Contacts of the helix formed by residues 541 - 552 (chain F) in PDB entry 4CYM
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 HIS 541 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504F CYS 3.9 7.0 + - - +
505F GLN 3.0 24.2 + - - -
506F LYS 3.4 7.2 + - - -
507F GLY* 2.7 32.9 - - - -
536F ALA* 3.0 10.4 + - + +
539F TYR* 3.1 32.6 + + + +
540F GLY* 1.3 70.6 - - - -
542F GLU* 1.3 63.6 + - - +
543F ASP* 3.2 15.3 - - - +
544F CYS* 3.0 14.4 + - + +
545F VAL* 3.0 24.8 + - - +
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Residues in contact with GLU 542 (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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540F GLY 3.2 7.5 + - - +
541F HIS* 1.3 72.9 - - - +
543F ASP* 1.3 63.8 + - - +
545F VAL* 3.5 3.1 - - + +
546F LYS* 3.0 57.0 + - + +
579F GLY* 3.6 30.4 - - - +
580F VAL* 3.6 30.4 + - + +
583F THR* 4.1 2.2 + - - +
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Residues in contact with ASP 543 (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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58C ILE* 5.6 11.1 - - + +
60C VAL 5.4 0.7 - - - +
507F GLY 3.9 12.2 - - - +
509F GLN* 3.0 52.4 + - - +
541F HIS* 3.6 19.1 - - - +
542F GLU* 1.3 74.2 + - - +
544F CYS* 1.3 60.4 + - - -
546F LYS* 3.8 9.1 - - - +
547F ALA 3.3 16.6 + - - -
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Residues in contact with CYS 544 (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 CYS* 4.5 8.1 - - - -
507F GLY* 3.5 24.9 - - - -
508F TYR 3.7 0.4 - - - -
509F GLN* 3.5 18.4 - - - -
512F THR* 3.2 33.3 + - + -
536F ALA* 4.2 10.5 - - + -
541F HIS* 3.0 14.4 + - + +
543F ASP* 1.3 80.7 + - - +
545F VAL* 1.3 67.1 + - - +
546F LYS 3.2 1.1 - - - -
547F ALA* 3.1 8.2 + - - +
548F LEU* 2.9 28.0 + - - +
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Residues in contact with VAL 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533F LEU* 4.1 18.6 - - + +
536F ALA* 3.9 28.2 - - + +
537F CYS* 4.0 12.1 - - - -
541F HIS 3.0 17.7 + - - +
542F GLU* 3.5 9.2 - - - +
544F CYS* 1.3 74.5 - - - +
546F LYS* 1.3 59.2 + - - +
548F LEU* 2.9 6.3 + - - +
549F VAL* 2.9 37.1 + - + +
580F VAL* 4.1 26.2 - - + -
583F THR* 4.4 14.4 - - + +
584F LEU* 4.5 7.4 - - + -
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Residues in contact with LYS 546 (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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60C VAL 5.7 0.7 - - - +
61C ASP* 2.9 32.7 + - - +
62C PHE* 3.5 31.6 + - + +
509F GLN* 6.0 0.2 - - - +
542F GLU* 3.0 45.2 + - - +
543F ASP* 3.8 7.1 - - - +
545F VAL* 1.3 77.8 - - - +
547F ALA* 1.3 67.0 + - - +
549F VAL* 3.1 3.2 + - - +
550F TYR* 2.8 38.3 + - + +
583F THR* 3.7 27.8 - - + +
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Residues in contact with ALA 547 (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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62C PHE* 3.9 13.6 - - + -
509F GLN* 4.1 7.6 - - + -
512F THR* 4.0 12.1 - - - +
513F LEU* 3.6 31.2 - - + -
516F LEU* 4.5 2.0 - - + -
543F ASP 3.3 11.9 + - - +
544F CYS 3.1 9.0 + - - +
546F LYS* 1.3 77.5 - - - +
548F LEU* 1.3 58.4 + - - +
551F TYR* 2.9 35.6 + - - +
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Residues in contact with LEU 548 (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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500F LEU* 4.3 8.1 - - + -
504F CYS* 3.7 29.4 - - - -
512F THR* 4.6 1.8 - - - +
516F LEU* 4.2 28.7 - - + -
522F ALA* 4.2 15.9 - - + -
532F PRO* 3.9 2.7 - - + +
533F LEU* 3.5 47.3 - - + +
536F ALA* 4.3 4.5 - - + -
544F CYS 2.9 17.4 + - - +
545F VAL 3.3 5.2 - - - +
547F ALA* 1.3 80.2 - - - +
549F VAL* 1.3 63.0 + - - +
550F TYR 3.4 0.2 + - - -
551F TYR 3.8 0.2 + - - -
552F ASP* 2.8 27.5 - - - +
556F CYS* 3.4 10.5 - - - -
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Residues in contact with VAL 549 (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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78C GLN* 4.6 0.9 + - - -
533F LEU* 4.7 7.4 - - + -
545F VAL* 2.9 33.6 + - + +
546F LYS* 3.8 4.3 - - - +
548F LEU* 1.3 79.0 - - - +
550F TYR* 1.3 67.7 + - + +
551F TYR 3.7 0.2 + - - -
552F ASP* 4.1 4.5 + - - +
554F GLU* 4.5 9.5 + - - -
556F CYS* 4.1 15.2 - - + +
558F LEU* 4.4 22.2 - - + -
583F THR* 4.8 5.2 - - + +
584F LEU* 4.4 9.2 - - + -
587F ASN* 3.6 42.1 + - + +
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Residues in contact with TYR 550 (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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62C PHE* 3.5 48.6 + + + -
63C ALA* 3.7 23.3 - - - -
64C LEU* 3.5 21.9 + - + +
78C GLN* 2.9 53.6 + - + +
79C LEU 5.3 0.4 - - - -
80C TRP* 3.6 5.6 - - - +
546F LYS* 2.8 33.5 + - + +
549F VAL* 1.3 76.0 - - + +
551F TYR* 1.3 68.9 + - - +
552F ASP 3.0 2.9 - - - -
583F THR* 4.2 18.6 - - + +
586F GLN* 4.7 8.3 + - - -
587F ASN* 3.3 34.7 + - - -
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Residues in contact with TYR 551 (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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27C LYS* 5.5 3.8 + - - -
78C GLN* 5.0 0.2 - - - +
80C TRP* 4.1 22.1 - + - -
94C VAL* 4.8 14.1 - - + -
97C LYS* 4.1 21.8 + - + +
513F LEU* 4.0 22.9 - - + -
516F LEU* 3.6 40.6 + - + -
517F HIS* 3.3 25.1 + - - +
547F ALA 2.9 20.1 + - - +
549F VAL 3.5 0.6 - - - -
550F TYR* 1.3 79.8 - - - +
552F ASP* 1.3 79.4 + - - +
553F VAL* 2.8 21.4 + - - +
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Residues in contact with ASP 552 (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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516F LEU* 4.0 12.7 - - - +
522F ALA* 4.1 11.5 - - - +
548F LEU* 2.8 23.5 - - - +
549F VAL 4.1 0.6 + - - +
550F TYR 3.0 2.0 - - - -
551F TYR* 1.3 99.3 - - - +
553F VAL* 1.4 72.4 + - - +
554F GLU 4.3 1.1 - - - +
555F SER* 3.5 38.0 + - - +
556F CYS* 3.2 22.2 - - + +
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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