 24.2 + - + +
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Residues in contact with VAL 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C ILE* 6.6 0.2 - - + -
574C ILE* 5.0 15.0 - - + -
613C ASN* 2.7 34.2 + - + +
614C THR* 4.9 0.7 - - - -
616C LEU* 1.3 79.0 - - + +
618C THR* 1.3 61.3 + - - +
620C ILE* 3.4 8.3 + - - +
621C ASP* 3.0 48.2 + - - +
659C ALA* 3.8 20.2 - - + +
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Residues in contact with THR 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C THR* 2.5 27.0 + - - +
615C TRP 3.5 3.6 - - - -
617C VAL* 1.3 78.3 - - - +
619C CYS* 1.3 64.1 + - - +
621C ASP* 3.0 17.1 + - + +
622C TYR* 3.2 27.0 + - + +
626C PHE* 4.0 17.5 - - + -
634C PHE* 4.0 25.6 - - + -
659C ALA* 3.7 14.9 - - - +
660C GLU* 4.5 7.0 + - + +
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Residues in contact with CYS 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C LEU* 4.1 2.9 - - + +
553C PHE* 4.5 14.6 - - + -
615C TRP* 2.8 46.4 + - - +
616C LEU* 3.1 10.1 + - - +
618C THR* 1.3 73.7 - - - +
620C ILE* 1.3 57.0 + - - +
622C TYR* 3.3 0.7 + - - -
623C GLN* 2.8 24.6 + - - -
624C THR 3.1 29.6 + - - +
625C LEU* 3.8 4.7 - - - -
626C PHE* 3.3 29.8 - - - -
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Residues in contact with ILE 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C LEU* 4.7 7.2 - - + -
553C PHE* 4.3 20.0 - - + -
574C ILE* 3.7 40.2 - - + +
578C ASN* 3.5 41.7 - - - +
616C LEU* 3.1 19.8 + - + +
617C VAL* 3.8 6.7 - - - +
618C THR 3.2 0.2 - - - -
619C CYS* 1.3 75.3 - - - +
621C ASP* 1.3 65.3 + - - +
623C GLN* 2.8 36.8 + - - +
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Residues in contact with ASP 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C VAL* 3.0 34.0 + - - +
618C THR* 3.0 8.4 + - + +
620C ILE* 1.3 81.9 - - - +
622C TYR* 1.3 71.5 + - + +
623C GLN* 5.1 1.6 - - - +
658C GLY* 5.3 3.5 - - - -
659C ALA* 4.8 9.2 + - - +
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Residues in contact with TYR 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C THR* 3.2 21.4 + - + +
619C CYS 4.1 0.7 - - - +
620C ILE 3.1 0.2 - - - -
621C ASP* 1.3 86.9 - - + +
623C GLN* 1.3 71.6 + - - +
624C THR* 3.3 11.5 + - - +
626C PHE* 3.3 42.4 - + + -
657C ALA* 5.6 6.1 - - - +
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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