Contacts of the helix formed by residues 57 - 74 (chain F) in PDB entry 6V01
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 SER 57 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU* 4.6 1.7 - - - +
145D ILE* 4.3 10.9 - - - +
148D TYR* 4.3 3.6 - - - -
54F ASP* 3.4 31.6 + - - -
55F ASP 3.4 3.6 + - - -
56F ASN* 1.3 73.7 - - - +
58F TYR* 1.3 61.6 + - - +
59F MET 3.2 1.1 + - - -
60F TYR* 3.9 5.5 + - - +
61F ILE* 4.0 7.1 - - - +
300G ALA* 3.2 27.0 - - - +
323J TRP* 3.2 36.7 - - - +
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Residues in contact with TYR 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 3.7 31.3 - - + +
148D TYR* 3.3 39.5 - + + -
56F ASN* 4.1 22.4 + - - -
57F SER* 1.3 75.8 - - - +
59F MET* 1.3 87.3 + - + +
60F TYR 3.3 0.4 - - - -
61F ILE* 3.5 2.9 + - - +
62F LEU* 2.9 43.6 + - + +
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Residues in contact with MET 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ASN* 3.1 24.4 + - + +
58F TYR* 1.3 107.4 - - + +
60F TYR* 1.3 56.5 + - - +
62F LEU* 3.5 15.6 - - + +
63F PHE* 2.9 30.5 + - - +
323J TRP 4.5 2.7 - - - +
324J VAL* 4.1 36.1 - - + +
327J THR* 3.5 15.3 + - + +
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Residues in contact with TYR 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ASN 4.5 0.6 + - - -
57F SER 3.9 5.2 + - - +
58F TYR 3.3 0.8 - - - -
59F MET* 1.3 80.8 - - - +
61F ILE* 1.3 57.4 + - - +
63F PHE* 3.2 1.7 + + - +
64F VAL* 3.0 52.2 + - + +
300G ALA* 4.3 5.6 - - + -
303G LEU* 3.7 18.4 - - + -
304G TRP* 3.1 47.0 - + - -
307G VAL* 3.2 13.0 - - - +
323J TRP* 3.8 28.4 + + + -
326J LYS* 3.2 25.4 - - + -
327J THR* 3.3 25.9 + - - +
330J SER* 3.0 26.1 + - - -
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Residues in contact with ILE 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ILE* 4.0 13.7 - - + +
141D VAL* 3.7 31.6 - - + +
142D LEU* 4.0 13.7 - - + -
145D ILE* 3.9 21.8 - - + -
57F SER 4.0 7.0 - - - +
58F TYR 3.5 4.3 + - - +
60F TYR* 1.3 72.8 - - - +
62F LEU* 1.3 64.1 + - - +
63F PHE 3.6 0.2 + - - -
64F VAL 4.3 0.4 - - - +
65F MET* 3.2 40.2 + - + +
299G TYR* 4.5 6.7 - - + -
300G ALA* 3.7 37.0 - - + +
303G LEU* 4.5 12.8 - - + -
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ILE* 4.8 17.6 - - + +
58F TYR* 2.9 34.7 + - + +
59F MET* 3.5 19.7 - - + +
61F ILE* 1.3 78.5 - - - +
63F PHE* 1.3 62.2 + - + +
65F MET* 4.8 0.5 - - - +
66F PHE* 3.2 27.6 + - + +
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Residues in contact with PHE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F MET 2.9 17.6 + - - +
60F TYR* 3.2 2.9 + + - +
62F LEU* 1.3 79.2 - - + +
64F VAL* 1.3 76.1 + - + +
66F PHE* 3.2 8.9 + + - +
67F LEU* 2.9 63.0 + - + +
327J THR* 3.7 27.8 - - + -
330J SER* 3.7 27.1 - - - -
331J CYS* 3.4 38.1 - - + -
334J VAL* 5.6 0.9 - - + -
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Residues in contact with VAL 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F TYR* 3.0 43.2 + - + +
63F PHE* 1.3 96.1 - - + +
65F MET* 1.3 58.3 + - - +
67F LEU* 3.3 4.8 + - - +
68F PHE* 2.9 27.0 + - - +
270G PHE* 4.7 11.2 - - + -
273G LEU* 3.8 28.7 - - + -
274G ILE* 4.5 9.0 - - + -
303G LEU* 4.0 16.2 - - + -
307G VAL* 4.5 2.9 - - + -
330J SER* 4.4 3.8 - - - +
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Residues in contact with MET 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 3.6 19.9 - - + +
137D LEU* 3.9 30.1 - - + -
138D ILE* 3.9 23.3 - - + -
141D VAL* 4.4 6.3 - - + -
238D MET* 5.6 0.2 - - - -
61F ILE* 3.2 39.4 + - + +
63F PHE 3.4 0.6 - - - -
64F VAL* 1.3 77.4 - - + +
66F PHE* 1.3 57.0 + - - +
68F PHE* 3.8 8.0 - - - +
69F ALA* 2.9 29.5 + - - +
274G ILE* 3.6 32.5 - - + -
299G TYR* 4.1 19.1 - - + +
303G LEU* 5.0 1.6 - - + -
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Residues in contact with PHE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 4.9 4.4 - - + +
138D ILE* 5.5 0.6 - - - +
62F LEU* 3.2 25.5 + - + +
63F PHE* 3.2 9.3 + + - +
65F MET* 1.3 79.7 - - - +
67F LEU* 1.3 75.9 + - + +
69F ALA* 3.2 7.7 + - + +
70F VAL* 2.9 50.6 + - + +
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Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F PHE* 2.9 52.5 + - + +
64F VAL* 3.3 6.2 + - - +
66F PHE* 1.3 96.8 - - + +
68F PHE* 1.3 55.8 + - - +
70F VAL* 4.1 9.5 - - + +
71F THR* 3.2 21.3 + - - +
270G PHE* 3.5 30.3 - - + -
331J CYS* 5.4 0.4 - - - -
334J VAL* 5.0 5.2 - - + -
335J PHE* 3.7 35.9 - - + -
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Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D PHE* 4.0 16.6 - + - -
134D LEU* 4.4 10.1 - - + -
238D MET* 4.0 29.6 - - + -
64F VAL* 2.9 15.5 + - + +
65F MET* 3.8 8.5 - - - +
66F PHE 3.2 0.2 - - - -
67F LEU* 1.3 76.1 - - - +
69F ALA* 1.3 60.7 + - - +
70F VAL 3.2 1.8 - - - -
71F THR* 2.9 19.8 + - - -
72F VAL* 3.0 35.9 + - + +
267G TYR* 3.8 22.7 - + - -
270G PHE* 3.7 29.4 - - + -
271G LEU* 3.9 27.4 - - + -
274G ILE* 4.8 17.0 - - + -
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Residues in contact with ALA 69 (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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127D PHE* 3.9 11.3 - - + -
130D PHE* 3.6 26.5 - - + -
131D LEU* 4.9 7.6 - - + -
134D LEU* 3.7 19.3 - - + -
65F MET 2.9 17.5 + - - +
66F PHE* 3.2 8.0 + - + +
68F PHE* 1.3 73.6 - - - +
70F VAL* 1.3 61.0 + - + +
72F VAL* 3.8 0.6 - - - +
73F GLY* 2.9 24.8 + - - -
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Residues in contact with VAL 70 (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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127D PHE* 6.0 0.2 - - - -
66F PHE* 2.9 47.7 + - + +
67F LEU* 4.4 10.1 - - + +
68F PHE 3.2 0.2 - - - -
69F ALA* 1.3 78.8 - - + +
71F THR* 1.3 63.6 + - + +
73F GLY* 3.1 15.4 + - - -
74F SER* 3.2 20.9 + - - +
263G ILE* 6.0 1.3 - - + -
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Residues in contact with THR 71 (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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67F LEU 3.2 18.1 + - - +
68F PHE* 2.9 21.9 + - - -
70F VAL* 1.3 80.7 - - + +
72F VAL* 1.3 57.7 + - - +
74F SER 4.3 1.1 - - - -
75F LEU* 3.9 5.0 + - - +
263G ILE* 3.7 38.7 - - + +
266G LEU* 3.8 40.0 + - + -
267G TYR* 4.2 13.7 - - - +
270G PHE* 3.9 7.7 - - + -
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Residues in contact with VAL 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D PHE* 3.6 35.0 - - + -
238D MET 5.9 1.8 - - - +
242D ASP* 5.7 7.0 - - + +
68F PHE* 3.0 37.7 + - + +
70F VAL 3.2 0.2 - - - -
71F THR* 1.3 75.6 - - - +
73F GLY* 1.3 56.1 + - - +
74F SER 3.1 4.3 - - - -
75F LEU* 2.8 23.6 + - + +
76F ILE* 3.0 34.7 + - + +
267G TYR* 3.6 31.4 - - + -
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Residues in contact with GLY 73 (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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123D PHE* 3.8 10.5 - - - -
127D PHE* 3.5 31.8 - - - -
69F ALA 2.9 14.0 + - - -
70F VAL* 3.1 4.4 + - - -
72F VAL* 1.3 75.5 - - - +
74F SER* 1.3 58.6 + - - +
76F ILE* 4.4 2.7 - - - -
77F LEU* 3.5 20.3 - - - +
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Residues in contact with SER 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F VAL* 3.2 16.8 + - - +
72F VAL 3.1 1.0 - - - -
73F GLY* 1.3 76.5 + - - +
75F LEU* 1.3 59.6 + - - +
76F ILE 3.6 0.4 - - - -
77F LEU* 4.4 8.8 - - - +
78F GLY* 3.4 19.3 + - - -
263G ILE* 3.9 31.8 - - - +
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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
------------------------------------------------------------
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