Contacts of the strand formed by residues 381 - 386 (chain A) in PDB entry 1U7V
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 ASN 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A PHE* 4.8 12.5 - - + -
347A ALA 3.1 14.6 - - - +
348A GLU* 4.1 17.3 + - + +
376A ILE* 4.1 5.1 - - - +
379A GLY 4.9 3.4 + - - -
380A CYS* 1.3 79.9 - - - +
382A LEU* 1.3 73.0 + - - +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A PHE* 3.3 7.6 - - - +
347A ALA 3.0 28.8 + - - -
357A VAL* 5.3 1.6 - - + -
362A CYS* 4.3 16.8 - - - -
366A TYR* 4.7 15.0 - - + +
368A TRP* 6.3 0.9 - - + -
374A CYS* 3.9 28.9 - - + -
375A LYS 5.9 0.7 - - - +
376A ILE* 4.0 17.5 - - + -
381A ASN* 1.3 83.5 + - - +
383A LYS* 1.3 70.7 + - - +
384A ILE* 3.0 30.1 + - + +
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A GLU* 2.4 42.9 + - + +
345A VAL 3.6 5.4 - - - +
346A PHE* 3.5 30.3 - - + -
362A CYS* 3.7 9.2 - - - -
365A ARG* 3.0 42.7 + - - +
366A TYR* 5.0 2.9 - - - +
382A LEU* 1.3 74.6 - - - +
384A ILE* 1.3 61.8 + - - +
385A PHE 3.8 16.8 - - - +
386A ASN* 4.6 6.3 - - - +
389A GLU* 5.3 0.4 - - - +
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Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LEU* 6.1 0.4 - - + -
345A VAL* 2.8 21.0 + - + +
347A ALA* 3.8 24.0 - - + -
357A VAL* 3.6 22.4 - - + -
359A SER* 2.6 30.7 + - - +
362A CYS* 3.6 10.0 + - - +
365A ARG* 4.2 1.1 - - - -
376A ILE* 4.2 4.7 - - + -
382A LEU* 3.0 49.4 + - + +
383A LYS* 1.3 73.2 - - - +
385A PHE* 1.3 58.8 + - + +
414A ILE* 3.0 35.7 - - + -
416A MET* 5.3 5.6 - - + -
440A LEU* 5.9 0.9 - - + -
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Residues in contact with PHE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A TYR* 5.9 0.2 - + - -
343A GLY 5.0 0.7 - - - -
344A GLU* 3.3 7.1 - - - +
345A VAL* 3.0 45.6 + - + +
361A ASN* 3.4 32.3 - - + -
365A ARG* 4.0 3.4 - - - +
383A LYS* 3.4 4.3 - - - +
384A ILE* 1.3 79.4 - - - +
386A ASN* 1.3 69.8 + - - +
387A ASN* 3.0 36.6 - - - -
390A PHE* 3.6 23.6 - + + -
411A MET 3.6 19.1 - - - -
414A ILE* 4.0 14.4 - - + -
442A LEU* 3.3 23.3 - - + -
445A PRO* 3.5 25.4 - - + -
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Residues in contact with ASN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A GLY 3.8 3.1 - - - -
344A GLU* 3.3 29.6 + - + +
361A ASN* 3.0 15.8 + - - +
365A ARG* 4.1 4.0 - - - +
383A LYS* 4.6 3.8 - - + +
385A PHE* 1.3 78.8 - - - +
387A ASN* 1.3 64.2 + - - +
388A GLN* 3.1 11.4 + - - +
389A GLU* 2.7 63.3 + - - +
390A PHE* 3.2 15.9 + - - +
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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