Contacts of the helix formed by residues 69 - 77 (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 THR 69 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ILE* 5.1 19.8 - - + +
168F THR* 5.6 0.9 - - - +
171F GLU* 5.0 11.2 - - + -
67Z LEU* 4.1 7.6 + - - +
68Z ILE* 1.3 79.8 + - - +
70Z PRO* 1.3 69.9 - - + +
71Z ALA* 3.7 15.0 - - + +
72Z VAL* 3.8 28.4 - - + +
73Z VAL* 2.6 41.0 + - - +
106Z GLN* 4.8 9.0 - - - +
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Residues in contact with PRO 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Z ILE 4.4 2.9 - - - +
69Z THR* 1.3 92.9 - - + +
71Z ALA* 1.3 49.4 + - - +
74Z SER* 2.4 42.0 + - - +
84Z ALA* 4.9 5.1 - - + +
88Z LEU* 4.6 10.5 - - + -
106Z GLN* 4.0 6.1 - - - +
107Z VAL* 3.1 53.6 - - + +
109Z TYR* 4.6 10.1 - - + -
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Residues in contact with ALA 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F ILE* 4.4 18.4 - - + +
167F LYS* 4.3 13.6 - - + +
168F THR* 4.6 12.3 - - + +
171F GLU* 3.1 27.8 - - - +
69Z THR* 3.3 6.6 - - + +
70Z PRO* 1.3 76.7 - - - +
72Z VAL* 1.3 59.7 + - - +
74Z SER* 4.1 2.6 - - - -
75Z GLU* 3.0 30.1 + - - +
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Residues in contact with VAL 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F GLU* 3.2 30.7 - - + +
65Z TYR* 6.4 2.7 - - + -
67Z LEU 6.1 0.9 - - - +
69Z THR* 3.3 23.6 + - + +
71Z ALA* 1.3 75.0 - - - +
73Z VAL* 1.3 65.4 + - + +
75Z GLU* 3.2 9.3 + - - +
76Z ARG* 2.9 49.6 + - + +
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Residues in contact with VAL 73 (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* 5.8 0.7 - - + -
62Z VAL* 4.6 15.0 - - + -
65Z TYR* 5.2 12.8 - - + -
67Z LEU 4.7 2.5 - - - +
68Z ILE* 3.8 25.8 - - + -
69Z THR 2.6 37.8 + - - +
72Z VAL* 1.3 74.8 - - + +
74Z SER* 1.3 50.7 - - - +
76Z ARG* 2.9 12.1 + - + -
77Z LEU* 2.7 58.7 + - + +
88Z LEU* 4.3 17.9 - - + -
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Residues in contact with SER 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F ILE* 5.6 7.4 - - - +
70Z PRO* 2.4 30.8 + - - +
71Z ALA* 4.1 3.8 - - - -
73Z VAL* 1.3 77.4 - - - +
75Z GLU* 1.3 61.1 + - - +
77Z LEU* 3.2 25.9 + - - +
78Z LYS* 3.7 2.8 + - - -
79Z ILE 3.6 13.0 + - - +
81Z GLY* 3.5 25.7 + - - -
84Z ALA* 3.5 14.3 - - - +
88Z LEU* 5.9 0.2 - - - +
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Residues in contact with GLU 75 (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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167F LYS* 3.9 24.5 + - - +
171F GLU* 4.9 2.3 - - - +
71Z ALA 3.0 21.7 + - - +
72Z VAL* 3.2 7.7 + - - +
74Z SER* 1.3 76.0 - - - +
76Z ARG* 1.3 67.3 + - + +
77Z LEU 3.1 0.2 - - - -
78Z LYS* 3.3 29.5 + - - +
68z G 3.4 32.6 + - - +
69z C 3.7 12.4 + - - +
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Residues in contact with ARG 76 (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* 5.0 5.9 - - - +
58Z LEU* 4.4 11.2 - - + +
65Z TYR* 4.0 34.3 + - + +
72Z VAL* 2.9 33.0 + - + +
73Z VAL* 2.9 14.4 + - + +
75Z GLU* 1.3 82.0 - - + +
77Z LEU* 1.3 60.8 + - + +
78Z LYS* 3.4 12.8 + - - +
67z C 4.9 11.1 + - - -
68z G 5.0 14.9 + - - -
100z G 3.1 39.2 + - - +
101z U 3.8 27.5 + - - -
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Residues in contact with LEU 77 (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* 4.7 9.0 - - - +
55Z TYR* 5.8 2.0 - - + -
58Z LEU* 3.0 44.9 - - + +
62Z VAL* 5.5 2.2 - - + -
73Z VAL* 2.7 37.6 + - + +
74Z SER* 3.3 26.5 - - - +
75Z GLU 3.1 1.4 - - - -
76Z ARG* 1.3 78.1 - - - +
78Z LYS* 1.3 59.1 + - - +
79Z ILE* 2.6 45.7 + - + +
84Z ALA* 3.8 24.0 - - + -
87Z ALA* 5.7 2.2 - - + -
88Z LEU* 4.3 8.7 - - + -
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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