Contacts of the helix formed by residues 109 - 131 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR 4.2 12.8 - - - +
30B SER* 4.0 10.1 - - - +
31B CYS 3.2 18.6 - - - +
32B GLN* 4.3 5.4 - - + +
33B ILE* 4.5 0.9 - - - -
108B GLU* 1.3 78.6 - - - +
110B PRO* 1.3 72.1 - - - +
111B LEU* 3.4 11.3 + - - +
112B GLN* 3.0 37.0 + - - +
113B LEU* 3.0 21.8 + - - +
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Residues in contact with PRO 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.6 24.5 - - + -
29A THR* 4.2 6.1 - - + -
26B GLN* 5.7 6.3 - - + +
29B THR* 5.6 1.1 - - - +
31B CYS* 3.4 37.0 - - + +
33B ILE* 4.0 22.6 - - + -
108B GLU 4.2 2.0 - - - +
109B THR* 1.3 85.8 - - - +
111B LEU* 1.3 58.4 + - + +
113B LEU* 3.5 3.0 - - + +
114B LEU* 2.9 39.4 + - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.7 36.5 - - + +
26B GLN* 4.1 17.5 - - + +
27B MET 4.3 7.9 - - - +
28B GLU* 4.0 37.9 - - + +
29B THR 5.3 1.6 - - - +
109B THR* 3.0 10.0 + - - +
110B PRO* 1.3 78.2 - - + +
112B GLN* 1.3 65.0 + - + +
114B LEU* 3.4 5.7 + - + +
115B GLU* 3.1 33.0 + - - +
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 5.4 2.1 + - - -
108B GLU* 3.2 39.1 + - + +
109B THR* 3.0 45.9 + - - +
111B LEU* 1.3 76.4 - - + +
113B LEU* 1.3 65.3 + - - +
115B GLU* 3.6 7.3 + - - +
116B LYS* 3.4 23.4 + - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 5.0 3.6 - - + -
33B ILE* 3.7 23.1 - - + -
35B PHE* 3.7 46.2 - - + -
37B PHE* 5.5 0.2 - - + -
60B ILE* 4.0 38.6 - - + -
64B THR* 4.0 11.2 - - + -
65B MET* 4.7 7.4 - - + -
108B GLU* 4.6 0.8 + - - -
109B THR 3.0 11.9 + - - +
110B PRO* 3.5 9.6 - - + +
112B GLN* 1.3 72.9 - - - +
114B LEU* 1.3 61.3 + - + +
115B GLU 3.0 1.1 - - - -
116B LYS* 2.7 37.8 + - + +
117B VAL* 3.1 8.5 + - + -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 4.7 11.2 - - - -
19B LEU* 5.4 4.1 - - + +
22B LEU* 3.6 27.1 - - + -
23B ILE* 3.9 25.1 - - + +
26B GLN* 3.8 22.7 - - + -
65B MET* 3.3 44.2 - - + -
110B PRO* 2.9 27.4 + - + +
111B LEU* 4.0 7.0 - - + +
113B LEU* 1.3 75.3 - - + +
115B GLU* 1.3 55.7 + - - +
117B VAL* 3.2 8.0 + - + +
118B LYS* 2.8 30.5 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 5.1 0.9 + - - -
23B ILE* 4.3 18.8 - - - +
111B LEU* 3.1 25.0 + - - +
112B GLN* 3.6 8.5 - - - +
113B LEU 2.9 0.4 + - - -
114B LEU* 1.3 74.7 - - - +
116B LYS* 1.3 66.1 + - + +
118B LYS* 3.1 36.8 + - - +
119B ASN* 3.0 40.6 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 4.1 16.8 - - + -
37B PHE* 3.6 42.1 - - + -
38B VAL 5.4 0.2 - - - -
49B TYR* 5.3 3.8 - - - +
106B PHE* 4.1 24.1 - - - -
108B GLU* 3.2 28.9 + - - -
112B GLN* 3.4 11.9 + - - +
113B LEU* 2.7 18.4 + - + +
115B GLU* 1.3 75.8 - - + +
117B VAL* 1.3 59.1 + - - +
119B ASN* 3.5 8.0 + - - +
120B VAL* 3.3 27.9 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.5 12.1 - - + -
37B PHE* 5.4 0.2 - - + -
57B VAL* 4.1 26.9 - - + -
60B ILE* 4.2 16.6 - - + -
61B MET* 5.0 2.0 - - + -
65B MET* 4.2 27.4 - - + -
113B LEU* 3.1 18.7 + - + +
114B LEU* 3.6 10.3 - - + +
115B GLU 3.2 0.2 - - - -
116B LYS* 1.3 75.4 - - + +
118B LYS* 1.3 65.3 + - - +
120B VAL* 3.3 9.9 + - - +
121B PHE* 3.1 45.3 + - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 5.1 5.1 - - + +
19B LEU* 4.2 24.7 - - + +
20B GLN* 3.1 33.7 + - + +
23B ILE* 3.6 18.2 - - + -
114B LEU 2.8 18.1 + - - +
115B GLU* 3.1 26.9 + - - +
117B VAL* 1.3 78.0 - - - +
119B ASN* 1.3 68.8 + - - +
121B PHE* 3.3 3.6 + - - +
122B ASN* 2.9 47.3 + - - +
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Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.6 0.6 - - - +
115B GLU* 3.0 31.6 + - - +
116B LYS* 3.9 7.3 - - - +
117B VAL 3.3 0.2 - - - -
118B LYS* 1.3 87.3 - - - +
120B VAL* 1.3 61.2 + - + +
122B ASN* 4.1 8.6 + - - +
123B GLU* 2.9 39.3 + - + +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.9 10.5 - - + -
49B TYR* 4.9 4.7 - - + -
50B LEU* 4.1 14.8 - - + +
53B ALA* 3.6 26.5 - - + -
54B PHE* 4.0 35.0 - - + +
57B VAL* 4.1 12.1 - - + -
116B LYS 3.3 14.8 + - - +
117B VAL 3.3 8.9 + - - +
118B LYS 3.2 0.6 - - - -
119B ASN* 1.3 77.9 - - + +
121B PHE* 1.3 59.7 + - + +
124B THR* 2.5 44.3 + - - +
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.9 21.3 - - + +
15B HIS* 6.4 0.7 - - + -
16B LEU* 4.3 9.4 - - + -
19B LEU* 3.7 26.5 - - + -
54B PHE* 4.5 15.5 - + - -
57B VAL* 3.8 21.3 - - + -
58B GLN* 4.7 1.1 - - - -
61B MET* 4.1 21.3 - - + -
80B LEU* 4.2 18.2 - - + -
83B LEU* 4.7 6.1 - - + -
84B SER* 4.0 13.0 - - - -
87B LEU* 4.6 5.2 - - + -
117B VAL* 3.1 40.7 + - + -
118B LYS 3.3 6.1 + - - +
120B VAL* 1.3 78.4 - - + +
122B ASN* 1.3 60.6 + - - +
124B THR* 3.7 4.2 - - - -
125B LYS* 2.9 31.4 + - - +
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.2 32.6 - - - +
118B LYS* 2.9 46.6 + - - +
119B ASN* 3.8 10.0 + - - +
121B PHE* 1.3 75.8 - - - +
123B GLU* 1.3 67.6 + - + +
125B LYS* 3.0 6.2 + - - +
126B ASN* 3.0 36.0 + - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.9 23.8 - - + -
119B ASN* 2.9 27.6 + - + +
122B ASN* 1.3 76.1 - - + +
124B THR* 1.3 63.2 + - - +
126B ASN* 3.4 17.5 + - - +
127B LEU* 3.1 38.1 + - + +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.5 20.4 - - + -
50B LEU* 4.2 10.1 + - - +
54B PHE* 5.0 3.6 - - + -
87B LEU* 4.9 3.4 - - + -
91B PHE* 4.0 17.2 - - + -
120B VAL* 2.5 34.9 + - - +
121B PHE* 3.7 4.7 - - - -
122B ASN 3.1 0.2 - - - -
123B GLU* 1.3 77.6 - - - +
125B LYS* 1.3 60.5 + - - +
127B LEU* 3.6 1.2 + - - +
128B LEU* 3.1 34.5 + - + +
135B PHE* 4.0 27.5 - - + -
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B SER 5.6 0.2 - - - -
9B HIS* 6.3 1.5 - - - -
11B ILE* 3.3 46.0 - - + +
12B GLY* 4.1 0.7 - - - -
13B SER* 4.0 26.1 + - - +
16B LEU* 3.7 25.1 - - + +
121B PHE 2.9 19.2 + - - +
122B ASN* 3.0 4.9 + - - +
124B THR* 1.3 75.6 - - - +
126B ASN* 1.3 72.2 + - - +
128B LEU* 3.3 2.8 + - - +
129B ASP* 2.9 52.1 + - - +
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASN* 3.0 31.2 + - - +
123B GLU* 3.9 20.4 + - - +
125B LYS* 1.3 89.2 + - - +
127B LEU* 1.3 64.1 + - + +
129B ASP* 3.8 6.0 + - - +
130B LYS* 3.3 46.1 + - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 6.2 2.2 - - + -
47B VAL* 5.2 4.7 - - + -
50B LEU* 3.7 29.6 - - + -
123B GLU* 3.1 24.0 + - + +
124B THR 4.2 2.2 - - - +
126B ASN* 1.3 81.7 - - + +
128B LEU* 1.3 57.1 + - - +
130B LYS* 4.0 10.7 - - + +
131B ASP* 2.7 38.7 + - - +
134B ILE* 3.7 35.1 - - + +
135B PHE* 4.5 5.4 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B CYS* 3.6 26.9 - - + +
8B SER* 3.2 26.9 - - - +
11B ILE* 4.8 4.7 - - + -
87B LEU* 3.9 25.6 - - + -
90B CYS* 4.6 7.2 - - + -
91B PHE* 5.2 0.7 - - + -
124B THR* 3.1 30.9 + - + +
125B LYS* 4.0 2.7 - - - +
127B LEU* 1.3 72.5 - - - +
129B ASP* 1.3 66.2 + - - +
130B LYS 3.1 2.1 + - - -
131B ASP 4.1 1.1 - - - -
132B TRP* 3.2 39.5 + - - +
134B ILE* 4.1 5.6 - - + -
135B PHE* 3.7 27.6 - - + -
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 2.6 37.6 - - - +
9B HIS* 4.1 30.5 + - + +
11B ILE 4.8 0.9 - - - +
125B LYS* 2.9 51.6 + - - +
126B ASN* 3.9 8.6 - - - +
128B LEU* 1.3 76.7 - - - +
130B LYS* 1.3 64.9 + - + +
132B TRP* 5.4 2.8 - - - -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASN* 3.3 36.8 + - + +
127B LEU* 4.0 12.1 - - + +
128B LEU 3.1 0.2 - - - -
129B ASP* 1.3 85.7 - - + +
131B ASP* 1.3 62.3 + - + +
132B TRP* 4.0 8.0 + - - -
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU 2.7 22.6 + - - +
128B LEU* 3.7 0.6 - - - -
130B LYS* 1.3 75.3 - - + +
132B TRP* 1.3 64.0 + - - +
133B ASN* 2.9 23.4 + - - +
134B ILE* 2.9 52.3 + - + +
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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