Contacts of the helix formed by residues 815 - 825 (chain C) in PDB entry 5UHA
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 815 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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813C GLU 3.8 0.6 + - - -
814C LEU* 1.3 72.8 - - - +
816C PRO* 1.3 58.4 - - + +
817C GLU* 3.0 28.7 - - + +
818C GLU* 2.6 24.1 + - - +
819C ARG* 2.4 38.0 + - - +
453F PHE* 3.5 33.9 - - + -
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Residues in contact with PRO 816 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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813C GLU 5.4 0.4 - - - +
814C LEU 3.3 7.4 - - - +
815C THR* 1.3 90.6 - - + +
817C GLU* 1.3 66.7 + - - +
818C GLU 3.3 0.2 - - - -
819C ARG* 3.8 15.6 - - + +
820C LEU* 3.4 22.9 + - - +
67D ARG* 6.0 3.4 - - - +
479F PHE* 3.2 33.4 - - - +
480F GLY 3.4 18.6 - - - +
481F LEU* 5.1 0.7 - - - -
484F GLY* 5.2 10.8 - - - +
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Residues in contact with GLU 817 (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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815C THR* 3.0 20.4 - - + +
816C PRO* 1.3 89.5 - - - +
818C GLU* 1.3 57.9 + - - +
820C LEU* 4.2 3.7 - - - +
821C LEU* 3.5 20.1 + - - +
453F PHE* 3.9 8.7 - - + -
456F LEU* 4.0 25.5 - - + +
457F GLN* 3.3 37.8 + - - +
460F LEU* 4.0 18.3 - - + +
480F GLY 5.1 0.2 - - - +
481F LEU* 4.7 25.6 - - + +
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Residues in contact with GLU 818 (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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814C LEU* 5.0 5.7 - - - +
815C THR* 2.6 32.2 + - - +
817C GLU* 1.3 74.6 - - - +
819C ARG* 1.3 61.9 + - - +
820C LEU 3.4 0.2 - - - -
821C LEU* 3.7 17.8 - - + +
822C ARG* 2.4 70.5 + - + +
453F PHE* 6.1 1.5 - - + -
456F LEU* 5.5 6.1 - - + +
526F TYR 5.2 5.9 - - - +
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Residues in contact with ARG 819 (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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813C GLU* 6.4 0.2 - - - -
814C LEU* 3.8 26.2 - - + +
815C THR 2.4 28.5 + - - +
816C PRO* 3.9 12.1 - - - +
818C GLU* 1.3 65.7 - - - +
820C LEU* 1.3 61.2 + - - +
822C ARG* 2.9 25.5 + - - +
823C ALA* 3.0 13.0 + - - +
67D ARG* 5.8 2.3 - - - +
478F ARG* 3.6 20.2 + - - +
479F PHE* 3.2 38.3 + - + +
486F PRO* 4.0 16.2 - - - +
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Residues in contact with LEU 820 (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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816C PRO 3.4 14.8 + - - +
817C GLU* 4.3 2.7 - - - +
819C ARG* 1.3 78.5 - - - +
821C LEU* 1.3 64.6 + - - +
823C ALA* 3.2 17.6 + - + +
824C ILE* 3.2 33.7 + - + +
460F LEU* 3.9 35.9 - - + -
463F VAL* 5.8 2.9 - - + -
475F VAL* 3.6 38.6 - - + +
479F PHE* 4.8 10.7 - - + +
514F LEU* 5.2 10.1 - - + -
523F LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 821 (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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817C GLU 3.5 16.2 + - - +
818C GLU* 3.9 17.7 - - + +
819C ARG 3.1 0.8 - - - -
820C LEU* 1.3 83.3 - - + +
822C ARG* 1.3 60.8 + - + +
824C ILE* 4.2 3.1 - - + -
825C PHE* 3.6 28.2 + - + +
456F LEU* 3.7 31.4 - - + -
460F LEU* 5.8 1.1 - - + -
523F LEU* 3.6 50.3 - - + +
526F TYR* 4.0 22.2 - - + +
527F LEU* 4.7 8.7 - - + +
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Residues in contact with ARG 822 (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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814C LEU* 3.4 27.8 - - - +
818C GLU* 2.4 69.2 + - + +
819C ARG* 2.9 10.5 + - - +
821C LEU* 1.3 80.9 - - + +
823C ALA* 1.3 59.4 + - - +
825C PHE* 5.4 0.7 - - - -
826C GLY* 3.2 24.5 + - - -
827C GLU* 3.4 26.8 + - + +
829C ALA* 3.3 36.0 - - - +
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Residues in contact with ALA 823 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819C ARG 3.0 9.3 + - - +
820C LEU* 3.2 12.7 + - - +
822C ARG* 1.3 79.1 - - - +
824C ILE* 1.3 67.1 + - + +
826C GLY* 3.4 9.0 + - - -
511F MET* 4.3 24.8 - - + +
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Residues in contact with ILE 824 (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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820C LEU* 3.2 24.2 + - + +
821C LEU* 4.3 2.9 - - - +
823C ALA* 1.3 80.1 - - + +
825C PHE* 1.3 73.4 + - + +
826C GLY 3.1 0.6 + - - -
463F VAL* 6.1 0.4 - - + -
511F MET* 4.8 11.5 - - + +
514F LEU* 3.8 52.7 - - + +
515F ARG* 3.2 26.9 + - - +
517F PRO* 5.8 0.4 - - + -
518F SER* 3.8 29.6 - - - +
523F LEU* 4.0 25.8 - - + -
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Residues in contact with PHE 825 (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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821C LEU* 3.6 24.8 + - + +
822C ARG* 5.4 0.2 - - - -
824C ILE* 1.3 88.3 - - + +
826C GLY* 1.3 60.5 + - - +
827C GLU* 3.0 26.8 + - + +
515F ARG* 5.0 4.9 - - - +
518F SER* 3.2 33.4 - - - -
521F GLN* 4.7 0.2 - - - -
523F LEU* 3.3 29.2 - - + -
524F ARG* 3.4 63.4 + - + +
527F LEU* 3.7 12.3 - - + -
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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