Contacts of the strand formed by residues 94 - 104 (chain E) in PDB entry 1RTA
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 ASN 94 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89E SER 4.7 1.2 - - - +
90E SER* 3.9 2.3 - - - -
91E LYS* 2.7 56.4 + - - +
93E PRO* 1.3 87.9 - - + +
95E CYS* 1.3 59.5 + - - +
96E ALA* 5.2 0.7 - - - +
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Residues in contact with CYS 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ASN* 3.4 11.7 - - - +
36E THR* 4.1 14.9 - - + +
40E CYS* 2.4 40.2 - - - -
90E SER* 3.0 11.2 - - - +
92E TYR* 3.6 12.6 - - - -
93E PRO 3.2 16.6 + - - -
94E ASN* 1.3 72.9 - - - +
96E ALA* 1.3 62.7 - - - +
97E TYR* 4.0 18.4 - - + -
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASN* 2.9 13.0 - - - +
87E THR* 3.0 38.5 + - + -
89E SER* 5.2 3.6 - - - +
90E SER* 2.7 24.6 + - - +
94E ASN 5.2 0.7 - - - +
95E CYS* 1.3 74.7 - - - +
97E TYR* 1.3 71.2 + - - +
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Residues in contact with TYR 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E SER 4.2 2.6 - - - +
26E CYS* 3.9 14.1 - - + +
27E ASN* 2.9 31.6 + - - +
30E MET* 3.5 45.7 - - + +
36E THR* 3.9 12.3 - - + +
40E CYS* 3.9 3.6 - - - -
41E LYS 2.9 43.1 + - - -
42E PRO 4.2 1.6 - - - -
84E CYS 4.1 6.5 - - - -
85E ARG 3.1 13.9 - - - +
86E GLU* 3.2 37.9 - - + -
87E THR* 3.9 6.1 - - - +
95E CYS* 4.0 20.4 - - + -
96E ALA* 1.3 85.2 - - - +
98E LYS* 1.3 62.1 + - - +
99E THR* 3.5 3.6 + - - -
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Residues in contact with LYS 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E SER* 4.6 18.3 - - - +
26E CYS* 4.3 0.2 - - - -
83E ASP 2.9 21.5 - - - +
84E CYS* 4.1 1.6 - - - -
85E ARG* 2.8 33.9 + - + +
87E THR* 4.8 6.8 - - - +
97E TYR* 1.3 72.8 - - - +
99E THR* 1.4 71.6 + - - +
100E THR* 3.4 11.2 + - + +
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Residues in contact with THR 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ALA* 3.6 20.0 - - + -
22E SER 3.8 8.5 - - - +
23E SER* 3.1 29.9 + - - +
25E TYR* 3.6 28.5 - - + -
26E CYS* 3.0 31.2 + - - +
82E THR* 3.6 8.1 - - + -
97E TYR 3.5 1.2 + - - -
98E LYS* 1.4 88.0 + - - +
100E THR* 1.3 59.9 + - - +
101E GLN 4.3 0.7 + - - +
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Residues in contact with THR 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E ILE 3.6 0.9 - - - +
82E THR* 3.0 5.4 - - - -
83E ASP* 2.7 47.6 + - - +
85E ARG* 4.1 21.2 + - - +
98E LYS* 3.5 11.1 + - + +
99E THR* 1.3 75.8 - - - +
101E GLN* 1.3 66.8 + - - +
102E ALA* 5.2 2.5 - - + +
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Residues in contact with GLN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ALA* 3.3 25.9 - - + +
20E ALA* 3.2 29.1 + - + +
48E HIS* 3.5 4.7 - - - -
80E SER* 3.8 10.7 - - - -
81E ILE 3.3 6.0 - - - +
82E THR* 3.2 15.9 + - - -
99E THR* 4.3 1.0 + - + -
100E THR* 1.3 79.9 - - - +
102E ALA* 1.3 98.3 + - - +
103E ASN* 5.0 0.6 + - - -
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Residues in contact with ALA 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E SER* 2.9 1.6 - - - -
81E ILE* 2.7 39.3 + - + +
83E ASP* 6.3 1.6 - - - -
100E THR* 5.2 3.1 - - + +
101E GLN* 1.3 92.2 + - - +
103E ASN* 1.3 57.1 + - - +
104E LYS* 3.8 33.2 - - + -
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Residues in contact with ASN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E THR* 3.4 29.8 + - + +
79E MET* 3.3 2.9 - - - -
80E SER* 3.2 28.2 + - - -
101E GLN* 5.0 0.8 + - - -
102E ALA* 1.3 72.4 - - - +
104E LYS* 1.3 63.0 + - - +
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Residues in contact with LYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E THR* 3.1 6.1 - - - +
79E MET* 2.6 33.9 + - - +
81E ILE* 3.6 30.1 - - + -
83E ASP* 4.9 7.9 + - - -
85E ARG* 5.4 4.9 - - - +
102E ALA* 3.8 19.7 - - + -
103E ASN* 1.3 76.9 - - - +
105E HIS* 1.3 71.5 + - - +
106E ILE* 4.9 0.2 - - - -
123E SER* 4.1 14.1 + - - -
124E VAL* 3.7 25.1 + - - +
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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