Contacts of the strand formed by residues 51 - 57 (chain E) in PDB entry 3DXA
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 GLU 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E TYR* 3.2 8.8 - - - +
43E ARG* 2.8 55.4 + - - +
45E THR* 3.6 22.2 + - - -
48E GLN* 4.4 9.8 - - + +
49E GLY 4.1 10.2 - - - +
50E PRO* 1.3 75.9 - - - +
52E PHE* 1.3 62.5 + - - +
71E LEU* 3.5 30.2 - - + +
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Residues in contact with PHE 52 (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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112D LYS* 3.5 50.5 - - + -
113D VAL 4.2 10.6 + - - +
114D THR* 6.3 0.2 - - - +
40E TYR* 4.2 8.5 - + - -
41E TRP 4.5 0.4 - - - -
42E TYR* 3.7 25.7 - + + -
50E PRO 4.1 0.8 + - - -
51E GLU* 1.3 72.7 - - - +
53E LEU* 1.3 78.6 + - - +
54E THR* 3.4 31.4 - - - -
55E TYR* 3.5 18.6 - - + -
67E GLU* 4.2 16.6 - - + -
68E LYS* 4.1 4.0 - - - -
69E SER* 3.0 35.0 + - - -
71E LEU* 3.8 12.0 - - - +
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Residues in contact with LEU 53 (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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41E TRP* 2.8 25.5 + - + +
42E TYR* 3.4 31.9 - - - +
43E ARG* 3.6 19.5 - - + +
52E PHE* 1.3 89.3 - - - +
54E THR* 1.3 61.2 + - - +
68E LYS* 3.6 2.1 - - - -
69E SER* 3.3 18.5 + - - -
71E LEU* 4.1 21.3 - - + -
72E LEU* 3.6 37.8 - - + +
76E PHE* 4.9 9.0 - - + -
89E LEU* 4.4 7.6 - - + -
102E TYR* 4.0 17.0 - - + -
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Residues in contact with THR 54 (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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40E TYR* 3.6 0.9 - - - -
41E TRP* 2.9 52.5 + - + -
52E PHE* 3.4 12.3 - - - -
53E LEU* 1.3 80.7 - - + +
55E TYR* 1.3 68.9 + - - +
56E PHE* 3.6 17.3 - - + -
61E GLN* 2.8 32.2 + - - +
67E GLU 3.1 8.7 + - - -
68E LYS* 3.7 0.5 - - - +
72E LEU* 3.9 9.4 - - - -
78E ALA* 3.6 8.7 - - + -
89E LEU* 6.1 0.4 - - + -
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Residues in contact with TYR 55 (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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65A GLN* 4.7 3.8 - - - -
69A THR* 4.9 2.6 + - - +
110D TYR* 4.1 19.3 + - - -
111D GLN 5.7 1.1 - - - -
112D LYS* 6.1 0.2 - - - -
31E ARG* 2.8 35.7 + - + +
39E LEU 3.6 6.5 - - - -
40E TYR* 3.4 40.2 - + + -
52E PHE* 3.5 19.3 - + + -
54E THR* 1.3 80.8 + - - +
56E PHE* 1.3 84.0 + - - +
57E GLN* 3.5 10.0 + - - -
61E GLN* 3.7 3.6 - - - +
66E LEU* 3.1 44.8 + - + +
67E GLU* 3.3 30.3 + - + +
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Residues in contact with PHE 56 (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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31E ARG* 3.3 1.4 - - - -
39E LEU* 2.9 44.7 + - + +
41E TRP* 4.5 0.4 - + - -
54E THR* 3.6 26.9 - - + -
55E TYR* 1.3 90.0 - - - +
57E GLN* 1.3 59.4 + - - +
58E ASN 4.2 0.9 - - - +
59E GLU 4.6 3.8 - - - -
60E ALA 3.2 24.0 - - - +
61E GLN* 3.6 23.6 - - + -
78E ALA* 3.6 14.6 - - + -
79E GLU* 3.7 24.2 - - - -
80E ARG* 3.7 43.3 - - + +
87E SER* 3.9 9.4 - - - -
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Residues in contact with GLN 57 (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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69A THR* 4.0 6.7 - - - +
72A GLN* 3.8 25.5 - - + +
73A THR* 3.9 10.2 + - - +
76A GLU* 2.8 25.1 + - - -
30E ASN* 3.3 15.2 - - - +
31E ARG* 3.4 38.6 + - + +
55E TYR* 3.5 7.4 + - - +
56E PHE* 1.3 72.6 - - - +
58E ASN* 1.3 76.7 + - - +
59E GLU 2.8 5.0 + - - -
60E ALA* 2.9 21.2 + - - +
66E LEU* 3.6 27.7 - - + +
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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