Contacts of the strand formed by residues 89 - 96 (chain E) in PDB entry 3N2N
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 GLY 89 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E VAL 3.5 6.7 - - - -
85E PHE* 4.0 7.0 - - - -
88E ARG* 1.3 73.1 - - - +
90E THR* 1.3 64.5 + - - -
122E GLU* 2.9 35.9 + - - +
123E GLY 4.1 0.7 - - - -
126E ARG* 2.8 32.0 + - - -
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Residues in contact with THR 90 (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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51E LYS* 6.0 1.2 + - - -
83E ILE* 3.5 1.9 - - - +
84E VAL* 2.9 46.4 + - - +
88E ARG* 4.5 9.9 + - - +
89E GLY* 1.3 77.8 + - - -
91E THR* 1.3 71.0 + - - +
92E LEU* 3.3 4.2 + - - +
126E ARG* 3.9 7.1 - - - +
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Residues in contact with THR 91 (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 SER* 3.9 1.8 - - - +
82E PHE 3.9 3.4 - - - +
83E ILE* 3.9 3.3 - - + +
90E THR* 1.3 79.8 - - - +
92E LEU* 1.3 62.0 + - - +
93E MET* 3.4 29.1 - - - +
94E LYS* 3.7 18.8 + - + +
126E ARG* 3.4 31.1 + - - +
130E GLN* 3.6 24.2 + - - +
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Residues in contact with LEU 92 (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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82E PHE* 2.8 31.4 + - + +
84E VAL* 4.2 22.9 - - + -
90E THR* 3.3 5.6 + - - -
91E THR* 1.3 73.4 - - - +
93E MET* 1.3 59.9 + - - +
105E GLY* 3.5 29.1 - - - +
108E GLU* 4.0 36.4 - - + +
109E LEU* 4.0 22.9 - - + +
112E VAL* 4.4 7.9 - - + -
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Residues in contact with MET 93 (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 MET* 3.2 32.8 - - + +
81E SER* 2.7 27.9 + - - -
82E PHE* 3.0 56.4 + - + +
91E THR* 3.4 5.1 - - - +
92E LEU* 1.3 83.5 - - + +
94E LYS* 1.3 62.6 + - - +
96E THR* 3.9 12.8 - - + -
101E GLN* 3.4 33.2 - - + +
102E ILE* 3.6 18.8 - - + -
105E GLY* 4.1 4.7 - - - -
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Residues in contact with LYS 94 (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 MET 3.7 0.7 - - - +
81E SER* 4.1 0.2 - - - -
91E THR* 3.8 18.4 - - + +
93E MET* 1.3 79.6 - - - +
95E LEU* 1.3 69.6 + - - +
96E THR* 3.2 17.0 + - - +
101E GLN* 5.1 1.6 - - - +
130E GLN* 3.6 20.4 - - - +
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Residues in contact with LEU 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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44E ASP* 3.4 33.0 - - + +
45E LEU 4.1 2.0 - - - +
46E TYR* 3.4 30.7 - - + +
79E ARG* 3.6 55.8 + - + +
80E MET* 3.4 12.6 - - - -
81E SER* 3.6 6.7 - - - +
94E LYS* 1.3 73.6 - - - +
96E THR* 1.3 60.0 + - - +
130E GLN* 2.9 19.3 + - + +
134E GLU* 3.7 16.8 - - + +
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Residues in contact with THR 96 (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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79E ARG* 3.2 8.9 - - - +
80E MET 2.9 28.2 + - - +
93E MET* 3.9 22.9 - - + -
94E LYS 3.5 12.3 - - - +
95E LEU* 1.3 78.0 - - - +
97E GLU* 1.3 58.6 + - - +
98E ASP* 3.0 15.6 + - - +
101E GLN* 3.1 45.6 + - + -
102E ILE* 3.9 11.9 - - + +
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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