Contacts of the strand formed by residues 115 - 121 (chain E) in PDB entry 3MVJ
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 115 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73E ILE* 3.9 11.6 - - + +
74E LEU 3.2 14.0 - - - +
75E ASP* 3.7 12.3 - - - +
76E LYS* 3.6 2.1 - - - +
111E LYS* 3.2 7.1 - - - +
112E ASP* 2.8 34.7 + - - +
114E SER* 1.3 96.8 - - - +
116E LEU* 1.3 67.6 + - - +
117E TYR* 2.8 36.5 + - + +
335E ILE* 3.7 22.2 - - - +
336E ARG 4.0 12.0 + - - +
337E VAL* 4.7 0.4 - - - +
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Residues in contact with LEU 116 (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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72E LYS 3.6 0.6 - - - +
73E ILE* 3.4 5.2 - - - -
74E LEU* 2.8 44.7 + - + +
76E LYS* 3.7 24.0 - - + -
79E VAL* 5.3 1.8 - - + -
88E THR* 3.5 32.5 - - + -
110E PHE 3.8 4.5 - - - -
111E LYS* 3.8 15.0 - - + -
115E ASN* 1.3 81.8 - - - +
117E TYR* 1.3 66.1 + - - +
118E MET* 6.1 0.2 - - - -
347E PHE* 3.8 29.6 - - + -
350E PHE* 3.7 27.4 - - + -
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Residues in contact with TYR 117 (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 LEU* 3.9 27.9 - - + +
71E MET* 3.9 16.2 - - + -
72E LYS 3.2 4.5 - - - +
73E ILE* 3.8 37.2 - - + -
109E SER* 3.2 25.2 - - - -
110E PHE* 2.9 57.5 + + + +
111E LYS* 4.1 1.1 - - - -
112E ASP* 2.8 33.5 + - - -
115E ASN* 2.8 38.0 + - + -
116E LEU* 1.3 77.0 - - - +
118E MET* 1.3 63.8 + - - +
119E VAL* 4.0 0.9 - - - -
335E ILE* 4.3 1.6 - - + +
337E VAL* 4.1 1.7 - - - +
350E PHE* 3.9 2.6 - - - -
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Residues in contact with MET 118 (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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71E MET* 3.4 0.9 - - - -
72E LYS* 2.7 73.3 + - + -
74E LEU* 3.8 24.0 - - + -
88E THR* 5.3 1.1 - - + +
91E GLU* 4.0 22.4 - - - +
92E LYS* 3.9 32.1 - - + -
95E LEU* 4.5 7.9 - - - -
106E LEU* 3.8 18.6 - - + -
108E PHE 3.6 3.6 - - - -
109E SER* 4.7 1.3 - - - -
117E TYR* 1.3 76.4 - - - +
119E VAL* 1.3 59.7 + - - +
120E MET* 3.6 11.0 - - + +
350E PHE* 4.3 10.3 - - + -
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Residues in contact with VAL 119 (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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43E PHE* 4.2 9.6 - - + -
69E TYR* 3.4 39.5 - - + -
70E ALA 3.4 4.5 - - - +
71E MET* 3.8 33.9 - - + +
106E LEU* 3.7 1.8 - - - +
107E GLU* 2.9 24.6 + - - -
108E PHE* 2.7 37.0 + - + +
110E PHE* 4.0 18.6 - - + -
117E TYR 4.9 0.2 - - - -
118E MET* 1.3 76.2 - - - +
120E MET* 1.3 60.8 + - - +
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Residues in contact with MET 120 (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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69E TYR* 3.3 12.2 - - - +
70E ALA 2.5 39.4 + - - +
72E LYS* 3.6 25.4 - - + +
95E LEU* 3.8 24.5 - - + -
104E VAL* 4.5 11.2 - - + -
105E LYS 3.4 13.0 - - - +
106E LEU* 3.8 15.5 - - + -
107E GLU* 4.3 0.7 - - - +
118E MET* 3.6 23.8 - - + +
119E VAL* 1.3 78.2 - - - +
121E GLU* 1.3 62.4 + - - +
122E TYR 3.2 0.7 + - - -
183E THR* 5.4 1.1 - - - -
184E ASP 6.1 1.1 - - - -
351E XFE 3.8 43.7 - - + -
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Residues in contact with GLU 121 (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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68E HIS 5.4 0.2 - - - -
69E TYR* 4.5 5.8 - - - -
70E ALA 4.2 0.2 - - - -
104E VAL* 4.1 7.2 - - + +
105E LYS* 3.3 39.5 + - + +
107E GLU* 4.0 19.7 - - - +
120E MET* 1.3 71.7 - - - +
122E TYR* 1.3 74.6 - - - +
123E VAL* 3.5 6.4 + - + +
181E GLN* 3.7 19.6 + - - +
351E XFE 3.1 21.7 + - - -
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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