Contacts of the strand formed by residues 78 - 85 (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 LEU 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E PHE* 3.6 32.5 - - + +
45E LEU* 3.8 24.0 - - + -
69E LEU 5.4 0.7 - - - +
73E PHE* 3.6 34.5 - - + +
75E SER* 3.0 9.5 + - - +
76E PRO 3.9 2.0 - - - +
77E GLN* 1.3 76.5 - - - +
79E ARG* 1.3 76.7 + - - +
80E MET* 3.8 22.7 - - + -
97E GLU* 4.1 0.3 - - - -
99E ARG* 2.8 34.0 + - - +
212E ILE* 4.4 7.4 - - + -
216E LEU* 4.1 15.6 - - + +
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Residues in contact with ARG 79 (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 2.9 9.0 + - - +
44E ASP* 2.8 42.4 + - - +
45E LEU* 2.8 27.5 + - - +
76E PRO 4.6 3.4 - - - +
77E GLN 3.8 2.2 + - - +
78E LEU* 1.3 74.9 - - - +
80E MET* 1.3 61.5 + - - +
95E LEU* 3.6 21.6 + - + +
96E THR* 3.2 11.2 - - - +
97E GLU* 3.7 35.0 - - + +
134E GLU* 2.7 36.9 + - - +
141E THR* 5.4 2.2 + - - -
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Residues in contact with MET 80 (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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45E LEU* 3.1 19.3 - - + +
47E PHE* 4.1 14.4 - - + -
69E LEU 5.4 0.4 - - - -
70E ALA* 3.9 31.6 - - + +
73E PHE 4.2 0.4 - - - +
78E LEU* 3.8 19.7 - - + -
79E ARG* 1.3 75.0 - - - +
81E SER* 1.3 60.4 + - - +
82E PHE* 3.8 24.0 - - + -
93E MET* 3.2 23.1 - - + +
95E LEU* 3.4 4.8 - - - -
96E THR 2.9 27.1 + - - +
99E ARG* 3.5 27.8 - - - +
102E ILE* 3.9 20.0 - - + -
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Residues in contact with SER 81 (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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45E LEU 2.8 6.7 + - - +
46E TYR* 3.8 24.5 - - - -
47E PHE* 2.9 27.4 + - - +
80E MET* 1.3 74.9 - - - +
82E PHE* 1.3 66.7 + - - +
83E ILE* 4.0 4.4 - - - +
91E THR* 3.9 2.6 - - - +
93E MET* 2.7 21.8 + - - -
95E LEU* 3.6 15.7 - - - -
130E GLN* 3.1 20.5 + - - -
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Residues in contact with PHE 82 (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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47E PHE* 3.6 22.9 - + + -
49E LEU* 5.0 1.1 - - + -
66E VAL* 3.6 17.5 - - + -
70E ALA* 4.9 0.2 - - + -
80E MET* 3.8 25.8 - - + -
81E SER* 1.3 77.7 - - - +
83E ILE* 1.3 61.8 + - - +
91E THR* 3.7 1.0 - - - -
92E LEU* 2.8 39.9 + - + -
93E MET* 3.0 41.0 + - + +
102E ILE* 4.0 5.2 - - + -
105E GLY 3.8 11.9 - - - -
106E LEU* 3.7 43.7 - - + -
109E LEU* 3.6 23.6 - - + -
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Residues in contact with ILE 83 (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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46E TYR* 4.6 6.7 - - + -
47E PHE 2.8 16.0 + - - +
48E ILE* 4.3 11.0 - - + -
49E LEU* 2.7 35.9 + - - +
81E SER* 4.0 8.5 - - - +
82E PHE* 1.3 77.0 - - - +
84E VAL* 1.3 66.4 + - - +
90E THR 3.5 11.2 - - - +
91E THR* 3.9 15.7 - - - +
123E GLY* 3.7 26.0 - - - +
126E ARG* 3.8 9.0 - - + -
127E ALA* 3.5 41.5 - - + +
130E GLN* 3.8 11.4 - - - +
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Residues in contact with VAL 84 (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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49E LEU* 3.4 9.2 - - + +
51E LYS* 3.8 32.1 - - + +
59E TRP* 4.4 11.7 - - + -
82E PHE 4.2 0.4 - - - -
83E ILE* 1.3 80.0 - - - +
85E PHE* 1.3 63.1 + - - +
88E ARG 4.0 0.2 - - - +
89E GLY* 3.5 0.5 - - - -
90E THR* 2.9 50.3 + - - +
92E LEU* 4.2 22.0 - - + -
109E LEU* 3.7 28.9 - - + -
112E VAL* 4.5 3.6 - - + -
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Residues in contact with PHE 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ILE* 3.7 27.4 - - + -
49E LEU 2.9 23.4 + - - -
50E ASP* 3.4 38.8 - - + -
51E LYS* 2.8 32.0 + - - +
52E SER 3.8 0.7 + - - -
84E VAL* 1.3 77.0 - - - +
86E SER* 1.3 62.7 + - - +
88E ARG 3.2 10.1 - - - +
89E GLY* 4.0 8.5 - - - -
118E THR* 3.6 20.4 - - + -
119E TYR 3.9 13.0 - - - +
120E MET* 3.5 57.4 - - + -
123E GLY* 4.3 5.4 - - - +
147E ALA* 5.9 0.7 - - + -
148E LEU 4.3 2.0 - - - -
149E THR* 4.4 1.1 - - - -
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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