Contacts of the helix formed by residues 501 - 512 (chain F) in PDB entry 5UH8
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 GLU 501 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490F ASP* 4.8 5.7 - - - +
493F GLY* 4.9 10.2 + - - -
498F VAL 5.3 0.2 - - - -
499F THR* 3.0 4.8 + - - +
500F ARG* 1.3 85.0 - - - +
502F ARG* 1.3 60.6 + - - +
503F ILE* 3.0 15.7 - - + +
504F ARG* 2.5 62.9 + - + +
505F GLN* 3.5 6.9 + - - +
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Residues in contact with ARG 502 (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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470F ARG* 4.2 9.9 - - - +
498F VAL* 3.6 21.1 + - + -
499F THR* 3.0 20.5 + - - +
500F ARG* 3.0 20.2 + - + +
501F GLU* 1.3 76.4 - - - +
503F ILE* 1.3 55.6 + - - +
504F ARG 3.1 0.2 - - - -
505F GLN* 2.9 39.2 + - - +
506F ILE* 2.8 34.5 + - + +
509F LYS* 5.5 3.4 - - - +
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Residues in contact with ILE 503 (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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470F ARG 3.5 24.2 - - - +
473F GLY 4.7 0.9 - - - -
474F VAL* 3.4 39.2 - - + +
477F LEU* 4.3 6.3 - - + -
489F LEU 5.7 0.9 - - - +
492F ILE* 4.2 8.1 - - + -
493F GLY* 3.7 32.1 - - - +
496F TYR* 3.6 37.4 - - + -
498F VAL 4.9 2.9 + - - +
501F GLU* 3.0 5.1 - - + -
502F ARG* 1.3 79.8 - - - +
504F ARG* 1.3 60.4 + - + +
506F ILE* 3.8 9.6 - - + +
507F GLU* 3.3 15.8 + - - +
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Residues in contact with ARG 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474F VAL* 5.5 1.3 - - - -
489F LEU* 3.3 33.3 - - - +
490F ASP* 4.8 6.5 + - - -
501F GLU* 2.5 55.2 + - + +
503F ILE* 1.3 79.7 - - + +
505F GLN* 1.3 61.5 + - - +
506F ILE 3.3 0.4 - - - -
507F GLU* 3.2 35.4 + - + +
508F SER* 3.6 4.2 + - - -
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Residues in contact with GLN 505 (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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501F GLU 3.5 2.7 + - - +
502F ARG* 2.9 46.7 + - - +
504F ARG* 1.3 79.8 - - - +
506F ILE* 1.3 55.9 + - - +
507F GLU 3.2 0.4 - - - -
508F SER* 3.1 27.5 + - - -
509F LYS* 3.2 40.6 - - - +
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Residues in contact with ILE 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470F ARG* 3.3 54.7 - - + +
471F GLU* 3.5 40.2 - - + +
474F VAL* 4.8 1.3 - - - -
496F TYR* 4.6 3.1 - - + -
502F ARG* 2.8 23.8 + - + +
503F ILE* 3.8 23.1 - - + +
504F ARG 3.3 0.2 - - - -
505F GLN* 1.3 75.8 - - - +
507F GLU* 1.3 61.7 + - - +
508F SER 3.4 0.2 - - - -
509F LYS* 3.2 29.8 + - + +
510F THR* 2.8 22.7 + - - -
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Residues in contact with GLU 507 (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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474F VAL* 4.1 20.9 - - + -
503F ILE 3.3 10.7 + - - +
504F ARG* 3.2 29.3 + - + +
505F GLN 3.2 0.6 - - - -
506F ILE* 1.3 78.8 - - - +
508F SER* 1.3 68.9 + - - +
510F THR* 3.1 7.5 + - - -
511F MET* 3.1 43.8 + - + +
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Residues in contact with SER 508 (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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504F ARG 3.6 3.5 + - - -
505F GLN* 3.1 26.0 + - - -
507F GLU* 1.3 87.1 + - - +
509F LYS* 1.3 60.9 + - - +
510F THR 3.0 6.0 + - - -
511F MET* 3.6 15.3 + - - +
512F SER* 4.2 7.4 + - - -
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Residues in contact with LYS 509 (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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470F ARG* 5.5 3.8 - - - +
471F GLU* 3.2 24.4 - - - +
502F ARG* 5.5 4.0 - - - +
505F GLN* 3.2 47.3 - - - +
506F ILE* 3.2 28.9 + - + +
507F GLU 3.2 1.0 - - - -
508F SER* 1.3 77.1 + - - +
510F THR* 1.3 57.6 + - - +
512F SER* 4.9 1.3 - - - -
513F LYS* 3.6 15.4 + - - +
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Residues in contact with THR 510 (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* 3.6 32.1 - - + -
471F GLU* 3.1 29.3 + - - +
474F VAL* 5.8 0.2 - - - -
475F VAL* 4.0 12.6 - - + -
506F ILE 2.8 16.9 + - - -
507F GLU* 3.2 12.0 - - - -
508F SER 3.0 0.2 - - - -
509F LYS* 1.3 78.1 - - - +
511F MET* 1.3 56.3 + - - +
512F SER 3.1 2.9 - - - -
513F LYS* 2.7 22.6 + - - -
514F LEU* 2.8 27.1 + - + +
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Residues in contact with MET 511 (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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823C ALA* 4.2 29.4 - - + +
824C ILE* 4.8 11.7 - - - +
507F GLU* 3.1 29.2 + - + +
508F SER* 3.6 9.3 + - - +
510F THR* 1.3 79.3 - - - +
512F SER* 1.3 58.6 + - - +
514F LEU* 3.7 23.0 - - + +
515F ARG* 3.9 10.1 + - - +
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Residues in contact with SER 512 (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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508F SER 4.2 7.6 + - - -
509F LYS 5.7 0.9 - - - -
510F THR 3.1 0.6 - - - +
511F MET* 1.3 75.5 - - - +
513F LYS* 1.3 58.1 + - - +
514F LEU 3.0 5.2 - - - -
515F ARG* 3.0 27.8 + - - +
516F HIS* 3.8 3.8 + - - +
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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