Contacts of the helix formed by residues 72 - 88 (chain A) in PDB entry 1RS2
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 LEU 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A HIS* 5.9 0.7 - - - -
18A ALA* 4.9 7.6 - - + -
70A VAL* 3.9 1.2 - - - +
71A ASN* 1.3 94.8 - - + +
73A LEU* 1.3 65.8 + - - +
74A GLU* 3.1 24.5 - - + +
75A HIS* 3.2 26.1 + - + +
76A LEU* 3.5 15.6 + - - +
1001A 209 3.1 26.5 - - + +
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Residues in contact with LEU 73 (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 HIS* 5.8 0.7 - - + -
29A PHE* 3.9 26.2 - - + -
72A LEU* 1.3 73.1 - - - +
74A GLU* 1.3 61.6 + - - +
76A LEU* 3.1 12.4 + - + +
77A ALA* 2.9 30.7 + - - +
98A ILE* 3.6 46.3 - - + +
100A LYS* 4.1 26.5 - - + -
112A VAL* 5.8 0.9 - - + -
113A GLY* 3.8 18.8 - - - -
114A ILE* 3.6 17.9 - - + +
1001A 209 2.9 20.8 + - + +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.1 15.4 - - + +
73A LEU* 1.3 80.8 + - - +
75A HIS* 1.3 55.4 + - - +
77A ALA* 4.0 1.1 - - - +
78A GLU* 3.1 33.1 + - - +
114A ILE* 3.6 32.9 - - + +
116A ILE* 5.5 7.1 - - + +
1001A 209 3.1 40.9 + - - -
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Residues in contact with HIS 75 (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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68A LYS* 5.6 1.2 + - - -
70A VAL* 3.5 32.6 - - + +
71A ASN 5.5 0.4 - - - -
72A LEU* 3.2 22.4 + - + +
73A LEU 3.1 0.8 - - - -
74A GLU* 1.3 78.6 - - - +
76A LEU* 1.3 62.2 + - - +
78A GLU* 4.0 4.6 - - - +
79A ARG* 3.0 56.3 + - + +
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Residues in contact with LEU 76 (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 HIS* 3.5 43.5 - - + +
29A PHE* 4.6 2.5 - - + -
64A ILE* 4.0 17.3 - - + +
65A MET* 4.3 13.7 - - + -
70A VAL* 3.2 28.7 - - + -
72A LEU 3.5 12.1 - - - +
73A LEU* 3.1 27.5 + - + +
75A HIS* 1.3 78.1 - - - +
77A ALA* 1.3 57.6 + - - +
79A ARG* 3.3 8.2 + - - +
80A ILE* 3.0 33.3 + - - +
98A ILE* 3.8 12.6 - - + -
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Residues in contact with ALA 77 (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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73A LEU 2.9 16.1 + - - +
74A GLU 4.3 1.6 - - - +
76A LEU* 1.3 77.3 - - - +
78A GLU* 1.3 57.4 + - - +
80A ILE 3.6 0.2 + - - -
81A ALA* 3.0 22.5 + - - +
96A VAL* 3.6 29.8 - - + +
98A ILE* 3.7 7.8 - - + +
114A ILE* 3.7 21.3 - - + -
116A ILE* 3.3 24.5 - - + +
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Residues in contact with GLU 78 (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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74A GLU* 3.1 22.6 + - - +
75A HIS* 4.0 8.7 - - - +
76A LEU 3.2 0.2 - - - -
77A ALA* 1.3 75.2 - - - +
79A ARG* 1.3 61.3 + - + +
81A ALA* 4.3 1.3 - - - +
82A ASN* 3.1 33.1 + - + +
116A ILE* 4.0 7.5 - - - +
118A ARG* 2.9 45.3 + - - -
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Residues in contact with ARG 79 (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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64A ILE* 3.3 25.0 - - + +
70A VAL* 5.3 5.4 - - - -
75A HIS* 3.0 53.3 + - + +
76A LEU* 3.3 6.9 + - - +
78A GLU* 1.3 77.0 - - + +
80A ILE* 1.3 58.6 + - - +
82A ASN* 4.2 4.8 - - - +
83A ARG* 2.9 61.7 + - - +
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Residues in contact with ILE 80 (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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31A VAL* 4.6 2.0 - - + -
33A VAL* 4.5 2.5 - - + -
60A GLU* 6.1 0.4 - - + -
61A VAL* 3.9 35.9 - - + +
64A ILE* 3.5 24.0 - - + -
65A MET* 4.0 21.8 - - + -
76A LEU 3.0 22.2 + - - +
77A ALA 3.8 4.0 - - - +
79A ARG* 1.3 75.2 - - - +
81A ALA* 1.3 60.1 + - - +
83A ARG* 3.7 1.4 - - - +
84A ILE* 2.9 50.2 + - + +
96A VAL* 4.1 27.1 - - + -
98A ILE* 4.4 3.4 - - + -
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Residues in contact with ALA 81 (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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77A ALA 3.0 18.6 + - - +
78A GLU* 4.3 2.2 - - - +
80A ILE* 1.3 75.7 - - - +
82A ASN* 1.3 63.9 + - - +
84A ILE* 3.2 2.3 + - - +
85A ASN* 3.0 30.7 + - - -
94A THR* 4.1 17.5 - - + +
96A VAL* 3.9 10.7 - - + +
116A ILE* 3.9 1.6 - - + -
118A ARG* 3.6 34.8 - - + -
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Residues in contact with ASN 82 (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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78A GLU* 3.1 22.3 + - + +
79A ARG* 4.2 4.2 - - - +
81A ALA* 1.3 79.4 - - - +
83A ARG* 1.3 57.7 + - - +
85A ASN* 3.6 6.6 + - - +
86A SER* 2.4 45.0 + - - -
118A ARG* 5.5 0.8 - - - +
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Residues in contact with ARG 83 (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 GLU* 3.3 31.3 + - + +
63A SER* 3.6 21.8 + - - -
64A ILE* 4.0 16.8 - - + +
79A ARG* 2.9 52.4 + - - +
80A ILE 3.7 3.8 - - - +
81A ALA 3.2 0.2 - - - -
82A ASN* 1.3 77.2 - - - +
84A ILE* 1.3 61.4 + - - +
86A SER* 3.7 3.6 + - - -
87A GLN* 3.0 60.5 + - - +
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Residues in contact with ILE 84 (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 VAL* 4.3 14.4 - - + -
35A LEU* 3.6 18.4 - - + -
57A VAL* 4.1 26.5 - - + -
60A GLU* 4.7 13.5 - - + -
61A VAL* 4.4 4.9 - - + -
80A ILE* 2.9 42.1 + - + +
81A ALA 3.8 2.9 - - - +
83A ARG* 1.3 78.7 - - - +
85A ASN* 1.3 63.9 + - - +
87A GLN 3.4 0.7 + - - -
88A TYR* 3.1 36.7 + - + +
91A VAL* 4.3 8.5 - - + -
94A THR* 3.4 26.2 - - + +
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Residues in contact with ASN 85 (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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81A ALA 3.0 25.0 + - - +
82A ASN* 4.1 6.0 - - - +
84A ILE* 1.3 74.3 - - - +
86A SER* 1.3 64.3 + - - +
88A TYR 3.4 8.4 + - - +
89A ASN* 5.2 0.3 - - - -
91A VAL* 3.5 10.6 - - - +
94A THR* 2.9 23.8 + - - -
118A ARG* 3.4 28.3 + - - +
119A GLU 4.3 4.0 + - - -
120A ASN* 3.0 46.7 + - - +
121A LYS 5.5 0.4 - - - +
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Residues in contact with SER 86 (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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82A ASN* 2.4 42.0 + - - -
83A ARG* 4.1 6.0 - - - -
84A ILE 3.3 0.4 - - - -
85A ASN* 1.3 77.7 - - - +
87A GLN* 1.3 62.5 + - - +
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Residues in contact with GLN 87 (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 GLU* 2.8 34.4 + - - +
83A ARG* 3.0 39.2 - - - +
84A ILE 3.4 1.2 + - - -
85A ASN 3.2 0.4 - - - -
86A SER* 1.3 84.3 - - - +
88A TYR* 1.3 84.1 + - + +
89A ASN 4.2 0.6 + - - -
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Residues in contact with TYR 88 (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 VAL* 3.9 31.0 - - + -
53A HIS 5.2 1.8 - - - -
56A GLU* 3.0 47.5 + - + +
57A VAL* 4.9 8.1 - - + -
60A GLU* 4.4 10.2 + - + -
84A ILE* 3.1 37.0 + - + +
85A ASN 3.4 3.4 - - - +
86A SER 3.6 0.8 - - - -
87A GLN* 1.3 106.7 + - + +
89A ASN* 1.3 62.3 + - - +
90A ARG* 4.6 1.6 - - + +
91A VAL* 3.5 22.6 + - + +
120A ASN* 3.0 24.3 + - - -
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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