Contacts of the strand formed by residues 381 - 388 (chain B) in PDB entry 1HPL
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 THR 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B ASP* 4.3 17.3 - - + +
344B VAL 3.2 16.2 - - - +
345B THR* 2.8 27.3 + - - +
379B ASP 4.0 1.6 + - - -
380B ASN* 1.3 77.3 - - - +
382B TYR* 1.3 76.0 + - - +
383B SER* 4.3 2.7 + - - +
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Residues in contact with TYR 382 (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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342B VAL 3.7 1.4 - - - +
343B ASP* 3.3 2.1 - - - -
344B VAL* 2.7 38.3 + - + +
346B LEU* 3.5 39.5 - - + -
355B VAL* 5.7 2.9 - - + -
371B ILE* 4.1 9.6 - - + +
372B PHE* 3.7 54.7 - + + -
375B THR 3.1 21.6 + - - -
376B LEU* 4.8 0.4 - - + -
377B LYS* 3.5 13.1 + - - +
380B ASN* 3.7 35.3 + - + -
381B THR* 1.3 79.4 - - - +
383B SER* 1.3 58.7 - - - +
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Residues in contact with SER 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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294B ASN* 4.7 3.9 + - - -
341B ARG* 4.5 13.9 - - - -
342B VAL 3.2 5.4 - - - -
343B ASP* 2.8 37.6 + - - -
371B ILE* 4.4 5.9 - - - +
381B THR* 4.3 4.2 + - - +
382B TYR* 1.3 73.9 - - - +
384B ASN* 1.3 64.7 + - - +
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Residues in contact with ASN 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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294B ASN* 3.2 21.8 + - - +
341B ARG* 3.7 3.9 - - - +
342B VAL* 3.1 30.4 + - - +
370B GLU 3.9 13.1 + - - +
371B ILE* 3.5 32.2 + - + +
383B SER* 1.3 77.9 - - - +
385B GLU* 1.3 81.5 + - - +
386B PHE* 5.0 4.9 - - + +
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Residues in contact with GLU 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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291B PHE* 4.4 2.6 - - - +
294B ASN* 3.2 35.4 + - + +
296B CYS 5.2 0.9 + - - -
297B PHE* 3.4 25.4 + - + +
339B ARG* 3.0 37.7 + - - +
340B TYR 3.1 11.2 - - - +
341B ARG* 2.7 45.5 + - + -
384B ASN* 1.3 94.5 + - - +
386B PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 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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339B ARG* 3.3 4.3 - - - +
340B TYR* 2.9 40.6 + + + -
342B VAL* 3.6 28.0 - - + -
357B VAL* 5.3 3.8 - - + -
359B LEU* 3.7 35.9 - - + -
369B TYR* 3.6 59.5 - + + -
370B GLU 5.4 2.5 - - - +
371B ILE* 4.2 18.6 - - + -
384B ASN* 5.0 4.5 - - + +
385B GLU* 1.3 77.7 - - - +
387B ASP* 1.3 66.3 + - - +
388B SER* 3.7 11.2 + - - -
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Residues in contact with ASP 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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291B PHE* 5.0 0.2 - - - -
328B ASN* 3.1 38.4 + - + +
337B ARG* 3.7 29.4 - - + +
338B TRP 3.7 5.6 - - - -
339B ARG* 3.1 38.2 + - - +
369B TYR* 3.9 10.9 + - - -
386B PHE* 1.3 76.1 - - - +
388B SER* 1.3 63.6 + - - +
389B ASP 3.6 1.2 + - - -
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Residues in contact with SER 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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337B ARG* 3.4 6.0 - - - -
338B TRP* 2.8 39.3 + - - -
340B TYR* 3.8 16.0 - - - -
366B SER* 3.7 19.3 - - - -
369B TYR* 3.3 11.6 + - - -
386B PHE* 3.7 12.7 + - - -
387B ASP* 1.3 72.9 - - - +
389B ASP* 1.3 59.9 + - - +
390B VAL 2.7 30.7 + - - -
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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