Contacts of the helix formed by residues 470 - 479 (chain F) in PDB entry 5UHE
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 ARG 470 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468F SER* 3.4 9.2 + - - +
469F GLU* 1.3 80.8 - - + +
471F GLU* 1.3 62.0 + - + +
473F GLY* 3.2 9.1 + - - -
474F VAL* 3.5 9.7 + - - +
496F TYR* 3.4 24.0 + - - +
498F VAL* 3.4 38.8 - - - +
502F ARG* 5.2 2.2 + - - +
503F ILE* 4.4 3.8 - - - +
506F ILE* 3.5 46.9 - - + +
509F LYS* 6.2 0.2 - - - +
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Residues in contact with GLU 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467F LEU* 3.7 21.5 - - + +
468F SER* 3.5 30.9 + - - +
470F ARG* 1.3 75.7 - - + +
472F ALA* 1.3 57.3 + - - +
473F GLY 3.1 6.4 + - - -
474F VAL* 3.8 2.6 - - - +
475F VAL* 3.1 26.5 + - - +
506F ILE* 3.6 18.6 - - + -
509F LYS* 3.2 33.7 - - + +
510F THR* 3.3 15.1 + - - +
513F LYS* 3.7 15.6 - - - +
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Residues in contact with ALA 472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464F LEU* 3.7 42.2 - - + +
467F LEU* 4.1 6.2 - - + +
468F SER 3.1 20.5 + - - +
469F GLU* 4.1 4.0 - - - +
471F GLU* 1.3 74.5 - - - +
473F GLY* 1.3 60.9 + - - +
475F VAL* 4.0 11.6 - - - +
476F ARG* 3.5 27.1 + - - +
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Residues in contact with GLY 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F GLU 3.3 13.0 + - - -
470F ARG* 3.2 9.3 + - - -
471F GLU 3.1 1.4 - - - -
472F ALA* 1.3 76.7 - - - +
474F VAL* 1.3 64.4 + - - +
475F VAL 3.2 1.1 - - - -
476F ARG* 3.2 26.2 + - - +
477F LEU* 3.2 23.1 - - - +
496F TYR* 6.2 2.9 - - - -
503F ILE* 5.2 0.9 - - - -
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Residues in contact with VAL 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470F ARG 3.5 8.7 + - - +
471F GLU 3.8 11.2 - - - +
473F GLY* 1.3 73.3 - - - +
475F VAL* 1.3 70.0 + - + +
477F LEU* 3.0 22.2 + - + +
478F ARG* 3.2 20.6 + - + +
492F ILE* 4.5 5.8 - - + -
503F ILE* 3.6 47.9 - - + +
506F ILE 4.5 4.7 - - - +
507F GLU* 4.3 24.2 - - + +
510F THR* 4.8 1.6 - - - +
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Residues in contact with VAL 475 (chain F).
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* 3.6 25.1 - - + +
463F VAL* 5.9 3.8 - - + -
464F LEU* 4.4 18.8 - - + -
467F LEU* 4.0 11.4 - - + -
471F GLU 3.1 23.1 - - - +
472F ALA* 4.0 7.6 - - - +
474F VAL* 1.3 83.1 - - + +
476F ARG* 1.3 59.2 + - - +
477F LEU 3.4 0.2 + - - -
479F PHE* 3.2 27.7 - - - +
481F LEU* 6.3 3.4 - - + -
510F THR* 3.8 22.2 - - + -
514F LEU* 5.1 5.2 - - + -
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Residues in contact with ARG 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464F LEU* 5.5 9.0 - - + +
469F GLU 5.4 3.2 + - - -
472F ALA 3.5 16.2 + - - +
473F GLY* 3.2 21.0 + - - +
475F VAL* 1.3 80.2 - - + +
477F LEU* 1.3 62.7 + - + +
480F GLY* 3.6 17.2 + - - -
481F LEU* 3.6 31.1 + - + +
482F THR* 4.5 19.1 + - - +
483F ASP* 4.8 7.8 + - - -
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Residues in contact with LEU 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473F GLY* 3.2 21.5 - - - +
474F VAL* 3.0 20.2 + - - +
475F VAL 3.1 0.2 - - - -
476F ARG* 1.3 84.4 - - + +
478F ARG* 1.3 62.4 + - - +
479F PHE 3.3 1.3 + - - -
480F GLY* 3.8 4.2 + - - -
483F ASP* 4.8 5.6 - - - +
485F GLN 4.0 4.5 - - - +
487F ARG* 3.8 27.6 + - - +
492F ILE* 3.5 48.2 - - + +
495F VAL* 4.8 12.6 - - + -
496F TYR* 4.8 10.8 - - + -
503F ILE* 4.3 8.7 - - + -
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Residues in contact with ARG 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819C ARG* 3.5 9.9 + - - +
474F VAL* 3.2 15.2 + - + +
477F LEU* 1.3 77.5 - - - +
479F PHE* 1.3 58.9 + - - +
480F GLY 3.5 0.2 - - - -
486F PRO* 3.4 21.0 - - + +
487F ARG 3.5 18.6 - - - +
489F LEU* 3.9 43.4 - - - +
492F ILE* 3.6 9.2 - - + -
507F GLU* 5.9 6.7 - - - +
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Residues in contact with PHE 479 (chain F).
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* 3.2 29.5 - - - +
819C ARG* 3.2 18.4 + - + +
820C LEU* 4.0 24.5 - - + +
474F VAL 4.6 0.4 + - - -
475F VAL 3.2 22.4 + - - +
477F LEU 3.3 0.2 - - - -
478F ARG* 1.3 80.7 - - - +
480F GLY* 1.3 64.4 + - - +
481F LEU* 5.0 2.2 - - + +
485F GLN 4.6 2.0 - - - -
486F PRO* 4.8 0.6 - - - +
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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