Contacts of the strand formed by residues 119 - 125 (chain E) in PDB entry 2I2X
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 LYS 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E LEU 3.5 6.1 - - - -
31E ASP* 2.6 54.1 + - + +
32E LEU* 4.0 13.5 - - + -
33E GLU 5.6 0.2 - - - +
38E TYR* 3.7 27.4 - - + +
79E PRO* 3.0 23.0 + - + +
80E ALA* 3.3 6.0 - - + -
81E ILE 3.2 19.4 + - - -
113E HIS* 4.9 0.4 - - - -
117E GLY 4.6 6.5 - - - +
118E ILE* 1.3 73.7 - - - +
120E CYS* 1.3 64.5 + - - +
27K LYS* 5.5 0.4 - - - +
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Residues in contact with CYS 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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29E GLY 3.7 0.2 - - - -
30E LEU* 2.8 54.4 + - - +
32E LEU* 3.8 10.9 - - - +
70E MET* 4.3 12.6 - - + -
81E ILE* 2.9 34.1 - - + +
83E LEU* 5.2 3.1 - - + -
106E LYS* 6.1 0.2 - - - -
109E MET* 4.3 27.6 - - - -
113E HIS* 4.8 0.2 - - - -
118E ILE 4.0 9.9 - - - -
119E LYS* 1.3 76.3 - - - +
121E ALA* 1.3 59.1 + - - +
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Residues in contact with ALA 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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28E ALA* 4.3 7.4 - - + +
29E GLY* 4.0 11.2 - - - +
30E LEU 4.7 0.2 - - - +
32E LEU* 3.6 19.4 - - + +
34E ILE* 5.8 0.2 - - + -
81E ILE 3.4 3.3 + - - +
82E ILE* 3.2 11.9 - - + +
83E LEU* 3.1 24.9 + - - +
106E LYS* 5.5 1.3 - - - +
109E MET* 4.7 4.9 - - - -
120E CYS* 1.3 79.5 - - - +
122E LEU* 1.3 60.5 + - - +
123E ARG 4.1 0.7 - - - -
159E ASP* 3.6 17.7 - - + +
160E LEU* 4.9 7.9 - - + -
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Residues in contact with LEU 122 (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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83E LEU 3.3 21.8 - - - +
85E THR* 3.7 4.3 - - - +
102E ALA* 3.6 24.7 - - - +
105E GLN* 3.5 25.1 - - + +
106E LYS* 4.5 3.8 - - + +
109E MET* 3.5 32.8 - - + -
121E ALA* 1.3 73.4 - - - +
123E ARG* 1.3 60.0 + - - +
124E HIS* 3.7 22.4 - - + +
157E GLY 3.6 19.3 - - - +
158E ALA* 3.7 4.0 - - - +
159E ASP* 2.8 44.2 + - - +
160E LEU* 3.1 6.9 + - - -
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Residues in contact with ARG 123 (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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42E GLU* 2.6 55.3 + - - +
82E ILE* 4.3 4.3 - - + +
83E LEU 2.8 8.8 + - - +
84E GLU* 3.3 26.6 - - - +
85E THR 2.7 31.5 + - - -
121E ALA 4.1 1.4 + - - -
122E LEU* 1.3 71.0 - - - +
124E HIS* 1.3 65.6 + - - +
125E THR* 3.7 8.3 - - - +
160E LEU* 3.4 38.1 - - + +
161E LEU 4.8 0.4 - - - +
162E SER* 3.7 15.2 + - - -
215E ALA* 4.0 5.3 - - - +
265E PRO* 2.5 39.8 + - - +
266E GLY 2.9 18.8 + - - -
267E LYS* 3.8 11.5 - - - +
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Residues in contact with HIS 124 (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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85E THR* 3.4 13.5 - - - +
87E HIS* 3.0 30.8 + + - +
98E GLY 3.8 3.8 + - - -
101E VAL* 4.2 4.2 - - - +
102E ALA* 3.3 30.9 + - + +
105E GLN* 3.2 30.0 + - - -
122E LEU* 3.7 12.7 + - + +
123E ARG* 1.3 82.2 + - - +
125E THR* 1.3 61.3 + - - +
126E ILE* 3.7 11.6 + - + +
153E CYS* 3.6 15.3 - - + -
158E ALA* 3.7 17.7 - - + -
160E LEU 2.7 12.5 + - - +
161E LEU* 3.5 3.7 - - + -
162E SER 2.9 23.7 + - - +
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Residues in contact with THR 125 (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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84E GLU* 2.7 30.4 + - - +
85E THR 3.0 12.4 + - - -
86E GLU* 3.7 8.8 - - + +
87E HIS* 3.0 25.7 + - - +
123E ARG* 3.7 2.1 - - - -
124E HIS* 1.3 71.4 - - - +
126E ILE* 1.3 67.6 + - - +
127E GLY 3.6 0.2 + - - -
162E SER* 3.2 28.7 - - - +
163E VAL* 3.8 11.9 - - - +
164E GLU* 4.5 7.9 - - - +
267E LYS* 3.8 20.8 - - - +
500F B13 5.8 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