Contacts of the helix formed by residues 75 - 87 (chain H) 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 ILE 75 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 4.5 28.3 - - + -
37H LYS 5.4 0.2 - - - -
38H ALA* 3.5 32.1 - - + +
39H GLN* 4.7 8.7 + - + +
71H SER 4.2 2.0 + - - -
72H PHE 3.9 3.0 + - - -
74H LYS* 1.3 99.0 - - + +
76H GLN* 1.3 66.1 + - - +
77H VAL* 2.7 33.0 - - + +
78H ARG* 4.7 2.5 - - + -
79H LEU* 3.9 16.8 - - + +
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Residues in contact with GLN 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 4.4 5.2 + - - +
72H PHE* 3.0 26.2 + - - +
73H GLN* 4.3 1.7 + - - +
74H LYS 3.7 2.0 + - - -
75H ILE* 1.3 77.4 - - - +
77H VAL* 1.3 64.6 + - + +
78H ARG 3.6 1.2 + - - -
79H LEU* 3.6 8.8 + - - +
80H VAL* 3.7 25.6 + - + +
94H PHE* 3.3 39.8 - - - +
135H PHE* 2.8 53.7 - - + +
136H PRO* 5.3 6.5 - - + -
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Residues in contact with VAL 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ILE* 2.7 38.5 - - + +
76H GLN* 1.3 80.3 - - + +
78H ARG* 1.3 69.3 + - + +
79H LEU 3.2 1.8 + - - -
80H VAL* 5.5 1.8 - - - -
81H ARG* 5.7 4.0 - - - +
136H PRO* 6.1 5.4 - - + -
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Residues in contact with ARG 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LEU* 3.7 37.8 - - + +
75H ILE* 4.7 3.6 - - + +
76H GLN 3.6 0.8 + - - -
77H VAL* 1.3 85.4 - - + +
79H LEU* 1.3 60.7 + - - +
80H VAL* 3.5 2.1 - - - +
81H ARG* 3.5 26.6 - - - +
82H GLU* 3.4 29.3 + - + +
157z C 4.9 24.2 + - - -
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LEU* 4.6 7.2 - - + -
30H LEU* 4.7 8.7 - - + -
36H LEU* 6.4 2.9 - - + -
39H GLN* 3.2 41.1 - - + +
40H LEU* 4.6 19.5 - - + -
43H LEU* 6.2 0.2 - - + -
75H ILE* 3.9 18.2 - - + +
76H GLN* 4.3 1.3 - - - +
77H VAL 3.2 5.0 + - - +
78H ARG* 1.3 74.8 - - - +
80H VAL* 1.3 62.3 + - - +
81H ARG 3.1 1.6 - - - -
82H GLU* 3.0 10.6 + - - +
83H LEU* 2.9 50.5 + - + -
94H PHE* 5.9 1.6 - - + -
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Residues in contact with VAL 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H GLN* 3.7 24.4 + - + +
77H VAL* 5.5 0.9 - - - -
78H ARG 5.2 1.6 - - - +
79H LEU* 1.3 79.5 - - + +
81H ARG* 1.3 66.4 + - + +
83H LEU* 3.2 9.9 + - + +
84H GLU* 2.9 39.2 + - - +
92H VAL* 3.8 33.0 - - + +
94H PHE* 4.2 18.4 - - + -
136H PRO* 6.5 1.3 - - + -
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Residues in contact with ARG 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H VAL* 5.7 4.2 - - - +
78H ARG* 3.5 26.7 - - - +
79H LEU 3.1 0.4 - - - -
80H VAL* 1.3 85.3 - - + +
82H GLU* 1.3 59.7 + - + +
84H GLU* 3.2 13.3 + - - +
85H LYS* 2.9 47.2 + - - +
165H ASN* 4.9 16.4 + - - +
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Residues in contact with GLU 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H LEU* 3.9 33.9 - - + +
78H ARG* 3.4 22.5 + - + +
79H LEU* 3.0 11.5 + - - +
81H ARG* 1.3 78.0 - - - +
83H LEU* 1.3 59.3 + - - +
85H LYS* 3.8 19.4 - - - +
86H LYS* 2.9 49.0 + - - +
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ILE* 4.3 21.1 - - + +
26H ALA* 5.2 7.6 - - + -
27H LEU* 4.0 24.5 - - + -
30H LEU* 4.5 7.4 - - + -
62H ILE* 5.2 4.0 - - + -
79H LEU* 2.9 34.0 + - + +
80H VAL* 3.5 14.6 - - + +
82H GLU* 1.3 76.5 - - - +
84H GLU* 1.3 58.1 + - - +
86H LYS* 4.8 2.0 - - - +
87H PHE* 2.7 32.1 + - + +
88H SER* 4.8 1.2 - - - -
92H VAL* 4.9 10.8 - - + +
94H PHE* 4.0 28.0 - - + -
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Residues in contact with GLU 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H VAL* 2.9 29.9 + - - +
81H ARG* 3.2 12.1 + - - +
83H LEU* 1.3 75.0 - - - +
85H LYS* 1.3 63.1 + - + +
87H PHE 2.9 15.2 - - - +
88H SER* 3.8 1.4 - - - +
89H GLY* 3.2 24.9 + - - +
90H LYS 3.9 17.9 - - - +
91H HIS* 4.1 3.7 - - - -
92H VAL* 3.9 26.1 + - + +
169H LYS* 3.9 18.8 + - - -
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Residues in contact with LYS 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H ARG* 2.9 30.8 + - - +
82H GLU* 3.2 24.4 + - - +
84H GLU* 1.3 79.3 - - + +
86H LYS* 1.3 70.8 - - + +
87H PHE 4.5 0.3 - - - +
88H SER 5.6 0.2 - - - +
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Residues in contact with LYS 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 4.9 16.2 - - + +
29H GLU* 4.6 26.1 + - + +
30H LEU* 4.4 20.2 - - + -
82H GLU* 2.9 36.6 + - - +
83H LEU* 4.8 1.8 - - - +
85H LYS* 1.3 83.7 - - + +
87H PHE* 1.3 61.0 + - + +
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Residues in contact with PHE 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 4.2 24.5 - - + -
22H GLY* 5.9 6.5 - - - +
23H ILE* 4.1 33.9 - - + -
26H ALA* 5.5 8.3 - - + -
50H GLU* 4.6 15.0 - - - -
60H ILE* 5.0 7.0 - - + -
83H LEU* 2.7 24.6 + - + +
84H GLU 2.9 14.6 - - - +
85H LYS 4.9 0.4 - - - -
86H LYS* 1.3 79.5 - - + +
88H SER* 1.3 96.6 + - - +
89H GLY 3.0 1.0 + - - -
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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