Contacts of the helix formed by residues 109 - 131 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR 3.9 17.3 - - - +
30A SER* 4.0 8.1 - - - +
31A CYS 3.1 17.7 - - - +
32A GLN* 4.1 6.4 - - + +
108A GLU* 1.3 77.0 - - - +
110A PRO* 1.3 75.3 - - - +
111A LEU* 3.9 7.5 + - - +
112A GLN* 2.9 49.3 + - - +
113A LEU* 3.1 10.4 + - - +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 6.1 3.4 - - + +
27A MET 6.1 0.9 - - - +
29A THR* 4.2 7.0 - - - +
31A CYS* 3.5 32.5 - - - +
33A ILE* 4.2 27.4 - - + -
108A GLU 3.8 1.3 - - - +
109A THR* 1.3 88.3 - - - +
111A LEU* 1.3 59.2 + - + +
113A LEU* 3.1 6.0 + - + +
114A LEU* 3.0 32.9 + - + +
27B MET* 3.8 21.4 - - + +
29B THR* 4.7 3.8 - - + +
31B CYS* 4.4 4.5 - - + -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.3 43.9 - - + +
26A GLN* 3.9 19.3 - - + +
27A MET 4.1 6.3 - - - +
28A GLU* 3.8 38.8 - - + -
29A THR 4.7 3.8 - - - +
109A THR* 3.2 7.7 + - - +
110A PRO* 1.3 79.4 - - + +
112A GLN* 1.3 60.7 + - + +
114A LEU* 3.3 6.5 + - + +
115A GLU* 2.9 35.9 + - - +
68B ARG* 5.5 4.0 - - - +
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Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN* 5.4 1.2 + - - -
108A GLU* 3.3 24.8 - - + +
109A THR* 2.9 50.9 + - - +
111A LEU* 1.3 78.3 - - + +
113A LEU* 1.3 62.3 + - - +
115A GLU* 3.5 7.6 + - - +
116A LYS* 3.2 26.3 + - - +
9C HIS* 4.1 32.0 + - - +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.7 24.7 - - + -
35A PHE* 3.6 51.3 - - + -
37A PHE* 5.7 0.7 - - + -
60A ILE* 4.1 27.6 - - + -
64A THR* 3.8 18.8 - - + -
65A MET* 4.8 6.7 - - + -
109A THR 3.1 9.4 + - - +
110A PRO* 3.1 9.8 + - + +
112A GLN* 1.3 74.7 - - - +
114A LEU* 1.3 67.1 + - + +
116A LYS* 2.9 19.2 + - + +
117A VAL* 3.0 15.7 + - + +
27B MET* 5.0 5.2 - - + -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.9 4.5 - - + +
22A LEU* 3.7 21.3 - - + -
23A ILE* 3.6 25.9 - - + +
26A GLN* 3.8 29.4 - - + -
65A MET* 3.5 37.2 - - + -
110A PRO* 3.0 18.5 + - + +
111A LEU* 3.3 11.4 + - + +
113A LEU* 1.3 77.2 - - + +
115A GLU* 1.3 56.7 + - - +
117A VAL* 3.4 6.1 + - + +
118A LYS* 3.0 27.5 + - - +
27B MET* 4.1 21.3 - - + -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLN* 4.4 7.8 + - - +
23A ILE* 4.2 26.1 - - - +
111A LEU* 2.9 21.0 + - - +
112A GLN* 3.6 9.4 - - - +
113A LEU 3.1 0.2 - - - -
114A LEU* 1.3 75.8 - - - +
116A LYS* 1.3 62.8 + - - +
118A LYS* 3.5 15.2 + - - +
119A ASN* 3.1 40.1 + - - +
68B ARG* 5.3 3.3 + - - -
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.3 12.1 - - + -
37A PHE* 3.7 34.3 - - + -
49A TYR* 5.6 1.3 - - - -
106A PHE* 3.7 26.5 - - - -
108A GLU* 3.2 31.9 + - - +
112A GLN* 3.2 11.9 + - - +
113A LEU* 2.9 12.9 + - + +
115A GLU* 1.3 76.2 - - - +
117A VAL* 1.3 65.8 + - - +
119A ASN* 3.2 9.6 + - - +
120A VAL* 3.1 27.4 + - - +
5C GLU* 4.4 12.3 + - - -
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.2 15.7 - - + -
37A PHE* 5.8 0.7 - - + -
57A VAL* 4.3 24.2 - - + -
60A ILE* 4.3 15.0 - - + -
61A MET* 5.2 1.8 - - + -
65A MET* 3.9 29.2 - - + -
80A LEU* 5.8 0.4 - - + -
113A LEU* 3.0 19.5 + - + +
114A LEU* 3.7 8.5 - - - +
115A GLU 3.3 0.2 - - - -
116A LYS* 1.3 76.3 - - + +
118A LYS* 1.3 63.6 + - - +
120A VAL* 3.1 11.4 + - - +
121A PHE* 3.3 36.7 + - + -
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.3 37.7 + - + +
19A LEU* 4.1 22.2 - - + +
20A GLN* 3.4 29.9 + - - +
23A ILE* 4.2 12.3 - - + -
114A LEU 3.0 17.0 + - - +
115A GLU* 3.6 18.6 - - - +
117A VAL* 1.3 78.2 - - - +
119A ASN* 1.3 57.0 + - - +
121A PHE* 3.3 3.5 + - - +
122A ASN* 2.7 50.6 + - + +
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 5.0 0.2 - - - +
115A GLU* 3.1 29.0 + - - +
116A LYS* 3.2 8.7 + - - +
118A LYS* 1.3 84.3 - - - +
120A VAL* 1.3 57.8 + - + +
122A ASN* 3.7 9.0 - - - +
123A GLU* 2.8 34.1 + - + +
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.7 25.1 - - + -
49A TYR* 5.3 4.3 - - + +
50A LEU* 4.5 13.6 - - + +
53A ALA* 3.9 11.9 - - + -
54A PHE* 4.2 26.0 - - + +
57A VAL* 4.2 20.4 - - + -
116A LYS 3.1 14.1 + - - +
117A VAL 3.1 8.1 + - - +
119A ASN* 1.3 77.8 - - + +
121A PHE* 1.3 62.2 + - + +
124A THR* 2.3 44.8 + - - +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.8 18.4 - - + +
15A HIS* 5.9 0.7 - - + -
16A LEU* 3.9 16.4 - - + -
19A LEU* 4.0 15.7 - - + -
54A PHE* 4.7 7.2 - + - -
57A VAL* 3.8 20.2 - - + -
58A GLN* 4.8 1.1 - - - -
61A MET* 4.5 9.0 - - - -
80A LEU* 4.4 12.8 - - + -
83A LEU* 3.7 30.5 - - + -
84A SER* 3.8 21.3 - - - -
87A LEU* 4.3 8.5 - - + -
117A VAL* 3.3 41.0 + - + -
118A LYS 3.9 5.2 - - - +
120A VAL* 1.3 79.5 - - + +
122A ASN* 1.3 61.3 + - - +
124A THR* 4.2 2.9 - - + -
125A LYS* 2.9 30.1 + - - +
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Residues in contact with ASN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.7 28.3 - - + +
118A LYS* 2.7 36.9 + - + +
119A ASN* 3.9 10.3 - - - +
121A PHE* 1.3 77.6 - - - +
123A GLU* 1.3 62.1 + - - +
125A LYS* 3.4 2.1 + - - +
126A ASN* 3.2 39.5 + - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.7 27.8 - - + +
119A ASN* 2.8 22.3 + - + +
122A ASN* 1.3 73.5 + - - +
124A THR* 1.3 64.7 + - - +
126A ASN* 3.6 15.1 + - - +
127A LEU* 3.3 39.9 + - + +
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.6 19.3 - - + -
50A LEU* 4.2 20.5 + - - +
54A PHE* 5.5 3.0 - - + -
87A LEU* 5.1 2.7 - - + -
91A PHE* 4.4 13.6 - - + -
120A VAL* 2.3 34.5 + - - +
121A PHE* 3.9 4.3 - - + -
123A GLU* 1.3 76.2 - - - +
125A LYS* 1.3 64.7 + - - +
127A LEU* 3.5 2.8 + - - +
128A LEU* 3.2 36.2 + - + +
135A PHE* 4.0 16.2 - - + -
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A HIS* 6.0 3.4 - - - -
11A ILE* 3.2 42.2 - - + +
12A GLY* 4.4 1.1 - - - -
13A SER* 4.2 22.6 + - - +
16A LEU* 3.8 24.0 - - + -
121A PHE 2.9 20.7 + - - +
122A ASN 3.6 4.7 - - - +
123A GLU 3.3 0.2 - - - -
124A THR* 1.3 78.3 - - - +
126A ASN* 1.3 71.8 + - - +
127A LEU 3.3 0.2 + - - -
128A LEU* 3.4 4.0 + - - +
129A ASP* 3.1 48.9 + - - +
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Residues in contact with ASN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASN* 3.2 32.0 + - - +
123A GLU* 3.8 19.3 + - - +
124A THR 3.3 0.4 - - - -
125A LYS* 1.3 90.0 + - - +
127A LEU* 1.3 65.8 + - + +
129A ASP* 3.7 8.4 + - - +
130A LYS* 3.5 36.4 + - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 6.1 2.7 - - + -
47A VAL* 5.3 5.2 - - + -
50A LEU* 3.5 31.9 - - + -
123A GLU* 3.3 27.8 - - - +
124A THR* 3.5 4.4 + - - +
125A LYS 3.3 0.2 - - - -
126A ASN* 1.3 80.7 - - + +
128A LEU* 1.3 55.2 + - - +
130A LYS* 3.2 14.6 + - + +
131A ASP* 2.7 38.5 + - - +
134A ILE* 4.0 30.1 - - + -
135A PHE* 4.7 4.9 - - + -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A CYS* 3.6 27.4 - - + +
8A SER* 3.6 7.3 + - - +
10A MET* 5.2 0.9 - - + +
11A ILE* 4.7 5.8 - - + +
87A LEU* 3.9 26.7 - - + -
90A CYS* 4.9 5.4 - - + -
91A PHE* 5.5 0.4 - - + -
124A THR* 3.2 32.4 + - + +
125A LYS* 3.4 4.9 + - - +
127A LEU* 1.3 75.0 - - - +
129A ASP* 1.3 67.0 + - - +
131A ASP 4.0 1.8 - - - -
132A TRP* 3.1 54.2 + - - +
134A ILE* 4.0 13.9 - - + -
135A PHE* 4.0 15.0 - - + +
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 2.7 36.1 + - - +
9A HIS* 3.7 29.8 + - + +
11A ILE 5.1 1.0 - - - +
125A LYS* 3.1 47.4 + - - +
126A ASN* 3.9 8.7 - - - +
127A LEU 3.3 0.2 - - - -
128A LEU* 1.3 76.1 - - - +
130A LYS* 1.3 62.7 + - + +
132A TRP* 5.4 2.1 - - - -
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 3.5 25.9 + - - +
127A LEU* 3.2 16.6 + - + +
128A LEU 3.1 0.6 - - - -
129A ASP* 1.3 82.9 - - + +
131A ASP* 1.3 61.7 + - + +
132A TRP* 4.1 3.5 - - - -
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU 2.7 14.8 + - - +
128A LEU* 3.5 2.6 - - - -
130A LYS* 1.3 78.4 - - + +
132A TRP* 1.3 57.2 + - - +
133A ASN* 3.2 18.0 + - - +
134A ILE* 2.9 53.9 + - + +
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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