Contacts of the strand formed by residues 409 - 415 (chain B) in PDB entry 1IZO
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 VAL 409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B GLU* 3.9 42.0 - - + +
132B VAL 3.6 7.4 - - - +
133B VAL* 4.2 14.6 - - + +
388B VAL* 4.2 2.0 - - - +
389B PRO* 3.3 12.4 - - + +
391B GLN* 2.7 43.4 + - + +
406B SER* 3.5 32.3 - - - +
408B PHE* 1.3 68.3 - - - +
410B MET* 1.3 61.5 + - - +
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Residues in contact with MET 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TRP* 4.3 16.8 - - + -
130B ASP 4.0 0.2 - - - +
131B GLU* 3.3 3.5 - - - -
132B VAL* 2.7 47.1 + - - +
134B LEU* 4.1 18.8 - - - -
380B LEU* 4.4 5.4 - - + -
384B ILE* 3.9 15.9 - - + -
386B TYR* 3.3 46.7 - - + -
387B ASP 3.5 8.5 - - - +
388B VAL* 5.3 1.3 - - + -
389B PRO* 4.5 0.2 - - - -
408B PHE* 3.7 36.8 - - + +
409B VAL* 1.3 74.3 - - - +
411B SER* 1.3 60.9 + - - +
413B ILE* 4.4 9.2 - - + +
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.4 22.0 - - - -
131B GLU* 4.5 6.7 - - - -
386B TYR* 3.7 1.9 - - - +
387B ASP* 2.8 38.4 + - - +
389B PRO* 3.5 26.7 - - - +
410B MET* 1.3 73.9 - - - +
412B GLY* 1.3 63.0 + - - +
413B ILE* 3.0 9.6 + - - +
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Residues in contact with GLY 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA 5.3 1.6 + - - -
130B ASP 4.0 5.7 + - - -
385B GLU 3.8 3.6 - - - +
386B TYR* 4.3 2.6 - - - -
387B ASP* 4.0 12.7 - - - +
411B SER* 1.3 76.4 + - - +
413B ILE* 1.3 67.4 + - - +
414B ARG* 3.1 26.3 + - - +
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Residues in contact with ILE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 5.1 0.9 - - + -
126B TRP* 3.5 53.3 + - + +
127B GLU* 3.7 25.0 + - + +
129B ALA 5.5 1.9 + - - +
130B ASP 5.5 1.1 - - - +
132B VAL* 3.4 39.9 - - + -
384B ILE* 4.4 18.2 - - + -
385B GLU 3.6 9.0 - - - +
386B TYR* 4.3 8.1 - - + -
410B MET* 4.4 10.3 - - + +
411B SER* 4.0 15.5 - - - +
412B GLY* 1.3 79.4 - - - +
414B ARG* 1.3 69.6 + - - +
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLU* 3.7 9.6 - - - +
384B ILE* 3.5 5.4 - - - -
385B GLU* 3.0 54.7 + - - +
386B TYR* 5.1 2.0 - - - +
387B ASP* 5.0 12.1 + - - -
412B GLY* 3.1 15.8 + - - +
413B ILE* 1.3 81.3 - - - +
415B ARG* 1.3 72.0 + - - +
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LYS* 4.6 6.3 + - - +
123B VAL* 3.8 31.4 - - + +
124B THR* 4.0 19.0 + - - +
127B GLU* 3.2 33.9 + - - +
383B GLN* 3.7 11.7 - - - +
384B ILE* 4.6 0.2 - - - +
385B GLU* 4.5 4.2 - - - +
414B ARG* 1.3 85.6 + - - +
416B LYS* 1.3 72.9 + - - +
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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