Contacts of the helix formed by residues 53 - 69 (chain A) in PDB entry 3UX9
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 ALA 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU 4.9 2.8 + - - -
51A ALA 3.4 5.7 + - - +
52A PRO* 1.3 71.2 - - - +
54A ILE* 1.3 66.4 + - - +
55A SER* 4.2 8.7 - - - +
56A VAL* 3.1 35.8 + - + +
57A LEU* 3.2 11.3 + - - +
113A ASN* 4.6 9.0 - - - +
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Residues in contact with ILE 54 (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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52A PRO 3.6 2.2 + - - -
53A ALA* 1.3 67.7 - - - +
55A SER* 1.3 63.7 + - - +
56A VAL 2.9 5.4 - - - -
57A LEU* 3.8 13.5 - - + -
58A HIS* 2.8 34.8 + - - +
96A LEU* 3.4 44.6 - - + +
99A CYS* 3.6 30.3 - - + +
100A VAL* 3.8 15.7 - - + -
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Residues in contact with SER 55 (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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53A ALA* 4.2 4.3 - - - +
54A ILE* 1.3 84.8 + - - +
56A VAL* 1.3 59.3 + - - +
58A HIS* 3.5 10.0 + - - +
59A GLU* 3.2 22.2 + - - +
100A VAL* 4.8 14.4 - - - +
113A ASN* 4.0 14.5 + - - -
117A ILE* 3.8 24.3 - - - +
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Residues in contact with VAL 56 (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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42A GLU* 4.4 14.8 - - + +
43A PHE* 3.9 26.4 - - + -
52A PRO 5.3 0.4 - - - -
53A ALA* 3.3 32.5 - - + +
54A ILE 2.9 0.2 - - - -
55A SER* 1.3 82.2 - - - +
57A LEU* 1.3 64.8 + - + +
58A HIS 3.2 0.7 - - - -
59A GLU* 3.3 9.2 + - + +
60A LEU* 2.9 27.4 + - - +
113A ASN* 4.5 5.2 - - - +
116A SER* 4.5 18.6 - - - -
117A ILE* 4.3 14.6 - - + -
120A VAL* 4.8 9.0 - - + +
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Residues in contact with LEU 57 (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 LEU* 5.5 18.2 - - + +
43A PHE* 3.9 27.1 - - + -
52A PRO* 3.7 25.4 - - + +
53A ALA 3.2 18.2 + - - +
54A ILE* 3.1 20.8 + - + +
56A VAL* 1.3 80.7 - - - +
58A HIS* 1.3 64.3 + - - +
60A LEU* 3.1 8.2 + - + +
61A ILE* 3.0 31.0 + - + +
96A LEU* 4.4 10.5 - - + -
155A SER* 4.5 15.9 - - - +
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Residues in contact with HIS 58 (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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54A ILE 2.8 20.4 + - - +
55A SER* 3.5 11.1 + - - +
57A LEU* 1.3 74.9 - - - +
59A GLU* 1.3 60.4 + - - +
61A ILE* 3.3 1.9 + - - +
62A GLN* 2.7 59.7 + - + +
93A LEU* 3.7 15.1 - - + +
96A LEU* 3.9 23.8 - - + +
97A GLU* 3.1 48.5 + - + +
100A VAL* 4.5 12.6 - - + +
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Residues in contact with GLU 59 (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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55A SER 3.2 14.9 + - - +
56A VAL* 3.8 9.4 - - - +
57A LEU 3.2 0.8 - - - -
58A HIS* 1.3 86.7 + - - +
60A LEU* 1.3 57.6 + - - +
62A GLN* 3.4 14.1 - - - +
63A GLN* 2.8 64.8 + - + +
117A ILE* 3.6 40.1 - - + +
120A VAL* 4.2 12.6 - - + -
121A LYS* 3.6 15.3 + - + -
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Residues in contact with LEU 60 (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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38A PHE* 4.6 17.0 - - + -
43A PHE* 4.0 15.5 - - + -
56A VAL 2.9 14.4 + - - +
57A LEU* 3.3 11.7 - - + +
59A GLU* 1.3 72.2 - - - +
61A ILE* 1.3 73.0 + - + +
63A GLN* 3.0 4.7 + - - +
64A ILE* 3.0 36.7 + - + +
120A VAL* 4.1 9.8 - - + +
124A PHE* 3.8 26.2 - - + -
151A SER* 4.5 10.8 - - - +
152A LEU* 4.5 12.8 - - + -
155A SER* 3.6 33.9 - - - +
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Residues in contact with ILE 61 (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 LEU 5.3 4.3 - - - +
11A ASN* 4.6 3.8 - - - +
57A LEU* 3.0 17.6 + - + +
58A HIS 3.7 4.0 - - - +
60A LEU* 1.3 80.7 - - + +
62A GLN* 1.3 63.1 + - - +
64A ILE* 3.3 7.7 + - + +
65A PHE* 2.9 22.3 + - - +
89A LEU* 3.9 18.1 - - + +
92A GLN* 3.6 37.5 - - + +
93A LEU* 3.9 23.8 - - + -
96A LEU* 3.6 18.2 - - + -
152A LEU* 4.3 23.8 - - + -
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Residues in contact with GLN 62 (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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58A HIS* 2.7 46.0 + - + +
59A GLU* 3.4 25.4 - - - +
61A ILE* 1.3 73.3 - - - +
63A GLN* 1.3 58.3 + - - +
65A PHE* 3.1 7.3 + - - +
66A ASN* 3.0 52.5 + - - +
93A LEU* 3.9 24.7 - - + +
97A GLU* 4.8 4.4 + - - -
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Residues in contact with GLN 63 (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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59A GLU* 2.8 47.2 + - + +
62A GLN* 1.3 74.6 - - - +
64A ILE* 1.3 67.9 + - - +
66A ASN* 2.9 25.2 + - - +
67A LEU* 2.8 22.7 + - - +
120A VAL* 4.3 7.0 - - + +
121A LYS* 3.6 26.0 - - - +
124A PHE* 3.4 48.5 - - + +
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Residues in contact with ILE 64 (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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60A LEU* 3.0 26.8 + - + +
61A ILE* 3.6 10.8 - - + +
63A GLN* 1.3 75.1 - - - +
65A PHE* 1.3 62.1 + - - +
67A LEU* 3.2 5.4 + - - +
68A PHE* 3.1 34.9 + - + +
85A PHE* 4.3 5.6 - - + -
89A LEU* 4.0 22.6 - - + +
124A PHE* 3.6 22.6 - - + -
148A ILE* 3.7 33.7 - - + +
151A SER* 6.0 0.4 - - - -
152A LEU* 3.8 26.5 - - + +
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Residues in contact with PHE 65 (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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61A ILE 2.9 13.9 + - - +
62A GLN* 3.3 15.0 - - - +
63A GLN 3.0 0.4 - - - -
64A ILE* 1.3 74.5 - - - +
66A ASN* 1.3 75.0 + - - +
67A LEU 3.2 0.2 + - - -
68A PHE 3.4 0.3 + - - -
69A THR* 2.9 56.0 + - + +
86A CYS* 3.9 18.2 - - + -
89A LEU* 3.9 30.7 - - + +
90A TYR* 4.6 20.2 - + + -
93A LEU* 4.2 18.8 - - + -
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Residues in contact with ASN 66 (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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62A GLN* 3.0 36.4 + - - +
63A GLN* 2.9 32.6 + - - +
65A PHE* 1.3 82.2 - - - +
67A LEU* 1.3 63.5 + - - +
68A PHE 3.5 0.2 + - - -
69A THR* 3.5 11.2 + - - -
70A THR* 3.5 18.7 - - - +
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Residues in contact with LEU 67 (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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63A GLN 2.8 12.1 + - - +
64A ILE* 3.4 10.1 - - - +
65A PHE 3.1 0.2 - - - -
66A ASN* 1.3 80.0 - - - +
68A PHE* 1.3 81.9 + - + +
70A THR* 3.3 21.4 + - + +
73A SER* 3.9 3.1 - - - -
124A PHE* 4.5 12.8 - - + -
127A ILE* 4.4 10.5 - - + -
128A THR* 4.4 22.7 - - + -
131A LEU* 4.4 19.1 - - + -
141A TRP* 4.4 8.5 - - + -
144A VAL* 4.2 16.8 - - + -
148A ILE* 4.3 15.7 - - + -
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Residues in contact with PHE 68 (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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18A LEU* 4.2 14.6 - - + -
21A MET* 3.7 15.5 - - + -
64A ILE* 3.1 27.1 + - + +
65A PHE 4.6 0.9 - - - +
67A LEU* 1.3 98.7 - - + +
69A THR* 1.3 59.8 + - - +
70A THR 3.4 2.0 - - - +
73A SER* 2.6 29.4 + - - -
77A TRP* 3.5 33.9 - + - -
82A LEU* 3.9 19.7 - - + +
85A PHE* 3.9 20.6 - + + -
86A CYS* 3.9 14.0 - - - -
89A LEU* 5.0 1.6 - - + -
141A TRP* 4.3 10.5 - + - -
144A VAL* 4.7 1.3 - - + -
145A ARG* 4.5 14.6 - - - -
148A ILE* 4.0 13.7 - - + -
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Residues in contact with THR 69 (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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65A PHE* 2.9 51.0 + - + +
66A ASN* 3.5 8.7 + - - -
67A LEU 3.4 0.6 - - - -
68A PHE* 1.3 80.2 - - - +
70A THR* 1.3 65.6 + - - +
86A CYS* 3.8 22.7 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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