Contacts of the strand formed by residues 431 - 436 (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 ILE 431 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B LEU* 4.2 17.7 - - + -
380B GLU* 4.5 13.9 + - + +
381B ASP 3.3 26.0 - - - +
382B THR* 4.1 22.7 - - + +
415B ALA* 4.2 6.7 - - + -
416B LEU 3.4 6.5 - - - +
417B ILE* 4.0 25.8 - - + -
429B TRP 4.5 0.2 + - - -
430B LYS* 1.3 72.6 - - - +
432B LEU* 1.3 62.2 + - - +
433B ASP 3.6 21.3 - - - +
434B SER* 5.0 3.4 - - - -
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Residues in contact with LEU 432 (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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400B PHE* 3.4 57.2 - - + +
403B VAL* 3.9 7.6 - - + -
416B LEU* 2.8 11.3 + - + +
418B GLY* 3.7 26.9 - - - +
426B ASP 5.4 0.2 - - - +
427B ASN* 3.7 42.2 - - + +
430B LYS* 3.4 18.8 - - + +
431B ILE* 1.3 74.5 - - - +
433B ASP* 1.3 64.6 + - + +
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Residues in contact with ASP 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B HIS* 5.0 2.3 + - - -
400B PHE* 4.0 19.2 - - + -
414B VAL 4.4 0.7 - - - -
415B ALA* 3.4 2.6 - - - -
416B LEU* 3.0 39.9 + - + +
431B ILE* 3.5 7.9 - - - +
432B LEU* 1.3 82.7 - - - +
434B SER* 1.3 75.6 + - - +
435B PHE* 3.7 20.9 - - + +
480B GLY* 4.6 9.0 + - - -
482B GLY* 4.6 11.8 + - - +
483B SER 4.4 14.0 - - - +
485B PRO* 4.8 3.6 - - - +
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Residues in contact with SER 434 (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 THR 4.6 12.8 + - - -
383B GLY* 5.6 3.2 - - - -
413B SER* 3.7 17.7 + - - -
414B VAL 3.1 12.1 + - - -
415B ALA* 4.7 3.7 - - - +
431B ILE* 5.0 3.6 - - - -
433B ASP* 1.3 86.1 + - - +
435B PHE* 1.3 64.1 + - - +
484B ASP* 3.8 7.3 - - - +
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Residues in contact with PHE 435 (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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413B SER* 3.4 4.4 - - - -
414B VAL* 2.8 53.2 + - + +
416B LEU* 4.2 26.0 - - + -
433B ASP* 3.7 18.6 - - + +
434B SER* 1.3 80.8 + - - +
436B PRO* 1.3 74.8 - - + +
454B LEU* 4.7 1.8 - - + -
473B PHE* 3.6 44.6 - + - -
478B MET* 4.3 16.8 - - + -
484B ASP* 3.7 5.8 - - + +
485B PRO* 3.5 36.6 - - + +
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Residues in contact with PRO 436 (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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412B ASP* 3.4 32.3 - - - +
435B PHE* 1.3 89.0 - - + +
437B ALA* 1.3 64.5 + - - +
473B PHE* 3.4 17.3 - - - -
484B ASP* 3.4 30.5 - - + +
485B PRO 4.7 2.1 - - - +
487B PHE* 3.7 11.1 - - + -
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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