Contacts of the helix formed by residues 64 - 77 (chain V) 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 GLU 64 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A PHE* 5.9 0.5 - - - -
33A GLN* 4.0 13.3 + - - +
59V ILE* 2.8 30.6 + - + +
62V MET* 3.3 10.0 - - + +
63V GLY* 1.3 74.7 - - - +
65V SER* 1.3 57.7 + - - +
66V ASP 3.2 3.5 + - - -
67V ASP* 3.4 28.0 + - - +
68V SER* 2.9 31.9 + - - -
71V ARG* 4.0 7.3 + - - -
4b ALA* 3.6 25.2 + - - +
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Residues in contact with SER 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL 2.4 35.1 + - - -
158A ASP* 3.8 13.5 + - - -
55V ILE* 3.9 24.5 - - - -
59V ILE* 3.3 10.4 + - - -
60V ARG* 4.2 14.8 - - - +
63V GLY* 4.6 3.1 - - - -
64V GLU* 1.3 79.5 - - - +
66V ASP* 1.3 57.0 + - - +
68V SER* 4.0 2.5 - - - -
69V ILE* 2.9 37.7 + - - +
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Residues in contact with ASP 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 4.9 3.4 - - + +
57A LYS* 4.2 4.5 + - - +
154A LEU* 3.2 38.5 - - + +
157A VAL* 2.7 28.3 - - - +
158A ASP 2.8 20.8 - - - +
159A ILE 3.4 2.3 + - - -
160A ALA* 3.2 32.1 + - + +
63V GLY 4.5 3.4 - - - +
64V GLU 3.2 0.4 - - - -
65V SER* 1.3 84.7 + - - +
67V ASP* 1.3 68.4 + - - +
69V ILE* 3.5 2.8 + - - +
70V LEU* 3.4 22.8 + - - +
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Residues in contact with ASP 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLN* 4.0 28.2 - - - +
36A GLN* 2.8 33.6 + - - +
37A TYR* 4.0 4.0 + - - -
154A LEU* 5.9 0.3 - - - +
63V GLY 5.1 0.4 + - - -
64V GLU* 3.4 30.1 + - - +
66V ASP* 1.3 79.2 - - - +
68V SER* 1.3 57.8 + - - +
69V ILE 3.4 0.2 - - - -
70V LEU* 3.3 8.8 - - + +
71V ARG* 2.9 53.5 + - - +
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Residues in contact with SER 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V ALA* 3.2 31.2 - - - +
55V ILE* 4.1 8.4 - - - +
59V ILE* 4.1 8.2 - - - +
64V GLU* 2.9 26.2 + - - -
65V SER* 3.7 9.2 - - - -
66V ASP 3.2 0.4 - - - -
67V ASP* 1.3 75.5 - - - +
69V ILE* 1.3 58.9 + - - +
71V ARG* 4.4 4.2 - - - +
72V LEU* 2.9 32.4 + - - +
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Residues in contact with ILE 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LYS* 6.0 1.3 - - - +
60A LEU* 5.1 14.4 - - + -
158A ASP* 3.3 47.1 - - + +
159A ILE* 5.1 8.1 - - + -
34V MET* 4.6 19.3 - - + -
36V VAL* 5.8 3.8 - - + -
53V TYR* 4.9 17.1 - - + -
55V ILE* 3.9 26.5 - - + -
65V SER 2.9 17.4 + - - +
66V ASP 4.1 3.6 - - - +
68V SER* 1.3 77.4 - - - +
70V LEU* 1.3 60.4 + - - +
72V LEU* 3.9 5.2 - - - +
73V ALA* 2.9 29.9 + - + +
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Residues in contact with LEU 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 3.3 23.8 - - - +
37A TYR* 3.3 20.2 - - + +
57A LYS* 3.2 34.7 - - - +
60A LEU* 5.7 1.1 - - - -
66V ASP 3.4 12.2 + - - +
67V ASP* 3.3 12.1 - - - +
69V ILE* 1.3 80.8 - - - +
71V ARG* 1.3 79.5 + - + +
73V ALA* 4.7 2.9 - - - -
74V LYS* 2.9 32.7 + - + +
79V VAL* 3.8 16.6 - - + +
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Residues in contact with ARG 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 3.6 22.6 + - - +
64V GLU* 4.0 7.9 + - - -
67V ASP* 2.9 34.9 + - - +
68V SER* 4.4 3.4 - - - +
70V LEU* 1.3 85.2 - - + +
72V LEU* 1.3 64.9 + - - +
74V LYS* 3.5 21.7 + - + +
75V ALA* 3.7 7.8 + - - +
4b ALA* 2.3 54.2 + - - +
5b LYS* 5.3 2.9 - - - +
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Residues in contact with LEU 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V SER* 3.7 42.8 - - - +
19V ALA* 5.1 2.2 - - + +
53V TYR* 3.7 42.7 + - + -
54V ALA 5.1 3.1 - - - +
55V ILE* 5.1 7.4 - - + -
68V SER* 2.9 22.2 + - - +
69V ILE* 3.9 4.5 - - - +
71V ARG* 1.3 79.9 - - - +
73V ALA* 1.3 59.4 + - - +
74V LYS 3.5 0.3 + - - -
75V ALA* 3.7 12.6 + - + +
76V ASP* 3.8 7.6 + - - +
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Residues in contact with ALA 73 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 5.2 4.5 - - + -
53V TYR* 3.9 30.5 - - + +
69V ILE* 2.9 20.6 + - + +
70V LEU* 4.7 0.4 - - - -
72V LEU* 1.3 73.6 - - - +
74V LYS* 1.3 60.2 + - - +
75V ALA 3.3 0.2 - - - -
76V ASP* 3.1 4.7 + - - +
77V GLY 2.8 23.4 + - - -
78V ILE* 3.7 10.0 + - + -
79V VAL* 3.5 25.4 - - + +
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Residues in contact with LYS 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70V LEU* 2.9 22.8 + - + +
71V ARG* 3.6 17.7 - - + +
72V LEU 3.2 0.6 - - - -
73V ALA* 1.3 75.9 - - - +
75V ALA* 1.3 65.0 + - - +
77V GLY* 3.2 13.1 + - - +
79V VAL* 3.7 9.0 - - + -
80V SER* 5.0 15.2 - - - +
81V LYS 5.3 8.5 - - - +
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Residues in contact with ALA 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71V ARG 3.7 6.7 + - - +
72V LEU* 3.7 10.8 + - + +
73V ALA 3.3 0.2 - - - -
74V LYS* 1.3 79.4 - - - +
76V ASP* 1.3 61.7 + - - +
77V GLY* 4.6 0.3 - - - -
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Residues in contact with ASP 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51V LYS* 2.6 38.8 + - - +
53V TYR* 2.9 27.7 + - + +
72V LEU 3.8 3.2 + - - +
73V ALA* 3.1 13.0 + - - +
75V ALA* 1.3 79.9 - - - +
77V GLY* 1.3 58.3 + - - +
78V ILE* 3.7 7.2 - - + +
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Residues in contact with GLY 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 5.0 4.9 + - - +
73V ALA 2.8 7.7 + - - -
74V LYS 3.2 12.6 + - - -
76V ASP* 1.3 77.5 - - - +
78V ILE* 1.3 61.3 + - - +
79V VAL 3.4 2.0 - - - -
80V SER 2.9 26.3 - - - +
81V LYS 5.4 2.7 - - - -
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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