Contacts of the helix formed by residues 333 - 345 (chain B) in PDB entry 5U7Z
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 ARG 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B CYS 3.0 39.6 + - - +
144B THR* 3.4 14.8 + - - +
162B ASP* 3.3 9.1 + - - -
319B THR* 4.1 14.1 + - + +
320B ASN* 2.5 32.3 + - - +
321B TYR* 5.7 0.4 - - - -
331B ASP* 3.6 24.6 + - + +
332B ASP* 1.3 72.4 - - - +
334B ARG* 1.3 63.7 + - - +
335B THR 3.4 0.2 - - - -
336B PRO* 3.5 5.8 - - - +
337B ALA* 3.2 22.7 + - - +
362B PRO* 3.3 37.9 - - + +
363B VAL* 3.6 14.8 - - - +
365B ASN* 3.7 13.9 - - - +
395B TRP 4.6 6.3 - - - -
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TYR* 4.9 6.9 + - - -
317B VAL* 2.6 46.0 + - + +
318B GLN* 4.3 8.5 + - - +
319B THR* 3.7 26.1 + - + +
321B TYR* 3.2 37.3 + - + +
323B ARG* 3.4 45.8 + - - +
332B ASP* 3.1 2.1 - - - +
333B ARG* 1.3 78.8 - - - +
335B THR* 1.3 64.5 + - - +
337B ALA* 3.1 7.3 + - - +
338B LYS* 3.0 62.9 + - + +
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Residues in contact with THR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B TYR* 4.8 3.1 + - - -
332B ASP* 2.6 30.0 + - - +
334B ARG* 1.3 78.2 - - - +
336B PRO* 1.3 68.2 - - + +
338B LYS* 3.2 12.5 + - + +
339B MET* 2.9 23.5 + - + +
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Residues in contact with PRO 336 (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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28A THR* 3.4 28.3 - - + -
332B ASP 2.7 31.2 - - - +
333B ARG 3.5 7.4 - - - +
335B THR* 1.3 86.2 - - + +
337B ALA* 1.3 54.7 + - - +
339B MET* 3.2 21.3 + - + +
340B CYS* 2.8 37.9 + - - -
360B THR* 5.7 1.3 - - + -
361B LYS 4.7 2.0 - - - +
362B PRO* 3.6 21.1 - - + -
363B VAL* 4.3 6.5 - - + -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 4.7 5.4 - - + -
146B ILE* 4.4 7.9 - - + -
317B VAL* 4.2 18.6 - - + -
333B ARG 3.2 12.4 + - - +
334B ARG 3.1 10.4 + - - +
336B PRO* 1.3 77.6 - - - +
338B LYS* 1.3 53.3 + - - +
340B CYS* 3.8 1.3 - - - +
341B LEU* 2.7 41.9 + - - +
357B VAL* 4.1 19.0 - - + +
363B VAL* 4.0 11.1 - - + +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B TYR* 3.6 33.7 - - + +
317B VAL* 4.4 9.4 - - + -
334B ARG* 3.0 54.9 + - + +
335B THR* 3.7 9.2 - - - +
337B ALA* 1.3 72.6 - - - +
339B MET* 1.3 57.6 + - - +
341B LEU* 3.7 3.3 - - - +
342B ASN* 2.6 44.6 + - - +
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Residues in contact with MET 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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28A THR* 5.0 9.9 - - - +
29A GLU 4.0 15.9 - - - +
30A ASP* 6.2 0.9 - - - -
31A CYS* 3.7 9.0 - - - -
335B THR* 2.9 15.6 + - + +
336B PRO* 3.5 32.3 - - + +
338B LYS* 1.3 76.9 - - - +
340B CYS* 1.3 74.3 + - - +
342B ASN* 3.6 7.6 - - - +
343B ARG* 3.0 27.5 + - + +
360B THR* 5.3 0.7 - - + -
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Residues in contact with CYS 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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31A CYS* 2.0 56.6 - - + +
336B PRO 2.8 19.7 + - - +
337B ALA* 3.9 1.3 - - - +
339B MET* 1.3 80.9 - - - +
341B LEU* 1.3 65.9 + - - +
343B ARG* 3.4 2.0 + - - +
344B THR* 3.0 28.1 + - - -
357B VAL* 3.8 24.2 - - + -
360B THR* 4.0 17.5 - - - -
363B VAL* 6.3 0.2 - - - -
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.6 29.4 - - + -
148B ALA* 5.2 0.2 - - + -
314B TRP* 3.0 29.2 - - + -
315B TYR* 3.6 26.5 - - + -
317B VAL* 3.4 33.7 - - + -
337B ALA 2.7 27.1 + - - +
338B LYS 3.7 1.3 - - - +
340B CYS* 1.3 70.8 - - - +
342B ASN* 1.3 62.3 + - - +
344B THR* 3.3 2.7 + - - -
345B SER 3.2 8.1 + - - -
349B ILE* 3.8 26.9 - - + -
354B MET* 4.7 3.8 - - + -
357B VAL* 3.9 18.4 - - + +
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Residues in contact with ASN 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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314B TRP* 4.5 6.4 + - - -
315B TYR* 2.8 29.0 + - - -
338B LYS* 2.6 28.2 + - - +
339B MET* 3.6 7.6 - - - +
341B LEU* 1.3 74.6 - - - +
343B ARG* 1.3 62.8 + - - +
345B SER* 3.1 16.1 + - - -
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Residues in contact with ARG 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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31A CYS* 4.9 11.9 - - + -
33A LYS* 5.7 8.7 - - - +
339B MET* 3.0 18.9 + - + +
340B CYS* 3.9 7.0 - - - +
341B LEU 3.4 0.2 - - - -
342B ASN* 1.3 75.8 - - - +
344B THR* 1.3 65.2 + - - +
345B SER* 4.2 3.3 - - - -
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Residues in contact with THR 344 (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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340B CYS 3.0 18.3 + - - -
341B LEU* 3.6 6.2 - - - -
342B ASN 3.2 0.4 - - - -
343B ARG* 1.3 76.0 - - - +
345B SER* 1.3 85.1 + - - +
348B ASN* 3.4 23.4 + - + +
349B ILE* 3.9 12.8 - - + -
353B THR* 3.6 42.2 + - + +
356B ASP* 5.9 1.0 - - - +
357B VAL* 4.5 7.6 - - - +
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Residues in contact with SER 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LYS* 6.1 0.4 - - - -
314B TRP* 3.8 11.8 - - - +
341B LEU 3.2 5.7 + - - -
342B ASN 3.1 15.8 + - - -
343B ARG 4.2 3.6 - - - -
344B THR* 1.3 96.2 + - - +
346B GLN* 1.3 65.5 + - - +
347B GLU* 3.2 30.2 + - - +
348B ASN* 3.2 9.5 + - - -
349B ILE 3.6 6.1 + - - -
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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