Contacts of the strand formed by residues 375 - 381 (chain A) in PDB entry 1DY7
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 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ILE* 4.1 7.6 - - - +
369A ILE* 3.4 0.6 - - - -
370A ASP* 2.8 38.0 + - + +
373A GLU* 3.5 25.3 - - + +
374A GLY* 1.3 82.8 - - - +
376A LEU* 1.3 68.8 + - - +
377A VAL* 4.1 2.0 - - + +
329B ASP* 4.3 11.6 + - - +
332B ASN* 3.5 25.1 - - + +
334B LYS* 6.2 4.5 - - - +
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Residues in contact with LEU 376 (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 ILE* 3.9 9.8 - - + +
339A SER 3.7 19.5 - - - +
340A ALA* 4.8 0.4 - - - -
367A VAL* 3.5 26.5 - - + -
368A VAL 3.5 17.9 - - - +
369A ILE* 4.1 7.2 - - + -
375A LYS* 1.3 79.4 - - - +
377A VAL* 1.3 61.1 + - - +
378A ALA 3.6 14.8 - - - +
379A ILE* 3.9 20.9 - - + -
331B ASP* 6.5 0.7 - - + -
332B ASN* 3.0 19.7 + - - +
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 4.8 4.7 - - + -
368A VAL* 2.8 22.8 + - + +
370A ASP* 3.9 28.3 - - + +
375A LYS* 4.1 2.9 - - + +
376A LEU* 1.3 79.5 - - - +
378A ALA* 1.3 60.5 + - + +
429A TRP* 3.3 44.8 - - + +
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Residues in contact with ALA 378 (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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366A LEU 4.3 1.6 - - - -
368A VAL* 2.9 34.2 + - + -
376A LEU* 3.6 5.7 - - - +
377A VAL* 1.3 83.5 - - + +
379A ILE* 1.3 68.3 + - - +
380A GLU* 4.8 7.9 - - + +
429A TRP* 3.7 36.3 - - + +
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Residues in contact with ILE 379 (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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289A TYR* 5.7 0.4 - - - +
340A ALA 3.4 32.1 - - - +
341A GLU* 4.6 8.7 - - + +
365A LYS* 3.8 33.6 - - + -
366A LEU 3.3 6.1 - - - +
367A VAL* 4.2 10.3 - - + -
376A LEU* 3.9 27.1 - - + -
378A ALA* 1.3 79.6 - - - +
380A GLU* 1.3 76.2 + - - +
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Residues in contact with GLU 380 (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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365A LYS* 3.3 5.6 - - - -
366A LEU* 2.7 41.2 + - - +
378A ALA* 4.8 6.4 - - + +
379A ILE* 1.3 86.6 + - - +
381A ASP* 1.3 64.5 + - - +
382A THR* 3.7 0.9 + - - +
417A ILE* 4.9 6.1 - - + -
429A TRP 3.2 28.3 - - - +
430A LYS* 4.8 6.3 - - - -
431A ILE* 4.2 21.3 + - + +
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Residues in contact with ASP 381 (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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363A ARG 3.8 2.9 - - - +
364A ASN* 3.4 23.0 + - - +
365A LYS* 2.9 34.0 + - + +
380A GLU* 1.3 75.5 + - - +
382A THR* 1.3 60.9 + - - +
383A GLY* 2.8 31.9 + - - -
384A GLY 4.7 0.2 - - - +
431A ILE* 3.3 16.2 - - - +
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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