Contacts of the helix formed by residues 377 - 387 (chain B) in PDB entry 1UPX
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 LEU 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ILE* 3.8 22.4 - - + -
369B PHE* 3.9 20.0 - - + -
373B GLN* 3.4 31.4 - - - +
374B VAL* 3.0 11.9 + - + +
376B ALA* 1.3 79.6 - - + +
378B ALA* 1.3 65.1 + - - +
379B ASP* 3.2 8.7 - - - +
380B LYS* 3.0 28.0 + - + +
381B VAL* 3.0 21.1 + - + +
443B ILE* 6.5 1.8 - - + -
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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
----------------------------------------------------------
374B VAL 3.2 6.1 + - - +
375B LEU* 3.1 25.0 + - + +
376B ALA 3.3 1.4 + - - -
377B LEU* 1.3 76.3 - - - +
379B ASP* 1.3 57.4 + - - +
381B VAL* 4.5 5.6 - - - -
382B ILE* 2.8 51.8 + - + +
464B LYS* 6.0 6.7 - - + -
468B VAL* 6.2 0.7 - - + -
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Residues in contact with ASP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ALA 4.3 5.4 - - - +
377B LEU* 3.8 10.2 - - - -
378B ALA* 1.3 74.7 - - - +
380B LYS* 1.3 79.1 + - - +
382B ILE* 4.2 4.8 - - - +
383B ASP* 3.0 39.8 + - - +
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Residues in contact with LYS 380 (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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377B LEU* 3.0 24.9 + - + +
379B ASP* 1.3 92.9 + - - +
381B VAL* 1.3 64.1 + - - +
383B ASP* 3.6 7.9 + - + +
384B ALA* 3.1 23.7 + - - +
441B GLY 5.6 6.4 + - - +
443B ILE* 3.8 18.7 - - + +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 4.6 19.7 - - + -
377B LEU* 3.0 27.6 + - + +
378B ALA* 3.9 5.2 - - - +
380B LYS* 1.3 75.8 - - + +
382B ILE* 1.3 65.1 + - + +
384B ALA* 3.1 4.2 + - - +
385B VAL* 3.0 24.9 + - + +
390B ILE* 4.7 2.4 - - + +
393B PHE* 4.0 28.0 - - + -
443B ILE* 4.1 22.2 - - + -
447B LEU* 5.8 5.2 - - + -
461B ILE* 6.4 0.7 - - + -
465B LEU* 4.7 15.7 - - + -
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Residues in contact with ILE 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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378B ALA* 2.8 43.0 + - + +
379B ASP* 4.2 4.3 - - - +
381B VAL* 1.3 71.7 - - + +
383B ASP* 1.3 58.7 + - - +
385B VAL* 3.2 6.6 + - - +
386B LYS* 2.9 50.7 + - + +
465B LEU* 4.6 14.4 - - + -
468B VAL* 3.7 42.8 - - + -
469B PHE* 4.3 6.3 - - + -
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Residues in contact with ASP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ASP* 3.0 28.3 + - - +
380B LYS* 3.7 8.2 - - + +
382B ILE* 1.3 78.8 - - - +
384B ALA* 1.3 56.4 + - - +
386B LYS* 3.4 13.5 + - - +
387B SER* 3.0 32.1 + - - -
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Residues in contact with ALA 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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380B LYS 3.1 18.3 + - - +
381B VAL 3.1 4.9 + - - +
383B ASP* 1.3 76.5 - - - +
385B VAL* 1.3 62.4 + - - +
387B SER* 3.8 6.1 - - - -
388B GLY 3.2 1.9 + - - -
389B ALA* 3.0 37.2 + - + -
390B ILE* 3.0 31.2 + - + -
440B ILE* 5.1 2.7 - - + +
443B ILE* 4.1 8.1 - - + -
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Residues in contact with VAL 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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381B VAL* 3.0 20.3 + - + +
382B ILE* 3.7 7.0 - - - +
384B ALA* 1.3 76.8 - - - +
386B LYS* 1.3 61.1 + - - +
388B GLY* 3.3 11.8 + - - -
390B ILE* 3.6 19.1 - - + +
393B PHE* 3.7 34.5 - - + -
465B LEU* 5.7 1.6 - - + -
469B PHE* 3.5 32.3 - - + -
478B PRO* 4.8 17.0 - - + -
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ILE* 2.9 37.0 + - + +
383B ASP* 3.9 13.3 + - - +
385B VAL* 1.3 78.8 - - - +
387B SER* 1.3 58.3 + - - +
388B GLY 3.6 0.2 + - - -
469B PHE* 4.1 19.7 - - + -
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Residues in contact with SER 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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383B ASP 3.0 18.6 + - - -
384B ALA* 3.3 3.3 + - - -
386B LYS* 1.3 76.5 - - - +
388B GLY* 1.3 60.3 + - - +
389B ALA* 3.3 20.4 + - - +
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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
------------------------------------------------------------
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