Contacts of the strand formed by residues 102 - 107 (chain E) in PDB entry 2ZSU
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 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B LYS* 3.4 33.5 + - + +
134B LYS* 4.6 9.2 - - - -
151D GLU* 5.0 1.0 - - - +
78E ARG 3.0 5.2 + - - +
79E ARG* 3.0 41.6 + - + -
80E VAL 2.9 25.1 + - - +
100E VAL* 3.8 1.2 - - - +
101E GLU* 1.3 84.3 - - + +
103E VAL* 1.3 69.0 + - - +
104E ILE* 4.2 20.9 - - + +
137E LYS* 3.2 10.1 - - - +
139E LYS* 5.3 4.8 - - + +
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Residues in contact with VAL 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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80E VAL* 3.4 9.6 - - + +
82E ILE* 3.7 34.5 - - + -
91E ILE* 3.9 15.7 - - + -
94E VAL* 3.7 16.6 - - + -
95E LEU* 4.0 14.1 - - + -
100E VAL* 3.5 28.3 - - + -
102E GLU* 1.3 74.2 - - - +
104E ILE* 1.3 62.3 + - - +
130E MET* 4.3 0.3 - - - +
137E LYS 2.7 12.0 + - - +
138E GLY* 3.2 6.5 - - - -
139E LYS* 2.7 34.0 + - - +
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Residues in contact with ILE 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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134B LYS* 6.2 2.7 - - - -
79E ARG* 3.7 28.3 - - - +
80E VAL 2.9 10.5 + - - +
81E LEU* 3.5 7.8 - - + +
82E ILE* 2.8 27.7 + - - +
102E GLU* 4.2 21.3 - - + +
103E VAL* 1.3 78.2 - - - +
105E MET* 1.3 61.7 + - - +
106E VAL* 4.2 7.0 - - + -
139E LYS* 3.4 16.8 - - + +
141E ILE* 3.9 28.3 - - + -
148E PHE* 4.0 17.3 - - + -
155E PHE* 3.9 13.0 - - + -
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Residues in contact with MET 105 (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 ILE* 3.3 16.2 - - + +
84E GLY 3.5 17.0 - - - +
85E GLY 3.8 24.7 - - - +
86E GLY* 4.3 3.1 - - - -
90E ALA* 6.5 0.2 - - - -
91E ILE* 4.6 30.7 - - + -
103E VAL 4.0 0.4 + - - -
104E ILE* 1.3 74.2 - - - +
106E VAL* 1.3 62.1 + - - +
107E GLU* 3.9 2.7 - - + -
113E ILE* 3.8 28.9 - - + -
127E LEU* 4.3 14.8 - - + -
130E MET* 4.2 15.9 - - + +
139E LYS 2.9 13.1 + - - +
140E LEU* 3.5 12.1 - - + +
141E ILE* 2.8 33.4 + - - +
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Residues in contact with VAL 106 (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 LEU* 4.1 13.2 - - + -
82E ILE 2.9 12.0 + - - +
83E ILE* 3.6 8.5 - - + +
84E GLY 2.8 27.5 + - - -
104E ILE* 4.2 8.1 - - + -
105E MET* 1.3 75.6 - - - +
107E GLU* 1.3 54.6 + - - +
108E ILE 4.3 0.5 + - - -
141E ILE* 3.3 12.6 - - + +
143E GLY* 3.4 27.4 - - - +
144E ASP 4.1 1.1 - - - -
145E GLY* 3.6 23.7 + - - +
148E PHE* 3.9 37.9 - - + -
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Residues in contact with GLU 107 (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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32E GLN* 4.7 3.5 + - - -
84E GLY* 3.5 21.2 - - - +
85E GLY 3.8 0.3 + - - -
86E GLY* 3.1 26.4 + - - -
105E MET* 3.9 6.2 - - + -
106E VAL* 1.3 73.8 - - - +
108E ILE* 1.3 67.7 + - - +
109E ASP* 3.1 44.2 + - - +
112E VAL* 4.6 6.5 - - - +
113E ILE* 3.8 28.9 - - + -
140E LEU* 4.7 1.1 - - + -
141E ILE 3.2 4.9 + - - -
142E ILE* 3.1 13.2 - - + +
143E GLY 3.0 18.2 + - - -
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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