Contacts of the helix formed by residues 337 - 348 (chain A) in PDB entry 3O5X
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 THR 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LYS* 4.0 30.7 - - + +
305A ILE* 5.0 8.4 - - + +
331A GLN* 4.6 4.1 + - - +
333A CYS* 3.7 5.8 - - - -
334A LEU* 2.8 33.1 + - + +
336A ASN* 1.3 99.9 - - - +
338A VAL* 1.3 66.2 + - - +
339A ASN 3.2 2.5 - - - -
340A ASP* 3.0 20.6 + - + +
341A PHE* 2.8 22.8 + - - +
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A CYS* 3.8 22.0 - - + -
334A LEU 3.3 15.5 + - - +
335A GLN* 4.1 11.9 + - - +
336A ASN 3.7 0.8 - - - -
337A THR* 1.3 77.7 - - - +
339A ASN* 1.3 65.1 + - - +
341A PHE* 3.0 13.9 + - - +
342A TRP* 3.1 18.9 + - + -
368A VAL* 4.5 15.0 - - + -
369A LYS 4.5 1.6 - - - +
370A TYR* 4.1 17.0 - - + -
380A TYR* 3.3 39.7 - - + -
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Residues in contact with ASN 339 (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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336A ASN 5.2 2.8 + - - +
337A THR 3.2 0.6 - - - -
338A VAL* 1.3 77.1 - - - +
340A ASP* 1.3 66.0 + - - +
342A TRP* 3.3 4.2 + - - +
343A ARG* 3.0 32.7 + - - +
380A TYR* 3.3 38.7 - - - +
381A GLY* 3.4 22.1 + - - +
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Residues in contact with ASP 340 (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 LYS* 4.8 9.6 - - - +
292A LEU* 3.6 15.0 - - + +
302A SER* 4.8 1.8 - - - +
304A TYR 4.4 13.1 - - - +
305A ILE* 3.8 10.0 - - + +
336A ASN 3.7 7.5 - - - +
337A THR* 3.0 29.1 + - + +
339A ASN* 1.3 77.0 - - - +
341A PHE* 1.3 66.0 + - - +
343A ARG* 2.9 32.4 + - - +
344A MET* 2.9 23.7 + - - +
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Residues in contact with PHE 341 (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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305A ILE* 3.8 12.3 - - + +
330A THR* 4.0 17.7 - - + -
331A GLN 5.0 3.8 - - - -
333A CYS* 3.3 28.0 - - - -
337A THR 2.8 8.0 + - - +
338A VAL 3.0 9.4 + - - +
340A ASP* 1.3 77.3 - - - +
342A TRP* 1.3 67.0 + + - +
344A MET* 3.1 28.7 + - + +
345A VAL* 2.9 51.6 + - + +
353A ILE* 3.9 14.6 - - + -
370A TYR* 3.5 45.1 - + - -
456A VAL* 4.1 9.6 - - + -
458A HIS* 4.3 7.9 - + - -
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Residues in contact with TRP 342 (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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338A VAL* 3.1 18.8 + - + -
339A ASN 3.9 6.3 - - - +
340A ASP 3.3 0.2 - - - -
341A PHE* 1.3 80.1 - + - +
343A ARG* 1.3 65.3 + - - +
345A VAL* 3.8 18.3 - - + +
346A PHE* 2.9 26.0 + - - +
353A ILE* 4.3 15.0 - - + -
370A TYR* 2.7 47.5 + + - +
380A TYR* 3.5 28.8 - + + -
383A MET* 4.0 21.2 - - + +
385A VAL* 3.7 27.1 - - + -
401A LEU* 3.8 26.7 - - + -
403A LEU* 3.7 35.3 - - + +
415A VAL* 4.5 5.4 - - + -
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Residues in contact with ARG 343 (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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292A LEU* 3.4 20.4 - - + +
293A HIS 3.0 28.2 + - - +
294A ASP 4.2 2.8 + - - -
295A GLY* 3.2 24.1 - - - +
296A ASP 5.3 1.0 - - - +
302A SER* 2.8 35.9 + - - -
339A ASN* 3.0 24.4 + - + +
340A ASP* 2.9 31.9 + - - +
342A TRP* 1.3 76.6 - - - +
344A MET* 1.3 57.5 + - - +
346A PHE* 3.7 1.7 - - - +
347A GLN* 2.8 32.9 + - - +
380A TYR 6.0 0.2 - - - +
382A VAL* 5.4 7.2 - - + -
383A MET* 4.1 24.3 - - + +
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Residues in contact with MET 344 (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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290A VAL* 4.0 17.5 - - + -
292A LEU* 3.6 17.9 - - + +
305A ILE* 4.0 15.5 - - + -
307A ALA* 3.6 24.9 - - - -
328A ILE* 3.7 26.9 - - + -
330A THR* 4.1 6.3 - - + -
340A ASP 2.9 13.4 + - - +
341A PHE* 3.1 42.4 + - + +
343A ARG* 1.3 74.7 - - - +
345A VAL* 1.3 69.1 + - + +
347A GLN* 3.2 2.2 + - - -
348A GLU* 2.9 31.5 + - + +
456A VAL* 4.1 10.8 - - + -
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Residues in contact with VAL 345 (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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341A PHE* 2.9 50.3 + - + +
342A TRP* 3.8 18.4 - - + +
344A MET* 1.3 77.0 - - + +
346A PHE* 1.3 62.3 + - - +
349A ASN* 3.2 3.1 + - - -
350A SER* 3.1 52.4 + - - +
353A ILE* 4.1 7.9 - - + -
403A LEU* 3.7 18.3 - - + +
413A ARG* 5.2 0.3 + - - -
415A VAL* 4.1 10.3 - - + -
456A VAL* 4.4 11.7 - - + -
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Residues in contact with PHE 346 (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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342A TRP 2.9 17.6 + - - +
343A ARG 3.7 1.3 - - - +
345A VAL* 1.3 76.2 - - - +
347A GLN* 1.3 70.7 + - - +
349A ASN* 3.2 12.6 + - - +
383A MET* 3.5 27.6 - - + -
403A LEU* 3.9 20.2 - - + +
405A LYS* 4.1 25.4 - - + -
408A GLN* 4.6 4.0 - - - -
411A THR* 3.6 36.6 - - + -
413A ARG* 3.3 42.1 + - - +
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Residues in contact with GLN 347 (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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290A VAL* 4.3 5.7 - - - +
291A VAL 2.7 25.4 + - - -
292A LEU* 3.4 7.1 - - - +
293A HIS* 2.8 49.3 + - + +
343A ARG 2.8 22.1 + - - +
344A MET* 3.7 4.0 - - - +
346A PHE* 1.3 81.3 - - + +
348A GLU* 1.3 81.0 + - - +
349A ASN* 3.3 3.6 + - - +
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Residues in contact with GLU 348 (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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290A VAL* 4.0 17.6 - - + +
309A ILE* 3.8 18.2 - - - +
328A ILE* 3.5 30.1 - - + -
344A MET* 2.9 19.8 + - + +
347A GLN* 1.3 106.1 + - + +
349A ASN* 1.3 69.8 + - - +
350A SER* 3.3 7.0 + - - +
453A GLY* 3.5 1.6 - - - -
454A PRO* 3.4 22.9 - - + +
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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