Contacts of the helix formed by residues 335 - 345 (chain B) in PDB entry 1U54
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 ASN 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLY 3.2 21.3 - - - +
334A LEU* 3.1 30.3 - - + +
338A GLN* 3.8 15.9 + - - +
294B PHE* 5.2 0.9 - - - -
333B GLY 3.9 1.9 + - - +
334B LEU* 1.3 72.3 - - - +
336B GLY* 1.3 64.6 + - - +
337B SER* 3.4 2.4 - - - +
338B GLN* 2.9 48.2 + - - +
339B ILE* 3.0 11.8 + - - -
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Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.9 8.0 - - - +
333A GLY* 3.9 5.1 - - - -
294B PHE* 3.4 44.9 - - - -
302B LEU* 4.7 3.9 - - - +
334B LEU 4.2 0.6 + - - -
335B ASN* 1.3 72.6 - - - +
337B SER* 1.3 57.6 + - - +
339B ILE* 3.8 5.2 - - - +
340B LEU* 3.0 30.1 + - - +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TRP* 3.5 20.8 + - - -
332A ILE* 2.9 36.7 + - - +
334A LEU* 4.2 11.9 - - - -
342A LYS* 6.3 2.0 - - - -
335B ASN* 2.9 12.8 + - - +
336B GLY* 1.3 74.6 - - - +
338B GLN* 1.3 59.7 + - - -
340B LEU* 3.4 4.3 + - - +
341B HIS* 3.2 23.2 + - - +
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Residues in contact with GLN 338 (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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333B GLY 3.9 2.9 - - - +
334B LEU* 3.1 32.0 - - + +
335B ASN* 2.9 50.7 + - - +
337B SER* 1.3 68.2 - - - +
339B ILE* 1.3 64.8 + - - +
341B HIS* 3.5 11.2 - - - +
342B LYS* 3.4 20.3 - - - +
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Residues in contact with ILE 339 (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 PHE* 4.3 6.5 - - + +
295B ALA* 3.7 28.0 - - + +
302B LEU* 4.4 15.3 - - + -
331B TRP* 3.6 40.8 - - + +
334B LEU* 3.7 29.6 - - + +
335B ASN 3.0 14.2 + - - +
336B GLY* 3.8 6.7 - - - +
338B GLN* 1.3 72.8 - - - +
340B LEU* 1.3 69.5 + - - +
342B LYS* 2.8 20.3 + - - +
343B ILE* 3.1 22.8 + - + +
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Residues in contact with LEU 340 (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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328A GLN* 3.8 22.9 - - + +
329A GLU 5.9 0.9 - - - +
332A ILE* 4.3 17.0 - - + -
299B PRO 4.3 4.0 - - - +
302B LEU* 4.2 30.7 - - + +
303B LYS* 3.8 21.8 - - + -
336B GLY 3.0 18.9 + - - +
337B SER* 3.4 5.8 + - - +
339B ILE* 1.3 75.7 - - - +
341B HIS* 1.3 56.7 + - - +
343B ILE* 3.4 10.3 + - + +
344B ASP* 2.9 54.8 + - + +
345B LYS* 5.2 6.3 - - + +
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Residues in contact with HIS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B SER 3.2 12.0 + - - +
338B GLN* 3.5 14.1 - - - +
340B LEU* 1.3 76.7 - - - +
342B LYS* 1.3 53.4 + - + +
345B LYS* 2.7 61.7 + - + +
346B GLU* 2.7 53.5 + - + +
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Residues in contact with LYS 342 (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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331B TRP* 3.3 34.1 - - + -
334B LEU* 4.1 17.9 - - + -
338B GLN* 3.4 13.9 - - - +
339B ILE* 2.8 11.4 + - - +
341B HIS* 1.3 76.2 - - + +
343B ILE* 1.3 54.2 + - + +
346B GLU* 3.3 16.5 + - - +
347B GLY 2.7 31.4 + - - -
348B GLU* 2.7 56.4 + - + +
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Residues in contact with ILE 343 (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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297B CYS 4.0 11.9 - - - +
299B PRO* 3.4 48.2 - - + +
302B LEU* 4.0 15.5 - - + -
314B TRP* 4.3 12.3 - - + -
331B TRP* 4.2 19.3 - - + +
339B ILE* 3.6 24.0 - - + +
340B LEU* 3.4 11.2 - - + +
342B LYS* 1.3 78.5 - - - +
344B ASP* 1.3 59.7 + - + +
347B GLY* 4.0 4.2 - - - -
348B GLU 3.5 15.9 - - - +
349B ARG* 2.8 26.6 + - - +
370B HIS* 4.4 5.7 - - - -
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Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLU* 5.3 5.4 - - - +
299B PRO* 3.9 3.8 - - + +
303B LYS* 2.8 44.5 + - - +
340B LEU* 2.9 26.1 + - + +
342B LYS 3.4 0.2 - - - -
343B ILE* 1.3 79.8 - - + +
345B LYS* 1.3 86.3 + - - +
346B GLU 3.5 0.7 - - - -
347B GLY* 4.4 3.2 + - - -
370B HIS* 3.0 26.4 + - - -
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Residues in contact with LYS 345 (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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328A GLN* 5.6 3.0 + - - -
351A PRO* 5.2 18.8 - - + -
354A GLU* 4.8 14.1 + - - +
303B LYS* 5.5 1.2 - - - +
340B LEU* 5.0 7.0 + - + +
341B HIS* 2.7 58.9 + - + +
344B ASP* 1.3 112.9 + - - +
346B GLU* 1.3 58.4 + - + +
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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