Contacts of the strand formed by residues 402 - 407 (chain B) in PDB entry 1E8U
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 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B GLY* 2.9 13.0 + - - +
303B GLY* 2.8 26.5 + - - -
315B SER* 3.2 17.4 + - - -
371B GLN* 5.5 1.6 - - - -
400B ALA 3.6 1.2 + - - -
401B GLU* 1.3 75.5 - - - +
403B ARG* 1.3 61.8 + - - -
414B TYR* 3.0 14.6 - - - -
415B GLN* 4.4 0.2 - - - -
470B TYR* 3.8 9.4 - - - -
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Residues in contact with ARG 403 (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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178B PHE 3.7 19.0 + - - -
179B ASP* 4.7 10.1 + - - +
180B MET 5.6 0.4 - - - +
303B GLY* 3.7 0.7 - - - -
304B GLY* 3.3 24.7 - - - +
315B SER* 3.6 4.0 + - - -
402B GLY* 1.3 72.0 - - - +
404B ILE* 1.3 68.7 + - - +
405B LEU* 3.9 31.1 - - + +
412B PHE 3.6 0.7 - - - +
413B LEU* 3.2 5.5 - - - +
414B TYR* 2.7 42.4 + - + +
470B TYR* 3.2 17.0 - - - +
472B ASP* 3.1 29.7 + - - -
473B PRO 5.8 0.2 + - - -
474B TYR* 4.2 12.5 - - - -
528B THR* 3.3 8.1 + - - -
529B SER 2.8 24.0 + - - -
530B THR* 2.9 24.6 + - - +
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Residues in contact with ILE 404 (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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179B ASP* 4.8 0.7 - - - +
304B GLY 3.0 17.7 + - - +
305B GLY 3.4 16.3 - - - +
306B SER* 3.5 16.1 - - - -
308B ILE* 4.8 1.3 - - + -
313B TRP* 3.6 22.7 - - + +
314B PHE 3.6 8.1 - - - -
315B SER* 3.6 31.0 - - - +
373B ILE* 3.8 21.3 - - + -
403B ARG* 1.3 78.2 + - - +
405B LEU* 1.3 66.9 + - - +
411B HIS* 5.7 0.4 - - + -
412B PHE 3.3 7.6 - - - +
413B LEU* 4.0 12.6 - - + -
429B MET* 3.9 28.3 - - + -
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 5.4 4.5 - - - +
306B SER* 4.1 4.5 - - - -
403B ARG* 3.9 40.8 - - + +
404B ILE* 1.3 79.4 - - - +
406B THR* 1.3 64.3 + - - +
407B VAL* 4.4 2.0 - - + -
411B HIS* 3.4 3.3 - - - +
412B PHE* 2.7 66.7 + - + +
414B TYR* 4.5 9.4 - - + +
426B LEU* 4.8 2.5 - - + -
472B ASP* 6.5 0.2 - - + -
473B PRO 4.4 6.3 - - - +
474B TYR* 3.7 24.0 - - + -
475B PRO* 3.7 29.4 - - + -
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Residues in contact with THR 406 (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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137B GLY* 4.0 10.8 - - - +
306B SER* 2.7 26.2 + - - -
307B PHE 5.4 1.8 - - - +
308B ILE* 3.9 3.1 - - - +
405B LEU* 1.3 75.3 - - - +
407B VAL* 1.3 69.0 + - - +
408B GLY 3.7 16.8 - - - +
409B THR 4.9 0.4 - - - -
410B SER 3.4 7.0 - - - +
411B HIS* 2.7 38.9 + - + +
474B TYR* 4.6 4.9 + - - -
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Residues in contact with VAL 407 (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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137B GLY 3.6 2.9 - - - -
138B LYS 3.4 25.1 - - - +
139B GLU* 4.2 5.0 - - - +
405B LEU* 4.4 4.9 - - + -
406B THR* 1.3 76.4 - - - +
408B GLY* 1.3 66.0 + - - +
409B THR 3.2 0.2 + - - -
410B SER* 3.0 24.7 + - - +
412B PHE* 4.1 10.4 - - + -
474B TYR* 3.9 21.5 - - + +
475B PRO* 3.7 43.5 - - + +
478B PHE* 3.6 24.1 - - + -
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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