Contacts of the helix formed by residues 345 - 352 (chain B) in PDB entry 4LUD
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 SER 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LYS 3.7 0.7 + - - +
344B GLY* 1.3 75.2 - - - -
346B LEU* 1.3 59.9 + - - +
347B LEU* 3.4 7.3 + - - +
348B ASP* 3.0 33.6 + - - +
349B PHE* 3.0 28.1 + - - +
389B ALA 4.1 2.5 - - - -
390B ALA* 3.8 15.8 - - - -
392B ILE 3.2 10.3 - - - -
393B LEU* 4.3 3.4 - - - -
394B VAL* 4.3 0.2 - - - -
601B SK8 3.5 27.6 - - - +
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Residues in contact with LEU 346 (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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344B GLY 3.9 0.2 + - - -
345B SER* 1.3 70.4 - - - +
347B LEU* 1.3 59.5 + - - +
349B PHE* 4.3 6.3 - - + -
350B LEU* 2.9 53.0 + - + +
366B PHE* 4.2 21.5 - - + -
370B ILE* 3.8 29.2 - - + -
389B ALA* 3.3 18.1 + - + +
392B ILE* 2.6 26.6 + - + +
394B VAL* 3.8 20.8 - - + +
400B CYS* 4.3 6.1 - - - -
451B LEU* 4.5 1.1 - - + -
455B ILE* 3.9 22.2 - - + -
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Residues in contact with LEU 347 (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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345B SER* 3.2 7.4 - - - +
346B LEU* 1.3 77.7 - - - +
348B ASP* 1.3 63.6 + - - +
350B LEU* 3.2 4.3 + - - +
351B LYS* 2.9 51.4 + - + +
389B ALA* 3.2 21.2 + - + +
390B ALA* 4.1 20.0 - - + +
428B TRP* 6.4 1.6 - - + -
454B GLU* 4.1 15.0 - - - +
459B GLY* 3.3 36.8 - - - +
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Residues in contact with ASP 348 (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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343B LYS 5.3 2.2 - - - +
344B GLY* 5.9 0.4 - - - -
345B SER* 3.0 26.0 + - - +
347B LEU* 1.3 87.1 - - - +
349B PHE* 1.3 56.4 + - - +
351B LYS* 3.4 10.2 + - - +
352B SER* 2.8 28.4 + - - -
601B SK8 4.1 11.8 - - - +
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Residues in contact with PHE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LYS* 3.7 38.5 + - + +
345B SER 3.0 17.9 + - - +
346B LEU* 3.8 20.0 - - + +
347B LEU 3.2 0.2 - - - -
348B ASP* 1.3 75.3 - - - +
350B LEU* 1.3 66.2 + - + +
352B SER* 2.6 29.6 + - - -
354B GLU* 3.8 28.3 - - + -
355B GLY* 3.2 17.5 - - - -
358B GLN* 4.0 34.5 - - + -
366B PHE* 4.0 16.6 - + - -
394B VAL* 4.5 8.3 - - + -
398B LEU* 3.5 22.7 - - + -
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 2.9 47.0 + - + +
347B LEU* 3.7 3.8 - - - +
349B PHE* 1.3 84.8 - - + +
351B LYS* 1.3 60.1 + - - +
352B SER 3.5 6.1 + - - +
355B GLY* 4.1 7.1 - - - +
356B SER* 4.0 10.9 + - - -
358B GLN* 5.7 0.2 - - + -
363B LEU* 3.8 28.9 - - + -
366B PHE* 5.1 2.0 - - + -
389B ALA* 5.1 3.1 - - + -
454B GLU 3.9 1.8 - - - +
455B ILE* 3.7 30.3 - - + +
458B TYR* 3.5 39.3 - - + +
459B GLY* 3.9 13.7 - - - +
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Residues in contact with LYS 351 (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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347B LEU* 2.9 37.7 + - + +
348B ASP* 3.6 9.6 - - - +
350B LEU* 1.3 73.0 - - - +
352B SER* 1.3 66.9 + - - +
458B TYR 4.1 11.4 - - - +
459B GLY 3.5 22.8 + - - -
460B ARG* 5.4 1.1 - - - +
461B ILE* 4.6 17.5 - - - +
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Residues in contact with SER 352 (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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348B ASP 2.8 14.5 + - - -
349B PHE* 2.6 31.0 + - - -
350B LEU 3.7 0.5 - - - +
351B LYS* 1.3 83.7 - - - +
353B ASP* 1.3 63.8 + - - +
354B GLU* 3.4 5.2 + - - +
355B GLY 3.2 9.4 + - - -
356B SER* 3.4 19.4 + - - -
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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
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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