Contacts of the strand formed by residues 375 - 381 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ASP* 3.7 11.2 - - - +
332A ASN* 3.5 27.1 - - + +
338B ILE* 4.1 7.5 - - - +
369B ILE* 3.5 0.8 - - - -
370B ASP* 2.9 32.3 + - + +
373B GLU* 3.5 22.0 - - + +
374B GLY* 1.3 83.3 - - - +
376B LEU* 1.3 70.3 + - - +
377B VAL* 3.5 5.7 + - + +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP* 6.4 1.6 - - + -
332A ASN* 2.9 20.3 + - - +
338B ILE* 3.9 11.2 - - + +
339B SER 3.8 17.9 - - - +
367B VAL* 3.5 26.2 - - + -
368B VAL 3.5 17.9 - - - +
369B ILE* 4.1 6.3 - - + -
375B LYS* 1.3 79.4 - - - +
377B VAL* 1.3 63.5 + - - +
378B ALA* 3.6 14.6 - - - +
379B ILE* 4.0 21.8 - - + -
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TYR* 4.4 6.7 - - + -
368B VAL* 2.8 41.9 + - + +
370B ASP* 3.9 30.3 - - + +
375B LYS* 3.5 6.5 + - + +
376B LEU* 1.3 80.0 - - - +
378B ALA* 1.3 63.4 + - - +
429B TRP* 4.1 22.0 - - + +
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU 4.4 0.4 - - - -
367B VAL* 3.6 0.2 - - - -
368B VAL* 2.9 37.2 + - + -
376B LEU* 3.6 6.3 - - - +
377B VAL* 1.3 82.8 - - - +
379B ILE* 1.3 69.9 + - - +
380B GLU* 4.3 7.2 - - + +
429B TRP* 3.6 37.0 - - + +
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Residues in contact with ILE 379 (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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289B TYR* 5.7 0.7 - - + +
340B ALA 3.4 30.3 - - - +
341B GLU* 4.7 7.9 - - + +
365B LYS* 3.9 31.1 - - + +
366B LEU 3.3 8.3 - - - +
367B VAL* 4.2 9.6 - - + -
376B LEU* 4.0 26.2 - - + -
378B ALA* 1.3 80.9 - - - +
380B GLU* 1.3 75.8 + - - +
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS* 3.9 4.7 - - - -
366B LEU* 2.8 41.1 + - + +
368B VAL* 6.3 0.2 - - + -
378B ALA* 4.6 7.1 - - + +
379B ILE* 1.3 88.2 + - - +
381B ASP* 1.3 69.7 + - - +
382B THR* 3.6 0.7 + - - +
417B ILE* 4.7 7.6 - - + -
429B TRP 3.0 28.7 - - - +
430B LYS* 4.9 17.8 + - - +
431B ILE* 4.5 17.2 + - + +
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Residues in contact with ASP 381 (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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364B ASN* 3.3 26.7 + - - +
365B LYS* 2.9 34.1 + - + +
380B GLU* 1.3 75.6 + - - +
382B THR* 1.3 62.1 + - - +
383B GLY* 2.8 31.7 + - - -
431B 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