Contacts of the helix formed by residues 109 - 131 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J THR 4.0 16.2 - - - +
30J SER* 4.1 4.9 - - - +
31J CYS 3.6 15.5 - - - +
32J GLN* 3.9 16.8 - - + +
33J ILE* 4.7 0.2 - - - -
108J GLU* 1.3 77.1 - - - +
110J PRO* 1.3 76.9 - - - +
111J LEU* 3.9 10.1 + - - +
112J GLN* 2.9 43.9 + - - +
113J LEU* 3.1 9.4 + - - +
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Residues in contact with PRO 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I MET* 3.6 26.1 - - + +
29I THR* 4.7 4.0 - - + -
31I CYS* 4.6 2.9 - - - -
26J GLN* 5.9 4.3 - - + +
29J THR* 5.0 4.3 - - - +
31J CYS* 3.3 33.2 - - - +
32J GLN* 4.6 0.4 - - - -
33J ILE* 4.2 26.7 - - + -
108J GLU 3.8 2.0 - - - +
109J THR* 1.3 85.4 - - - +
111J LEU* 1.3 63.5 + - + +
113J LEU* 3.2 6.3 + - + +
114J LEU* 3.1 29.4 + - + +
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Residues in contact with LEU 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ARG* 4.6 10.1 - - - +
23J ILE* 4.1 22.5 - - + +
26J GLN* 3.7 34.5 - - + +
27J MET 4.4 3.4 - - - +
28J GLU* 4.0 38.4 - - + +
29J THR 4.9 4.7 - - - +
109J THR* 3.1 9.5 + - - +
110J PRO* 1.3 79.8 - - + +
112J GLN* 1.3 64.7 + - + +
113J LEU 3.0 0.2 - - - -
114J LEU* 3.0 18.5 + - + +
115J GLU* 3.0 18.0 + - + +
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Residues in contact with GLN 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J GLN* 5.5 1.4 + - - -
108J GLU* 3.5 30.9 + - + +
109J THR* 2.9 40.8 + - - +
111J LEU* 1.3 79.9 - - + +
113J LEU* 1.3 60.2 + - - +
115J GLU* 4.0 9.0 + - - +
116J LYS* 3.5 27.9 + - - +
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Residues in contact with LEU 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I MET* 5.0 3.8 - - + -
33J ILE* 3.7 15.3 - - + -
35J PHE* 3.7 48.9 - - + -
37J PHE* 5.7 0.2 - - + -
60J ILE* 4.0 31.9 - - + -
64J THR* 3.6 31.4 - - + -
65J MET* 4.9 6.1 - - + -
108J GLU* 4.7 0.2 + - - -
109J THR 3.1 7.4 + - - +
110J PRO* 3.3 11.4 - - + +
111J LEU 3.0 0.4 - - - -
112J GLN* 1.3 77.6 - - - +
114J LEU* 1.3 66.3 + - + +
116J LYS* 3.2 8.1 + - + +
117J VAL* 3.2 18.8 + - + +
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Residues in contact with LEU 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I MET* 4.7 12.6 - - + -
19J LEU* 5.1 3.4 - - + +
22J LEU* 3.4 29.4 - - + -
23J ILE* 3.6 22.3 - - + +
26J GLN* 3.5 33.4 - - + -
65J MET* 3.4 35.7 - - + -
110J PRO* 3.1 18.5 + - + +
111J LEU* 3.0 11.7 + - + +
113J LEU* 1.3 75.8 - - + +
115J GLU* 1.3 55.4 + - - +
117J VAL* 2.9 7.9 + - - +
118J LYS* 2.8 34.1 + - - +
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Residues in contact with GLU 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ARG* 4.9 11.6 + - - +
23J ILE* 4.0 17.7 - - + +
111J LEU* 3.0 18.6 + - + +
112J GLN* 4.1 8.7 - - - +
114J LEU* 1.3 75.6 - - - +
116J LYS* 1.3 64.0 + - + +
118J LYS* 3.1 30.8 + - - +
119J ASN* 2.9 40.4 + - - +
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Residues in contact with LYS 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J PHE* 4.2 12.6 - - + -
37J PHE* 3.7 40.6 - - + -
40J GLN* 6.2 2.9 - - - +
49J TYR* 5.5 2.0 - - - +
106J PHE* 4.1 20.5 - - - -
108J GLU* 2.8 33.5 + - - +
112J GLN* 3.5 14.3 + - - +
113J LEU* 3.2 9.8 + - + +
114J LEU 3.2 0.4 - - - -
115J GLU* 1.3 79.7 - - + +
117J VAL* 1.3 63.3 + - + +
119J ASN* 3.4 5.2 + - - +
120J VAL* 3.1 28.9 + - - +
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Residues in contact with VAL 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J LEU* 4.3 8.7 - - + -
37J PHE* 5.5 2.0 - - + -
57J VAL* 3.6 28.5 - - + -
60J ILE* 4.1 19.5 - - + -
61J MET* 5.0 1.8 - - + -
65J MET* 3.8 35.7 - - + -
113J LEU* 3.2 17.7 + - + +
114J LEU* 2.9 8.5 + - - +
116J LYS* 1.3 76.5 - - + +
118J LYS* 1.3 64.9 + - - +
120J VAL* 3.3 8.3 + - - +
121J PHE* 3.3 32.8 + - + -
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Residues in contact with LYS 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J LEU* 5.2 6.6 - - + +
19J LEU* 3.5 27.7 - - + +
20J GLN* 3.0 39.3 + - + +
23J ILE* 3.9 16.0 - - + +
114J LEU 2.8 14.9 + - - +
115J GLU* 3.1 33.8 + - - +
117J VAL* 1.3 72.9 - - - +
119J ASN* 1.3 67.2 + - - +
121J PHE* 3.2 5.7 + - - +
122J ASN* 2.7 42.4 + - + +
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Residues in contact with ASN 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J LEU* 5.3 0.2 - - - -
115J GLU* 2.9 35.9 + - - +
116J LYS* 4.0 5.6 - - - +
118J LYS* 1.3 86.9 - - - +
120J VAL* 1.3 60.3 + - + +
122J ASN* 3.7 14.9 + - - +
123J GLU* 2.8 33.3 + - - +
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Residues in contact with VAL 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J PHE* 3.9 24.2 - - + -
49J TYR* 5.3 4.7 - - + -
50J LEU* 4.0 15.1 - - + +
53J ALA* 4.0 16.2 - - + +
54J PHE* 4.5 29.6 - - + +
57J VAL* 4.9 10.1 - - + -
116J LYS 3.1 17.0 + - - +
117J VAL* 3.5 10.5 - - - +
118J LYS 3.2 0.4 - - - -
119J ASN* 1.3 77.2 - - - +
121J PHE* 1.3 61.6 + - + +
124J THR* 2.6 40.5 + - - +
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Residues in contact with PHE 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ILE* 3.9 15.9 - - + +
16J LEU* 4.3 11.4 - - + -
19J LEU* 3.6 19.7 - - + -
54J PHE* 4.8 6.5 - + - -
57J VAL* 3.9 28.3 - - + -
61J MET* 4.1 16.2 - - + -
80J LEU* 4.3 18.4 - - + -
83J LEU* 4.2 25.1 - - + -
84J SER* 3.8 23.3 - - - -
87J LEU* 4.4 9.9 - - + -
117J VAL* 3.3 24.4 + - + -
118J LYS 3.2 6.6 + - - +
120J VAL* 1.3 79.5 - - + +
122J ASN* 1.3 65.1 + - - +
124J THR* 3.4 5.9 + - + -
125J LYS* 3.0 25.6 + - - +
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Residues in contact with ASN 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 3.6 23.0 + - - -
16J LEU* 3.7 22.9 - - + +
118J LYS* 2.7 28.0 + - + +
119J ASN* 3.7 19.2 + - - +
121J PHE* 1.3 74.8 - - - +
123J GLU* 1.3 66.5 + - - +
125J LYS* 3.3 4.2 + - - +
126J ASN* 3.0 44.9 + - - +
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Residues in contact with GLU 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J PRO* 6.3 2.0 - - + -
50J LEU* 3.7 29.6 - - + -
119J ASN* 2.8 21.8 + - + +
122J ASN* 1.3 74.4 + - - +
124J THR* 1.3 66.9 + - - +
126J ASN* 3.1 18.4 + - - +
127J LEU* 3.0 45.6 + - + +
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Residues in contact with THR 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ILE* 3.4 21.1 - - + -
50J LEU* 4.3 9.9 + - - +
54J PHE* 5.2 3.8 - - + -
87J LEU* 4.9 4.0 - - + -
91J PHE* 4.1 27.3 - - + -
120J VAL* 2.6 29.8 + - - +
121J PHE* 3.5 6.5 - - - -
123J GLU* 1.3 77.7 - - - +
125J LYS* 1.3 61.3 + - - +
127J LEU* 3.6 1.0 + - - +
128J LEU* 3.1 43.1 + - + +
135J PHE* 4.2 15.3 - - + -
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Residues in contact with LYS 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 6.1 2.4 - - - -
8J SER 5.5 0.4 - - - +
11J ILE* 3.4 44.8 - - + +
12J GLY* 4.4 9.4 - - - -
13J SER* 4.4 9.2 + - - +
16J LEU* 3.5 29.8 - - + +
121J PHE 3.0 13.3 + - - +
122J ASN* 3.5 7.9 - - - +
123J GLU 3.2 0.2 - - - -
124J THR* 1.3 76.9 - - - +
126J ASN* 1.3 73.4 + - - +
128J LEU* 3.2 5.3 + - - +
129J ASP* 3.0 48.4 + - - +
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Residues in contact with ASN 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ASN* 3.0 34.8 + - - +
123J GLU* 3.5 26.0 + - - +
125J LYS* 1.3 93.8 + - - +
127J LEU* 1.3 60.4 + - + +
129J ASP* 3.4 11.9 + - - +
130J LYS* 2.9 41.4 + - - +
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Residues in contact with LEU 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J PRO* 5.9 4.7 - - + -
47J VAL* 4.9 7.4 - - + +
50J LEU* 3.9 25.6 - - + -
123J GLU* 3.0 33.6 + - + +
124J THR 4.2 2.2 - - - +
126J ASN* 1.3 75.2 - - + +
128J LEU* 1.3 66.0 + - - +
129J ASP 3.1 2.2 + - - -
130J LYS* 3.2 13.1 + - + +
131J ASP* 3.0 26.0 + - - +
134J ILE* 4.1 32.7 - - + +
135J PHE* 4.6 5.8 - - + -
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Residues in contact with LEU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J CYS* 3.6 30.1 - - + +
8J SER* 3.3 13.5 - - - +
11J ILE* 4.4 5.8 - - + -
87J LEU* 4.3 16.6 - - + -
90J CYS* 4.8 7.6 - - + -
91J PHE* 5.2 0.9 - - + -
124J THR* 3.1 43.9 + - + +
125J LYS* 3.2 5.4 + - - +
127J LEU* 1.3 77.1 - - - +
129J ASP* 1.3 61.6 + - - +
131J ASP 4.0 2.5 - - - -
132J TRP* 3.1 48.0 + - - +
134J ILE* 4.2 1.6 - - + -
135J PHE* 3.7 25.4 - - + -
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Residues in contact with ASP 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J SER* 2.5 39.3 - - - +
9J HIS* 5.1 11.5 + - + -
11J ILE 5.4 0.3 - - - +
125J LYS* 3.0 44.5 + - - +
126J ASN* 3.5 11.6 - - - +
127J LEU 3.1 0.6 - - - -
128J LEU* 1.3 79.2 - - - +
130J LYS* 1.3 64.8 + - + +
132J TRP* 5.2 2.1 + - - -
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Residues in contact with LYS 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J ASN* 2.9 47.9 + - - +
127J LEU* 3.2 15.7 + - + +
129J ASP* 1.3 84.0 - - + +
131J ASP* 1.3 62.6 + - + +
132J TRP* 4.1 2.5 - - - -
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Residues in contact with ASP 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J LEU 3.0 8.6 + - - +
128J LEU* 3.6 2.2 - - - -
130J LYS* 1.3 81.9 - - + +
132J TRP* 1.3 67.5 + - - +
133J ASN* 3.1 17.6 + - - +
134J ILE* 3.0 50.7 + - + +
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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