Contacts of the helix formed by residues 323 - 336 (chain A) in PDB entry 5YVT
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 LYS 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ASP* 3.3 46.3 - - + +
274A MET* 4.8 9.2 - - + +
315A THR* 4.3 3.6 - - - -
321A ASN 4.1 0.4 + - - -
322A ALA* 1.3 75.9 - - - +
324A CYS* 1.3 65.2 + - - +
325A SER* 4.1 2.9 - - - +
326A ASP* 3.2 30.4 + - - +
327A PHE* 3.2 20.3 + - - +
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Residues in contact with CYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 4.7 14.6 - - - +
19A ILE* 4.7 5.2 - - - -
22A ALA* 4.5 7.9 - - - -
273A ASP* 2.8 17.3 + - - +
274A MET* 3.9 12.2 - - - +
275A ALA* 3.2 30.3 - - - +
277A PRO* 3.9 15.5 - - - -
315A THR* 4.2 8.9 - - - +
323A LYS* 1.3 71.3 - - - +
325A SER* 1.3 50.2 + - - +
327A PHE* 3.3 4.0 + - - +
328A THR* 2.7 49.4 + - - -
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Residues in contact with SER 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 5.6 1.6 - - - -
273A ASP* 2.7 34.9 + - - -
323A LYS* 4.1 3.1 - - - +
324A CYS* 1.3 75.0 - - - +
326A ASP* 1.3 63.6 + - - +
328A THR* 3.6 7.6 - - - -
329A GLU* 2.8 34.3 + - - +
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A SER* 4.9 7.7 + - - -
322A ALA* 4.5 10.9 - - + +
323A LYS* 3.2 39.4 + - - +
325A SER* 1.3 80.8 + - - +
327A PHE* 1.3 59.4 + - - +
329A GLU* 3.2 7.2 + - - +
330A GLU* 3.0 29.6 + - - +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ASN* 3.7 7.4 - - - -
277A PRO* 3.7 25.1 - - + -
278A THR* 3.4 27.4 - - - -
304A CYS* 4.8 1.1 - - - -
307A THR* 4.0 16.8 - - + +
308A ILE* 3.8 28.5 - - + -
313A SER* 3.3 29.5 + - - +
314A LEU* 4.1 17.0 - - + -
315A THR* 4.0 13.2 - - + -
318A LEU* 5.1 4.0 - - + -
323A LYS 3.2 8.5 + - - +
324A CYS 3.5 6.7 - - - +
326A ASP* 1.3 78.1 - - - +
328A THR* 1.3 61.4 + - - +
330A GLU* 3.4 3.8 + - - +
331A ILE* 3.3 48.8 + - + +
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.4 48.9 - - + +
25A LYS* 4.3 19.5 - - + -
26A ILE* 3.3 16.5 - - + +
277A PRO* 3.9 5.6 - - - +
324A CYS* 2.7 32.1 + - - -
325A SER* 3.6 9.4 - - - -
327A PHE* 1.3 74.8 - - - +
329A GLU* 1.3 61.7 + - - +
331A ILE* 3.3 5.6 + - - -
332A CYS* 3.1 25.7 + - - -
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.5 27.7 + - - +
325A SER 2.8 21.7 + - - +
326A ASP* 3.2 8.7 + - - +
328A THR* 1.3 72.8 - - - +
330A GLU* 1.3 57.5 + - - +
332A CYS* 3.3 11.7 + - - +
333A ARG* 3.0 38.6 + - + +
336A LYS* 5.8 2.3 - - - -
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A THR* 3.8 16.3 - - + +
310A ASP* 5.3 1.7 - - - +
312A LYS* 3.9 22.4 + - - +
313A SER* 2.7 30.0 + - - +
326A ASP 3.0 15.6 + - - +
327A PHE 3.9 4.7 - - - +
328A THR 3.3 0.4 - - - -
329A GLU* 1.3 73.2 - - - +
331A ILE* 1.3 63.7 + - - +
333A ARG* 3.3 29.8 + - - +
334A ARG* 3.0 66.3 + - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.6 33.7 - - + -
277A PRO* 5.7 2.2 - - + -
281A LEU* 4.2 20.2 - - + -
300A ILE 4.6 1.1 - - - +
303A ALA* 3.8 24.0 - - + +
304A CYS* 3.9 12.3 - - + +
307A THR* 3.4 23.3 - - - +
327A PHE* 3.3 46.6 + - + +
328A THR* 3.3 2.5 + - - +
330A GLU* 1.3 72.5 - - - +
332A CYS* 1.3 64.8 + - - +
334A ARG* 3.3 1.3 + - - -
335A VAL* 3.1 24.5 + - - +
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Residues in contact with CYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.8 46.9 - - - +
26A ILE* 3.6 17.7 - - - -
29A ALA* 3.9 9.1 - - + +
328A THR 3.1 19.0 + - - -
329A GLU* 3.4 16.2 - - - +
331A ILE* 1.3 76.3 - - - +
333A ARG* 1.3 59.5 + - - +
335A VAL* 3.5 16.8 - - - +
336A LYS* 3.4 29.4 - - - +
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLU* 3.0 27.9 + - - +
330A GLU* 3.3 50.4 + - - +
331A ILE 3.2 0.2 - - - -
332A CYS* 1.3 79.1 - - - +
334A ARG* 1.3 75.7 + - - +
335A VAL 3.6 0.2 + - - -
336A LYS* 3.7 21.2 + - - +
337A ASP* 4.2 7.8 - - - +
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 4.1 17.2 - - + +
306A ALA* 3.5 26.4 + - + +
307A THR* 3.4 24.2 - - - +
310A ASP* 2.7 37.3 + - - -
330A GLU* 3.0 32.0 + - - +
331A ILE 3.3 3.1 + - - +
333A ARG* 1.3 93.6 - - - +
335A VAL* 1.3 61.9 + - - +
337A ASP* 3.4 26.1 + - - +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.3 7.0 - - + +
29A ALA* 3.9 4.5 - - + -
30A ALA* 3.7 40.6 - - + +
299A ARG* 3.1 60.0 + - + +
300A ILE* 4.1 5.8 - - + -
303A ALA* 3.8 10.7 - - + +
331A ILE* 3.1 16.7 + - + +
332A CYS* 3.5 19.7 - - - +
334A ARG* 1.3 73.4 - - - +
336A LYS* 1.3 64.1 + - - +
337A ASP 3.2 8.1 + - - -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.0 31.4 + - - +
299A ARG* 5.2 2.5 + - - +
329A GLU* 5.8 2.2 - - - -
332A CYS* 3.4 26.0 - - - +
333A ARG* 3.7 14.8 - - - +
334A ARG 3.3 0.8 - - - -
335A VAL* 1.3 77.6 - - - +
337A ASP* 1.3 63.9 + - - +
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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