Contacts of the helix formed by residues 109 - 131 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C TYR* 6.5 0.7 - - + -
27G MET 5.9 0.4 - - - -
28G GLU 4.5 11.4 - - - +
30G SER* 3.1 30.1 - - - +
31G CYS 3.9 2.7 - - - +
32G GLN* 3.7 18.1 + - + +
108G GLU* 1.3 78.4 - - - +
110G PRO* 1.3 74.4 - - - +
111G LEU* 3.1 11.5 + - - +
112G GLN* 3.1 29.9 + - - +
113G LEU* 3.1 18.7 + - - +
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Residues in contact with PRO 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLN* 4.4 14.4 - - + +
30G SER* 3.8 15.5 - - - +
31G CYS 3.6 14.6 - - - +
33G ILE* 4.3 11.2 - - + -
108G GLU 4.4 1.3 - - - +
109G THR* 1.3 88.2 - - - +
111G LEU* 1.3 56.2 + - - +
113G LEU* 3.5 8.4 + - + +
114G LEU* 2.9 36.0 + - - +
27H MET* 3.9 24.2 - - + +
29H THR* 3.9 26.5 - - + -
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Residues in contact with LEU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ILE* 3.5 38.6 - - + +
24G ASP* 5.8 0.4 - - - +
26G GLN* 4.1 19.4 - - + +
27G MET 4.9 2.7 - - - +
28G GLU* 4.0 37.5 - - + +
109G THR* 3.0 10.4 - - - +
110G PRO* 1.3 78.6 - - - +
112G GLN* 1.3 64.8 + - + +
114G LEU* 3.1 12.5 + - - +
115G GLU* 2.9 32.0 + - - +
68H ARG* 6.2 2.5 - - + -
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Residues in contact with GLN 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G GLN* 3.4 11.1 - - - +
108G GLU* 3.3 33.8 - - + +
109G THR* 3.1 34.6 + - - +
111G LEU* 1.3 77.5 - - + +
113G LEU* 1.3 61.6 + - - +
115G GLU* 2.8 26.4 + - - +
116G LYS* 3.0 14.6 + - - +
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Residues in contact with LEU 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ILE* 3.7 25.8 - - + -
35G PHE* 3.5 50.7 - - + -
37G PHE* 5.3 0.7 - - + -
60G ILE* 4.1 25.4 - - + -
64G THR* 4.1 10.8 - - + -
65G MET* 4.0 9.4 - - + -
108G GLU* 4.2 1.4 + - - -
109G THR 3.1 10.6 + - - +
110G PRO 3.5 8.3 - - - +
112G GLN* 1.3 76.1 - - - +
114G LEU* 1.3 60.8 + - - +
116G LYS* 3.4 8.2 + - + +
117G VAL* 3.3 22.0 + - + +
27H MET* 4.0 17.3 - - + -
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Residues in contact with LEU 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 5.1 6.9 - - + +
22G LEU* 3.1 37.0 - - + +
23G ILE* 3.5 19.5 - - + +
26G GLN* 3.5 34.8 - - + +
65G MET* 3.4 31.9 - - + -
110G PRO 2.9 27.4 + - - +
111G LEU* 3.3 6.7 - - - +
112G GLN 3.0 0.2 - - - -
113G LEU* 1.3 73.7 - - - +
115G GLU* 1.3 65.4 + - - +
116G LYS 3.3 0.2 - - - -
117G VAL* 4.0 3.4 - - + +
118G LYS* 3.2 22.0 + - - +
27H MET* 4.5 10.5 - - - -
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Residues in contact with GLU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLN* 5.4 4.5 + - - +
23G ILE* 3.8 30.8 - - - +
111G LEU* 2.9 16.2 + - - +
112G GLN* 2.8 14.5 + - - +
114G LEU* 1.3 76.5 - - - +
116G LYS* 1.3 58.8 + - - +
118G LYS* 3.4 8.9 + - - +
119G ASN* 3.0 28.4 + - - +
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Residues in contact with LYS 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G PHE* 4.2 13.0 - - + -
37G PHE* 3.5 38.5 - - + -
38G VAL 5.0 1.1 - - - -
49G TYR* 5.4 3.6 + - - +
106G PHE* 3.6 29.4 - - - -
108G GLU* 3.2 33.5 + - - +
112G GLN 3.0 12.2 + - - +
113G LEU* 3.5 9.9 - - + +
115G GLU* 1.3 76.3 - - - +
117G VAL* 1.3 61.8 + - - +
119G ASN* 3.2 9.4 + - - +
120G VAL* 3.1 26.0 + - - +
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Residues in contact with VAL 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 4.1 13.0 - - + -
37G PHE* 4.9 4.9 - - + -
57G VAL* 4.1 21.1 - - + -
60G ILE* 4.9 5.2 - - + -
61G MET* 5.2 6.7 - - + -
65G MET* 3.5 32.1 - - + -
80G LEU* 5.6 0.2 - - + -
113G LEU* 3.3 14.6 + - + +
114G LEU* 3.7 4.7 + - + +
116G LYS* 1.3 73.2 - - - +
118G LYS* 1.3 66.4 + - - +
120G VAL* 3.1 8.6 + - - +
121G PHE* 3.0 51.2 + - + -
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Residues in contact with LYS 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU* 3.5 43.6 - - - +
19G LEU* 3.5 32.8 - - + +
20G GLN* 3.8 23.1 - - - +
23G ILE* 3.9 17.0 - - + -
114G LEU 3.2 13.7 + - - +
115G GLU* 3.4 15.0 - - - +
117G VAL* 1.3 79.0 - - - +
119G ASN* 1.3 53.1 + - - +
121G PHE* 3.4 1.9 + - - +
122G ASN* 2.8 53.2 + - + +
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Residues in contact with ASN 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G GLN* 5.5 7.9 + - - +
49G TYR* 5.2 11.7 + - - -
115G GLU 3.0 13.8 + - - +
116G LYS* 3.3 12.8 - - - +
118G LYS* 1.3 77.6 - - - +
120G VAL* 1.3 54.6 + - + +
122G ASN* 4.1 8.8 + - - +
123G GLU* 2.7 69.9 + - - +
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Residues in contact with VAL 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G PHE* 3.9 23.6 - - + -
49G TYR* 4.5 7.4 - - + +
50G LEU* 3.8 22.8 - - + +
53G ALA* 3.9 19.7 - - + -
54G PHE* 4.6 17.3 - - + +
57G VAL* 4.5 15.3 - - + -
116G LYS 3.1 14.7 + - - +
117G VAL* 3.1 8.9 + - - +
119G ASN* 1.3 75.9 - - + +
121G PHE* 1.3 68.1 + - + +
124G THR* 2.8 35.3 + - - +
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Residues in contact with PHE 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 3.6 15.5 - - + +
15G HIS* 6.5 0.2 - - + -
16G LEU* 4.4 7.0 - - + -
19G LEU* 3.9 25.1 - - + -
54G PHE* 4.7 6.1 - + - -
57G VAL* 4.5 12.8 - - + -
61G MET* 4.1 20.2 - - + -
80G LEU* 4.3 11.9 - - + -
83G LEU* 3.6 33.0 - - + -
84G SER* 3.5 25.4 - - - -
87G LEU* 4.6 11.9 - - + -
117G VAL* 3.0 46.9 + - + +
120G VAL* 1.3 83.5 - - + +
122G ASN* 1.3 61.8 + - - +
124G THR* 4.4 4.3 - - - -
125G LYS* 3.2 20.1 + - - +
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Residues in contact with ASN 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU* 4.0 22.1 - - - +
118G LYS* 2.8 39.2 + - + +
119G ASN* 3.5 12.1 + - - +
121G PHE* 1.3 75.5 - - - +
123G GLU* 1.3 67.0 + - - +
125G LYS* 3.2 4.8 + - - +
126G ASN* 3.2 38.6 + - - +
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Residues in contact with GLU 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G GLN* 5.9 1.2 + - - -
46G PRO* 5.0 7.1 - - - +
49G TYR* 4.8 5.9 - - - -
50G LEU* 3.5 35.4 - - + +
119G ASN* 2.7 55.2 + - - +
122G ASN* 1.3 74.8 - - + +
124G THR* 1.3 61.3 + - - +
126G ASN* 3.3 11.0 + - - +
127G LEU* 3.2 30.0 + - + +
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Residues in contact with THR 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 3.5 17.7 - - + -
50G LEU* 4.2 13.6 + - - +
54G PHE* 5.3 4.4 - - + -
87G LEU* 4.9 5.2 - - + -
91G PHE* 4.2 15.3 - - + -
120G VAL* 2.8 30.4 + - - +
121G PHE* 3.7 7.2 - - - -
123G GLU* 1.3 77.4 - - - +
125G LYS* 1.3 62.1 + - - +
127G LEU* 3.4 1.7 + - - +
128G LEU* 3.1 39.6 + - + +
135G PHE* 3.9 20.7 - - + -
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Residues in contact with LYS 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER 5.7 1.6 - - - +
11G ILE* 3.1 45.3 - - + +
12G GLY* 4.5 8.7 - - - -
13G SER* 4.6 10.0 + - - +
16G LEU* 3.9 24.1 - - + +
121G PHE 3.2 11.0 + - - +
122G ASN* 3.2 9.8 + - - +
124G THR* 1.3 79.7 - - - +
126G ASN* 1.3 70.3 + - - +
128G LEU* 4.0 4.4 - - - +
129G ASP* 2.9 48.4 + - - +
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Residues in contact with ASN 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G ASN* 3.2 35.0 + - - +
123G GLU* 3.7 12.2 - - - +
124G THR 3.3 0.4 - - - -
125G LYS* 1.3 89.9 + - - +
127G LEU* 1.3 62.3 + - + +
129G ASP* 3.9 6.8 - - - +
130G LYS* 3.0 44.5 + - - +
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Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G PRO* 5.4 5.8 - - + -
47G VAL* 4.6 11.2 - - + +
50G LEU* 3.9 21.5 - - + -
123G GLU* 3.2 19.3 + - + +
124G THR 4.1 2.5 - - - +
125G LYS 3.3 0.2 - - - -
126G ASN* 1.3 80.8 - - + +
128G LEU* 1.3 61.0 + - - +
129G ASP 3.2 1.8 - - - -
130G LYS* 3.1 16.5 + - + +
131G ASP* 2.8 31.3 + - - +
134G ILE* 4.1 33.7 - - + +
135G PHE* 4.3 8.7 - - + -
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Residues in contact with LEU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G CYS* 3.6 29.6 - - + +
8G SER* 3.1 27.7 - - - -
11G ILE* 4.5 4.7 - - + -
87G LEU* 4.2 15.9 - - + -
90G CYS* 4.8 6.5 - - + -
91G PHE* 5.4 0.9 - - + -
124G THR* 3.1 38.8 + - + +
125G LYS* 4.0 4.3 - - - +
127G LEU* 1.3 74.0 - - - +
129G ASP* 1.3 65.5 + - - +
131G ASP 3.8 3.6 - - - +
132G TRP* 3.3 43.9 + - - +
135G PHE* 3.9 24.0 - - + -
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Residues in contact with ASP 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G SER* 2.9 30.5 - - - +
125G LYS* 2.9 43.4 + - - +
126G ASN* 3.9 9.8 - - - +
127G LEU 3.2 0.2 - - - -
128G LEU* 1.3 77.8 - - - +
130G LYS* 1.3 64.0 + - + +
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Residues in contact with LYS 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G ASN* 3.0 35.9 + - - +
127G LEU* 3.1 19.5 + - + +
129G ASP* 1.3 83.5 - - + +
131G ASP* 1.3 61.6 + - + +
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Residues in contact with ASP 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G LEU 2.8 12.0 + - - +
128G LEU* 3.5 3.5 - - - -
130G LYS* 1.3 77.9 - - + +
132G TRP* 1.3 70.5 + - - +
133G ASN* 2.8 22.4 + - - +
134G ILE* 3.1 42.4 + - + +
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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