Contacts of the helix formed by residues 109 - 131 (chain F) in PDB entry 3UF2
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 109 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F THR 4.2 14.4 - - - +
30F SER* 4.6 2.5 - - - +
31F CYS 3.4 13.7 - - - +
32F GLN* 3.8 17.2 - - + +
33F ILE* 4.9 0.4 - - - -
108F GLU* 1.3 78.2 - - - +
110F PRO* 1.3 74.8 - - - +
111F LEU* 3.8 12.6 + - - +
112F GLN* 3.1 42.3 + - - +
113F LEU* 3.2 10.0 + - - +
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Residues in contact with PRO 110 (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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27E MET* 3.6 26.0 - - + -
29E THR* 4.4 6.3 - - + -
26F GLN* 5.5 6.5 - - + +
29F THR* 5.5 3.4 - - - +
31F CYS* 3.0 39.0 - - + +
32F GLN* 4.3 0.9 - - - -
33F ILE* 4.3 11.9 - - + -
108F GLU 3.8 2.0 - - - +
109F THR* 1.3 86.3 - - - +
111F LEU* 1.3 60.7 + - + +
113F LEU* 3.1 10.4 + - + +
114F LEU* 2.9 37.0 + - + +
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ILE* 3.8 24.2 - - + +
26F GLN* 3.7 34.1 - - + +
27F MET 4.5 3.1 - - - +
28F GLU* 4.0 35.4 - - + -
29F THR 4.9 4.5 - - - +
109F THR* 3.1 12.9 - - + +
110F PRO* 1.3 77.6 - - + +
112F GLN* 1.3 60.2 + - + +
114F LEU* 3.2 6.4 + - + +
115F GLU* 2.9 34.7 + - + +
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Residues in contact with GLN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F GLN* 4.7 4.2 + - - -
108F GLU* 3.1 45.9 - - + +
109F THR* 3.1 31.7 + - - +
111F LEU* 1.3 78.6 - - + +
113F LEU* 1.3 62.3 + - - +
115F GLU* 3.4 6.4 + - - +
116F LYS* 3.1 29.3 + - - +
6I TYR* 3.5 28.3 - - - +
9I HIS* 5.6 5.4 - - - +
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Residues in contact with LEU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 4.8 4.5 - - + -
33F ILE* 3.8 12.6 - - + -
35F PHE* 3.8 35.0 - - + -
60F ILE* 3.8 39.3 - - + -
64F THR* 3.5 32.1 - - + -
65F MET* 4.4 9.4 - - + -
108F GLU* 4.4 0.8 + - - -
109F THR 3.2 7.2 + - - +
110F PRO* 3.1 11.3 + - + +
112F GLN* 1.3 79.5 - - - +
114F LEU* 1.3 58.4 + - + +
116F LYS* 3.1 11.0 + - + +
117F VAL* 3.0 29.8 + - + +
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 4.5 12.1 - - - -
19F LEU* 5.1 3.9 - - + +
22F LEU* 3.6 23.1 - - + +
23F ILE* 3.6 22.2 - - + +
26F GLN* 3.5 33.7 - - + -
65F MET* 3.6 38.8 - - + -
110F PRO* 2.9 22.6 + - + +
111F LEU* 3.2 9.6 + - + +
113F LEU* 1.3 75.5 - - + +
115F GLU* 1.3 60.1 + - - +
117F VAL* 3.3 5.0 + - + +
118F LYS* 2.9 30.5 + - - +
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Residues in contact with GLU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F GLN* 4.9 2.4 + - - -
23F ILE* 4.3 18.5 - - + +
111F LEU* 2.9 18.8 + - + +
112F GLN* 3.9 6.7 - - - +
114F LEU* 1.3 76.9 - - - +
116F LYS* 1.3 57.5 + - - +
118F LYS* 3.2 36.1 + - - -
119F ASN* 2.8 49.0 + - - +
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Residues in contact with LYS 116 (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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35F PHE* 4.4 11.9 - - + -
37F PHE* 3.9 40.8 - - + -
40F GLN* 6.0 0.4 + - - -
49F TYR* 5.7 0.9 - - - -
106F PHE* 4.2 15.3 - - - -
108F GLU* 3.4 36.7 + - - +
112F GLN* 3.1 15.4 + - - +
113F LEU* 3.2 11.7 - - + +
115F GLU* 1.3 76.7 - - - +
117F VAL* 1.3 64.9 + - - +
119F ASN* 3.6 6.9 + - - +
120F VAL* 3.4 27.4 + - - +
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Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 4.3 11.2 - - + -
37F PHE* 5.7 0.4 - - + -
57F VAL* 4.1 20.2 - - + -
60F ILE* 4.0 22.0 - - + -
61F MET* 4.9 2.7 - - + -
65F MET* 3.8 31.2 - - + -
113F LEU* 3.0 22.2 + - + +
114F LEU* 3.3 7.4 + - - +
116F LYS* 1.3 75.4 - - + +
118F LYS* 1.3 65.5 + - - +
120F VAL* 3.3 11.1 + - - +
121F PHE* 3.2 42.7 + - + -
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Residues in contact with LYS 118 (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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16F LEU 4.8 3.4 - - - +
19F LEU* 4.1 33.0 - - + +
20F GLN* 2.6 34.1 + - - +
23F ILE* 3.7 12.3 - - + +
114F LEU 2.9 17.9 + - - +
115F GLU* 3.2 38.7 + - - +
117F VAL* 1.3 76.8 - - - +
119F ASN* 1.3 66.3 + - - +
121F PHE* 2.8 20.8 + - - +
122F ASN* 2.9 31.9 + - - +
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Residues in contact with ASN 119 (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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115F GLU* 2.8 41.3 + - - +
116F LYS* 3.9 6.6 - - - +
117F VAL 3.4 0.4 - - - -
118F LYS* 1.3 86.2 - - - +
120F VAL* 1.3 58.2 + - + +
122F ASN* 4.3 8.6 + - - +
123F GLU* 2.9 52.5 + - + +
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Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 4.0 11.7 - - + -
49F TYR* 5.2 5.4 - - + -
50F LEU* 4.1 17.6 - - + +
53F ALA* 3.9 20.4 - - + -
54F PHE* 4.2 32.1 - - + +
57F VAL* 4.2 11.7 - - + -
116F LYS 3.4 15.0 + - - +
117F VAL 3.3 8.7 + - - +
118F LYS 3.1 0.8 - - - -
119F ASN* 1.3 78.4 - - + +
121F PHE* 1.3 58.7 + - + +
123F GLU* 4.0 0.4 - - - -
124F THR* 2.6 45.3 + - - +
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Residues in contact with PHE 121 (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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11F ILE* 4.0 19.4 - - + +
16F LEU* 3.8 18.4 - - + +
19F LEU* 3.6 21.3 - - + -
54F PHE* 4.5 15.7 - + - -
57F VAL* 3.7 21.5 - - + -
61F MET* 4.2 13.7 - - + -
80F LEU* 4.5 11.2 - - + -
83F LEU* 4.3 18.4 - - + -
84F SER* 4.0 20.9 - - - -
117F VAL* 3.2 40.5 + - + -
118F LYS 2.8 7.0 + - - +
120F VAL* 1.3 78.2 - - + +
122F ASN* 1.3 64.7 + - - +
124F THR* 3.4 3.6 + - - -
125F LYS* 3.0 24.6 + - - +
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Residues in contact with ASN 122 (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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16F LEU* 3.5 34.4 + - - +
118F LYS* 2.9 42.0 + - - +
119F ASN* 3.8 9.3 + - - +
121F PHE* 1.3 77.6 - - - +
123F GLU* 1.3 59.0 + - + +
125F LYS* 3.3 2.9 + - - +
126F ASN* 3.1 43.3 + - - +
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Residues in contact with GLU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F TYR* 5.5 4.5 - - - -
50F LEU* 3.7 32.6 - - + +
119F ASN* 2.9 40.6 + - - +
120F VAL* 5.1 0.2 - - - -
122F ASN* 1.3 76.1 - - + +
124F THR* 1.3 64.5 + - - +
126F ASN* 3.4 11.1 + - - +
127F LEU* 3.2 29.8 + - + +
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Residues in contact with THR 124 (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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11F ILE* 3.5 20.0 - - + -
50F LEU* 4.2 11.4 + - - +
54F PHE* 4.7 8.4 - - + -
87F LEU* 4.9 3.6 - - + -
91F PHE* 4.2 11.6 - - + -
120F VAL* 2.6 31.3 + - - +
121F PHE* 3.8 5.4 - - - -
122F ASN 3.3 0.2 - - - -
123F GLU* 1.3 77.3 - - - +
125F LYS* 1.3 62.4 + - - +
127F LEU* 3.5 1.7 + - - +
128F LEU* 3.1 34.8 + - + +
135F PHE* 3.9 24.6 - - + -
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Residues in contact with LYS 125 (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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8F SER 5.5 0.9 - - - +
11F ILE* 3.2 43.0 - - + +
12F GLY* 4.7 0.9 - - - -
13F SER* 4.2 23.4 + - - +
16F LEU* 3.5 25.9 - - + +
121F PHE 3.0 18.0 + - - +
122F ASN 3.6 4.5 - - - +
123F GLU 3.3 0.2 - - - -
124F THR* 1.3 77.0 - - - +
126F ASN* 1.3 68.1 + - - +
128F LEU* 3.9 3.7 - - - +
129F ASP* 2.9 52.9 + - - +
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Residues in contact with ASN 126 (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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122F ASN* 3.1 27.8 + - - +
123F GLU* 3.4 12.2 + - - +
124F THR 3.3 0.4 - - - -
125F LYS* 1.3 87.1 + - - +
127F LEU* 1.3 65.1 + - + +
129F ASP* 3.9 6.9 + - - +
130F LYS* 3.0 47.2 + - - +
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Residues in contact with LEU 127 (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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46F PRO* 5.9 1.6 - - + -
47F VAL* 4.9 7.2 - - + +
50F LEU* 3.5 30.3 - - + -
123F GLU* 3.2 14.2 + - + +
124F THR 3.5 3.6 + - - +
125F LYS 3.2 0.2 - - - -
126F ASN* 1.3 82.1 - - + +
128F LEU* 1.3 61.0 + - - +
129F ASP 3.3 0.4 - - - -
130F LYS* 3.5 11.1 + - + +
131F ASP* 2.8 34.2 + - - +
134F ILE* 3.9 33.7 - - + +
135F PHE* 4.3 10.3 - - + -
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Residues in contact with LEU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F CYS* 3.6 41.1 - - + +
8F SER* 3.6 17.0 - - - +
11F ILE* 4.3 7.6 - - + -
87F LEU* 3.9 18.8 - - + -
90F CYS* 4.7 5.4 - - + -
91F PHE* 5.5 0.2 - - + -
124F THR* 3.1 34.5 + - + +
125F LYS* 3.4 4.9 + - - +
127F LEU* 1.3 74.0 - - - +
129F ASP* 1.3 67.2 + - - +
130F LYS 3.2 1.1 + - - -
131F ASP 3.8 4.7 - - - +
132F TRP* 3.4 31.5 + - - +
135F PHE* 3.8 26.9 - - + -
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Residues in contact with ASP 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F SER* 3.0 33.7 - - - +
125F LYS* 2.9 51.5 + - - +
126F ASN* 4.0 9.3 - - - +
128F LEU* 1.3 76.5 - - - +
130F LYS* 1.3 65.4 + - + +
132F TRP* 5.5 4.0 - - - -
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Residues in contact with LYS 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F ASN* 3.0 38.8 + - - +
127F LEU* 3.5 12.7 + - + +
128F LEU 4.1 0.4 - - - -
129F ASP* 1.3 84.2 - - + +
131F ASP* 1.3 61.6 + - + +
132F TRP* 4.2 4.2 - - - -
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Residues in contact with ASP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F LEU 2.8 21.8 + - - +
128F LEU* 3.6 1.2 - - - -
130F LYS* 1.3 80.8 - - + +
132F TRP* 1.3 59.3 + - - +
133F ASN* 3.2 16.2 + - - +
134F ILE* 3.2 49.2 + - + +
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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
------------------------------------------------------------
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