Contacts of the helix formed by residues 52 - 62 (chain Z) in PDB entry 5FLX
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 LYS 52 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4S VAL* 4.4 20.8 - - - +
6S PRO* 3.6 47.0 + - + +
51Z ASP* 1.3 73.6 - - - +
53Z ALA* 1.3 64.7 + - - +
55Z TYR* 4.1 12.0 - - + -
56Z ASP* 3.3 22.8 + - + +
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Residues in contact with ALA 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Z ASP* 3.4 7.7 - - + -
52Z LYS* 1.3 78.9 - - - +
54Z THR* 1.3 68.0 + - - +
56Z ASP* 3.5 10.9 + - - +
57Z LYS* 4.0 4.7 + - - +
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Residues in contact with THR 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Z ASP* 4.8 8.3 + - - +
53Z ALA* 1.3 75.3 - - - +
55Z TYR* 1.3 57.6 + - - +
56Z ASP 3.1 5.5 + - - -
57Z LYS* 3.1 20.2 + - + +
58Z LEU* 3.0 38.8 + - + +
76Z ARG 5.0 7.4 - - - +
77Z LEU 4.7 12.1 - - - +
78Z LYS* 5.6 6.8 - - + +
79Z ILE* 5.9 2.7 - - - -
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Residues in contact with TYR 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S VAL* 5.3 14.6 - - + -
51Z ASP* 3.1 27.8 + - + +
52Z LYS* 4.4 9.6 - - + -
53Z ALA 3.3 1.8 - - - +
54Z THR* 1.3 77.7 - - - +
56Z ASP* 1.3 58.0 + - - +
58Z LEU* 3.4 24.1 - - + +
59Z CYS* 2.9 49.8 + - - -
77Z LEU* 5.8 1.6 - - + -
79Z ILE* 5.9 7.3 - - + +
87Z ALA* 4.7 18.8 + - + +
90Z GLU* 4.5 13.2 + - - -
91Z LEU* 3.8 23.8 - - + +
94Z LYS* 5.6 2.6 - - - +
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Residues in contact with ASP 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Z LYS* 3.3 25.5 + - + +
53Z ALA 3.6 6.1 - - - +
54Z THR 3.1 0.6 - - - -
55Z TYR* 1.3 76.1 - - - +
57Z LYS* 1.3 67.4 + - - +
58Z LEU 3.0 1.1 - - - -
59Z CYS* 3.1 19.2 + - - +
60Z LYS* 3.1 19.3 + - - +
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Residues in contact with LYS 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Z ALA 4.0 4.4 + - - +
54Z THR* 3.1 22.4 + - + +
56Z ASP* 1.3 81.1 + - - +
58Z LEU* 1.3 58.3 + - + +
60Z LYS* 2.9 34.9 - - - +
61Z GLU* 2.7 56.2 + - + +
65Z TYR* 5.7 0.9 - - - -
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Residues in contact with LEU 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Z THR* 3.0 22.2 + - + +
55Z TYR* 3.4 35.0 - - + +
56Z ASP 3.0 0.2 - - - -
57Z LYS* 1.3 81.5 - - + +
59Z CYS* 1.3 59.7 + - - +
61Z GLU* 4.3 14.1 - - - +
62Z VAL* 2.4 52.1 + - + +
65Z TYR* 4.8 8.3 - - + +
73Z VAL* 5.8 0.2 - - + -
76Z ARG* 4.4 10.8 - - + +
77Z LEU* 3.0 50.0 - - + +
79Z ILE* 5.5 2.5 - - + -
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Residues in contact with CYS 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z TYR* 2.9 59.2 + - - -
56Z ASP* 3.4 13.2 - - - +
58Z LEU* 1.3 77.1 - - - +
60Z LYS* 1.3 59.6 + - - +
62Z VAL* 4.1 6.9 - - - +
63Z PRO* 3.8 12.8 - - - +
91Z LEU* 6.0 2.0 - - - -
94Z LYS* 6.4 1.8 - - - -
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Residues in contact with LYS 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Z ASP* 3.1 12.9 + - - +
57Z LYS* 2.9 52.8 - - - +
59Z CYS* 1.3 76.9 - - - +
61Z GLU* 1.3 64.3 + - - +
62Z VAL 3.6 0.2 - - - -
63Z PRO* 3.5 10.2 - - - +
64Z ASN* 4.0 9.1 + - - +
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Residues in contact with GLU 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Z LYS* 2.7 44.3 + - + +
58Z LEU* 4.3 6.2 - - - +
60Z LYS* 1.3 79.7 - - + +
62Z VAL* 1.3 64.2 + - - +
63Z PRO* 3.4 1.8 - - - -
64Z ASN* 3.1 27.0 + - - +
65Z TYR* 3.0 48.5 + - - -
101z U 4.0 0.7 + - - -
102z G 3.8 37.6 - - - +
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Residues in contact with VAL 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Z LEU* 2.4 51.7 + - + +
59Z CYS* 4.1 7.4 - - - +
61Z GLU* 1.3 68.9 - - - +
63Z PRO* 1.3 74.4 - - + +
64Z ASN 3.1 1.0 + - - -
65Z TYR* 3.1 36.3 + - + +
68Z ILE* 3.9 10.2 - - + +
73Z VAL* 4.6 18.2 - - + -
77Z LEU* 5.5 2.0 - - + -
88Z LEU* 6.0 3.1 - - + -
91Z LEU* 3.9 29.2 - - + -
97Z ILE* 4.6 7.2 - - + +
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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