Contacts of the strand formed by residues 381 - 388 (chain B) in PDB entry 1O23
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 MET 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B TYR* 1.3 81.4 - - - +
382B VAL* 1.3 65.8 + - - +
383B LEU* 3.5 10.7 + - + +
396B VAL* 3.3 2.6 - - - -
397B ASP* 2.8 68.3 + - + +
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Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 3.8 19.7 - - - +
241B LYS* 4.7 6.5 - - - +
380B TYR* 3.7 26.0 - - + -
381B MET* 1.3 73.0 - - - +
383B LEU* 1.3 64.3 + - - +
384B GLU 3.9 8.7 - - - +
385B VAL* 3.8 28.3 - - + -
394B ILE* 4.2 3.4 - - + -
395B THR 3.9 7.2 - - - +
396B VAL* 4.0 5.6 - - + -
561D GLU* 5.3 3.1 - - - +
569D LEU* 4.7 16.2 - - + +
791D PRO* 5.1 7.6 - - - +
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Residues in contact with LEU 383 (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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221B ALA* 3.5 30.7 - - + -
381B MET* 4.3 19.1 - - + +
382B VAL* 1.3 77.9 - - - +
384B GLU* 1.3 65.1 + - + +
395B THR* 3.0 19.2 + - + +
397B ASP* 4.3 17.5 - - + +
558D LYS* 4.9 22.4 - - + +
561D GLU* 6.0 3.1 - - - +
569D LEU* 5.8 0.7 - - - -
790D TYR* 4.0 4.7 - - - -
791D PRO* 3.4 27.8 - - + +
812D UDP 5.9 0.9 - - - -
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Residues in contact with GLU 384 (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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382B VAL* 3.6 3.8 - - - +
383B LEU* 1.3 84.6 - - + +
385B VAL* 1.3 65.6 + - - +
386B GLN* 2.9 35.4 + - + +
393B LYS 3.8 1.0 - - - +
394B ILE* 3.4 4.2 - - - +
395B THR* 2.8 44.7 + - - +
811B UDP 5.4 0.9 + - - -
569D LEU* 5.6 0.4 - - - -
788D GLN* 2.9 23.3 - - + +
789D ARG 3.6 10.5 - - - +
790D TYR* 3.5 32.5 + - + -
812D UDP 4.9 4.9 + - - -
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Residues in contact with VAL 385 (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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238B GLU* 4.7 6.7 - - - +
382B VAL* 3.8 19.7 - - + -
384B GLU* 1.3 75.6 - - - +
386B GLN* 1.3 61.5 + - - +
387B ARG* 3.7 36.3 - - - +
392B THR* 4.6 8.3 - - + -
393B LYS 3.8 2.9 - - - -
394B ILE* 4.2 15.3 - - + +
569D LEU* 4.7 13.9 - - + +
787D VAL 3.7 1.4 - - - +
788D GLN* 3.5 1.0 - - - -
789D ARG* 2.7 54.0 + - + +
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Residues in contact with GLN 386 (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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384B GLU* 2.9 39.1 + - + +
385B VAL* 1.3 75.0 - - - +
387B ARG* 1.3 63.2 + - - +
388B TYR* 3.0 24.6 + - + -
392B THR* 3.3 5.7 - - - +
393B LYS* 2.9 64.2 + - + +
395B THR* 4.2 6.5 + - - -
811B UDP 3.4 24.0 + - - -
786D GLU* 2.7 29.2 - - - +
787D VAL 3.5 3.8 - - - -
788D GLN* 4.2 4.4 - - + +
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Residues in contact with ARG 387 (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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167B LEU* 3.3 33.0 - - + +
168B GLY* 4.4 6.1 - - - -
242B ASP* 2.7 43.0 + - - -
385B VAL* 3.7 23.9 - - + +
386B GLN* 1.3 71.9 - - - +
388B TYR* 1.3 62.5 + - - +
391B TYR 4.0 3.4 - - - -
392B THR* 3.2 33.6 + - - +
394B ILE* 6.4 0.2 - - - +
786D GLU* 3.5 3.1 - - - +
787D VAL* 2.7 48.1 + - + +
789D ARG* 5.7 4.2 - - + +
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Residues in contact with TYR 388 (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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167B LEU* 3.7 2.2 - - - -
168B GLY 2.7 23.7 + - - -
386B GLN* 3.0 36.5 + - + -
387B ARG* 1.3 76.1 - - - +
389B PRO* 1.3 71.1 - - + +
390B LEU 3.4 1.3 - - - +
391B TYR* 2.9 47.4 + + + +
393B LYS* 4.8 1.3 - - + -
811B UDP 3.3 84.2 + + + +
785D LEU 4.0 14.1 - - - -
786D GLU* 3.1 29.9 + - + -
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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