Contacts of the helix formed by residues 298 - 305 (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 ALA 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TRP 3.9 0.4 + - - -
297B CYS* 1.3 76.6 - - - +
299B PRO* 1.3 72.8 - - + +
300B GLU* 3.0 29.4 - - - +
301B SER* 2.9 22.6 + - - +
302B LEU* 3.2 8.7 + - - +
311B SER* 4.1 6.3 + - - -
314B TRP* 3.5 32.8 - - + -
315B MET* 5.0 2.6 - - - +
375B ARG* 4.1 1.1 - - - +
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Residues in contact with PRO 299 (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 3.6 0.4 - - - -
298B ALA* 1.3 86.1 - - + +
300B GLU* 1.3 65.7 + - - +
302B LEU* 3.2 6.4 + - + +
303B LYS* 3.0 30.7 + - - +
314B TRP* 3.4 34.5 - - + -
340B LEU* 4.3 1.1 - - + +
343B ILE* 3.4 36.8 - - + +
344B ASP* 3.9 22.4 - - + +
370B HIS* 4.8 11.9 - - + +
375B ARG* 4.0 2.7 - - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ALA* 3.0 21.6 - - - +
299B PRO* 1.3 78.9 - - - +
301B SER* 1.3 55.9 + - - +
303B LYS* 4.2 11.6 - - - +
304B THR* 2.9 35.3 + - - +
305B ARG 3.6 1.2 + - - -
306B THR* 3.7 26.9 + - + +
308B SER* 4.0 5.5 + - - -
311B SER* 3.7 15.8 + - - -
370B HIS 4.8 1.0 - - - +
372B PRO* 3.7 24.2 - - + +
375B ARG* 3.2 28.1 + - - -
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Residues in contact with SER 301 (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* 4.1 6.3 - - - -
298B ALA* 2.9 22.4 + - - +
300B GLU* 1.3 77.4 - - - +
302B LEU* 1.3 59.2 + - - +
305B ARG* 3.0 26.6 + - - +
306B THR 2.8 25.0 + - - +
307B PHE* 3.7 33.5 - - - -
311B SER* 3.9 10.4 - - - -
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Residues in contact with LEU 302 (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* 5.3 1.0 - - - +
329A GLU* 5.0 4.5 + - - +
332A ILE* 3.4 29.5 - - + +
294B PHE* 3.5 46.4 - - + +
297B CYS* 3.8 25.6 - - + +
298B ALA 3.2 3.7 + - - +
299B PRO 3.2 6.5 + - - +
301B SER* 1.3 76.4 - - - +
303B LYS* 1.3 61.9 + - - +
305B ARG* 5.9 0.5 - - - +
336B GLY 4.7 3.6 - - - +
339B ILE* 4.4 9.2 - - + -
340B LEU* 4.2 31.6 - - + +
343B ILE* 4.0 25.6 - - + -
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Residues in contact with LYS 303 (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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327A GLY 3.5 1.0 - - - +
328A GLN* 3.1 59.0 - - - +
329A GLU 4.1 0.7 + - - -
299B PRO* 3.0 26.2 + - - +
300B GLU* 3.2 9.1 + - - +
302B LEU* 1.3 80.1 - - - +
304B THR* 1.3 66.1 + - + +
305B ARG* 3.8 0.7 - - - -
340B LEU* 3.8 15.3 - - + -
344B ASP* 2.8 40.5 + - - +
345B LYS* 5.5 0.7 - - - +
370B HIS* 4.0 13.9 + - - -
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Residues in contact with THR 304 (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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218A ARG* 3.6 20.3 - - - +
221A GLN* 3.4 28.7 + - - +
325A THR 3.9 10.8 - - - +
326A TYR 3.2 27.1 - - - +
327A GLY 4.3 5.4 - - - -
285B VAL* 3.9 1.7 - - - +
300B GLU* 2.9 11.1 + - - +
303B LYS* 1.3 85.4 - - + +
305B ARG* 1.3 74.6 + - - +
306B THR* 3.1 18.0 + - - -
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Residues in contact with ARG 305 (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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218A ARG* 4.1 24.9 - - - +
329A GLU* 5.7 3.0 + - - -
285B VAL* 3.3 15.0 - - + -
286B MET* 2.8 56.4 + - + +
287B GLN 2.5 32.1 + - - -
288B GLU* 3.6 15.5 + - - +
290B ARG 3.1 24.9 + - - -
291B LYS* 3.9 13.9 - - - +
292B VAL 5.6 0.4 - - - +
294B PHE* 5.9 5.3 - - - -
301B SER 3.0 19.9 + - - +
302B LEU 5.9 0.7 - - - +
303B LYS 3.8 0.8 - - - -
304B THR* 1.3 79.5 - - - +
306B THR* 1.3 62.2 + - - +
307B PHE* 3.3 10.8 - - + -
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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