Contacts of the helix formed by residues 51 - 66 (chain A) in PDB entry 2RIO
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 PHE 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A SER 5.3 0.9 - - - -
28A SER* 3.4 45.3 - - - -
30A THR* 5.4 2.2 - - - -
47A MET* 4.1 31.9 - - + -
48A LEU* 2.9 29.4 + - + +
50A ASP* 1.3 83.6 - - + +
52A CYS* 1.3 51.9 + - - +
53A ASP 3.3 3.6 + - - -
54A ILE* 3.3 35.0 + - + +
55A ALA* 2.8 34.9 + - - +
84A LEU* 4.9 0.9 - - + -
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Residues in contact with CYS 52 (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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48A LEU 4.5 0.4 + - - -
49A ILE* 3.2 38.1 + - + +
50A ASP 3.4 1.2 - - - -
51A PHE* 1.3 75.4 - - - +
53A ASP* 1.3 68.8 + - - +
55A ALA* 3.5 0.5 + - - +
56A LEU* 3.1 40.3 + - - +
79A THR* 3.8 15.5 - - - -
84A LEU* 4.1 20.5 - - - +
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Residues in contact with ASP 53 (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 ASP 4.7 3.9 + - - +
51A PHE 3.3 0.8 - - - -
52A CYS* 1.3 83.3 - - - +
54A ILE* 1.3 54.5 + - + +
56A LEU* 3.2 26.8 + - - +
57A MET* 2.7 35.4 - - + +
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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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47A MET* 6.4 0.4 - - + -
51A PHE* 3.5 42.1 - - + +
53A ASP* 1.3 77.3 - - + +
55A ALA* 1.3 61.3 + - - +
56A LEU 3.3 0.3 + - - -
57A MET* 3.5 19.9 + - + +
58A GLU* 3.3 22.2 + - - +
173A GLY 5.4 10.0 - - - +
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Residues in contact with ALA 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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47A MET* 4.7 5.2 - - + -
51A PHE* 2.8 22.7 + - + +
52A CYS 3.8 3.1 - - - +
53A ASP 3.2 0.4 - - - -
54A ILE* 1.3 73.6 - - - +
56A LEU* 1.3 58.0 + - - +
58A GLU* 3.2 18.4 - - - +
59A ILE* 2.9 41.9 + - + +
84A LEU* 3.4 31.0 - - + -
86A ILE* 4.7 4.7 - - + -
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Residues in contact with LEU 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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52A CYS* 3.1 36.6 - - - +
53A ASP* 3.2 26.6 + - - +
55A ALA* 1.3 78.2 - - + +
57A MET* 1.3 61.4 + - + +
59A ILE* 4.2 14.1 - - + +
60A LYS* 3.3 26.5 + - - +
84A LEU* 5.3 3.6 - - + -
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Residues in contact with MET 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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53A ASP* 2.7 38.6 - - + +
54A ILE* 3.5 22.2 - - + +
56A LEU* 1.3 73.1 - - - +
58A GLU* 1.3 68.2 + - - +
60A LYS* 3.2 10.5 + - + +
61A LEU* 3.2 30.9 + - + +
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Residues in contact with GLU 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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45A LYS* 3.5 24.3 + - - +
47A MET* 4.4 15.3 - - - +
54A ILE* 3.3 12.5 + - - +
55A ALA* 3.2 26.0 + - - +
57A MET* 1.3 79.6 - - - +
59A ILE* 1.3 68.7 + - + +
61A LEU* 3.1 4.2 + - - +
62A LEU* 3.0 23.1 + - + +
86A ILE* 4.9 6.3 - - - +
172A PHE* 3.8 34.0 + - + +
173A GLY* 3.6 28.8 + - - +
175A CYS* 4.5 4.2 - - - -
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Residues in contact with ILE 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 ALA* 2.9 39.1 + - + +
56A LEU* 4.2 13.9 - - + +
58A GLU* 1.3 79.4 - - + +
60A LYS* 1.3 54.8 + - - +
62A LEU* 3.6 8.4 - - + +
63A THR* 2.8 35.6 + - - +
74A TYR* 3.5 41.5 - - + +
77A SER* 3.7 21.3 - - - +
84A LEU* 4.8 2.2 - - + -
86A ILE* 4.2 15.5 - - + -
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Residues in contact with LYS 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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56A LEU 3.3 17.4 + - - +
57A MET* 3.2 10.0 + - - +
58A GLU 3.2 1.0 - - - -
59A ILE* 1.3 80.0 - - - +
61A LEU* 1.3 71.0 + - + +
63A THR* 3.4 12.0 - - + +
64A GLU* 3.2 25.8 + - - +
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Residues in contact with LEU 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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57A MET* 3.2 17.7 + - + +
58A GLU 3.1 2.5 + - - +
60A LYS* 1.3 87.0 - - + +
62A LEU* 1.3 60.3 + - - +
64A GLU* 3.5 11.3 + - - +
65A SER* 2.7 32.4 + - - -
136A ILE* 3.6 13.5 - - + +
172A PHE* 4.5 2.4 - - - -
175A CYS* 3.6 43.1 - - - +
176A LYS* 4.4 0.9 - - - +
177A LYS* 3.7 48.5 - - + +
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Residues in contact with LEU 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 GLU* 3.0 15.2 + - + +
59A ILE* 3.6 12.8 - - + +
61A LEU* 1.3 76.7 - - - +
63A THR* 1.3 57.7 + - - +
65A SER* 2.8 18.2 + - - -
66A ASP* 2.9 24.8 + - + +
71A VAL* 4.0 13.2 - - + -
72A ILE* 3.1 33.7 - - + +
74A TYR* 4.0 23.8 - - + -
86A ILE* 6.0 0.7 - - + -
88A LEU* 4.3 17.9 - - + -
171A ASP 6.2 0.2 - - - +
172A PHE* 3.8 35.3 - - + +
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Residues in contact with THR 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 ILE* 2.8 25.5 + - - +
60A LYS* 3.4 14.4 - - + +
62A LEU* 1.3 71.0 - - - +
64A GLU* 1.3 60.1 + - + +
65A SER 3.3 0.5 + - - -
66A ASP* 3.7 4.4 + - - +
74A TYR* 3.8 12.5 - - - +
40B ARG* 3.5 42.2 + - + +
153B ARG* 2.9 34.5 + - - +
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Residues in contact with GLU 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 LYS* 3.2 14.9 + - - +
61A LEU* 3.7 18.8 - - - +
62A LEU 3.2 0.6 - - - -
63A THR* 1.3 81.5 - - + +
65A SER* 1.3 56.6 + - - +
66A ASP 3.7 0.2 - - - -
67A ASP 5.4 0.2 + - - -
130A HIS* 4.6 0.2 - - - -
134A LEU* 3.4 32.4 - - + +
136A ILE* 4.2 7.4 - - + -
177A LYS* 3.4 35.4 + - - -
152B SER* 5.1 5.9 + - - -
153B ARG* 3.7 35.7 + - + +
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Residues in contact with SER 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 LEU 2.7 20.9 + - - -
62A LEU 2.8 4.5 + - - -
64A GLU* 1.3 74.6 - - - +
66A ASP* 1.3 63.2 + - - +
67A ASP 3.2 2.6 + - - -
68A HIS 3.5 3.1 + - - -
71A VAL* 3.5 14.1 - - - +
130A HIS* 3.1 28.2 + - - -
131A LEU* 3.8 25.6 - - - +
134A LEU* 3.9 5.4 - - - +
136A ILE* 3.3 18.9 - - - +
172A PHE* 4.2 5.1 - - - -
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Residues in contact with ASP 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 LEU* 2.9 19.6 + - + +
63A THR 4.1 1.6 - - - -
64A GLU 3.7 1.8 - - - -
65A SER* 1.3 76.4 - - - +
67A ASP* 1.3 62.1 + - - +
68A HIS 3.3 7.4 + - - +
71A VAL* 3.8 11.2 - - - +
72A ILE 3.1 23.3 - - - +
73A ARG* 3.9 8.6 - - - +
74A TYR* 2.9 25.2 + - - +
40B ARG* 2.9 22.3 + - - -
73B ARG* 2.7 25.1 + - - -
153B ARG* 3.1 12.5 + - - -
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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