Contacts of the helix formed by residues 338 - 352 (chain A) in PDB entry 4AY1
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 ASP 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A TYR* 4.6 10.3 - - + +
318A ARG* 2.2 39.6 + - - -
325A PRO* 3.8 9.8 - - - +
336A TYR* 4.0 15.6 + - + -
337A ASP* 1.3 74.1 - - - +
339A VAL* 1.3 66.5 + - - +
340A LYS* 3.4 3.0 + - - -
341A SER* 2.9 22.6 + - - -
342A MET* 3.0 24.4 + - - +
379A LEU* 3.8 11.2 - - - -
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 5.1 0.6 + - - +
338A ASP* 1.3 75.7 - - - +
340A LYS* 1.3 59.4 + - + +
342A MET* 3.3 3.6 + - - +
343A GLU* 2.9 54.7 + - - +
374A GLN* 3.8 25.5 - - - +
378A PRO* 3.9 23.3 - - + +
379A LEU* 3.8 13.1 - - + +
382A ALA* 3.7 16.9 - - + +
385A ARG* 5.0 5.8 - - - +
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG* 3.2 43.1 - - - +
338A ASP* 3.2 9.4 + - - +
339A VAL* 1.3 80.0 - - + +
341A SER* 1.3 62.1 + - - +
343A GLU* 3.3 17.2 + - - +
344A THR* 3.2 24.9 + - - -
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG* 3.9 3.3 - - - +
323A GLN 3.7 23.6 - - - +
324A VAL* 4.0 3.6 - - - -
325A PRO* 3.9 13.5 - - - -
337A ASP* 2.8 26.9 + - - -
338A ASP* 2.9 31.3 + - - -
340A LYS* 1.3 77.1 - - - +
342A MET* 1.3 57.6 + - - +
344A THR* 3.3 6.0 + - - -
345A LYS* 3.0 31.7 + - - +
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Residues in contact with MET 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 3.6 27.5 - - + +
267A PRO 3.2 28.0 - - - +
268A THR* 4.6 3.1 - - + -
337A ASP* 3.6 18.2 - - + +
338A ASP 3.0 18.3 + - - +
339A VAL* 3.7 4.9 - - - +
341A SER* 1.3 75.9 - - - +
343A GLU* 1.3 59.5 + - - +
345A LYS* 3.2 7.2 + - + +
346A VAL* 2.9 33.1 + - - +
359A ILE* 5.5 2.0 - - + -
379A LEU* 3.7 43.3 - - + +
382A ALA* 5.4 2.7 - - + -
383A VAL* 3.8 27.8 - - + -
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL* 2.9 38.0 + - + +
340A LYS* 3.3 17.4 + - - +
342A MET* 1.3 74.9 - - - +
344A THR* 1.3 62.8 + - - +
346A VAL* 3.3 2.2 + - - +
347A GLN* 3.0 33.4 + - + +
382A ALA* 4.7 6.1 - - + +
385A ARG* 3.6 22.5 + - - -
386A SER* 3.4 24.5 + - - +
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Residues in contact with THR 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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230A LEU* 3.8 21.5 - - + -
323A GLN* 4.2 27.2 + - + +
340A LYS 3.2 13.3 + - - -
341A SER* 3.6 10.8 - - - -
342A MET 3.2 0.2 - - - -
343A GLU* 1.3 77.0 - - - +
345A LYS* 1.3 63.6 + - - +
347A GLN* 3.1 11.2 + - + +
348A PHE* 3.0 21.5 + - - +
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Residues in contact with LYS 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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228A SER* 2.7 41.4 + - - -
230A LEU* 4.4 26.0 - - + +
245A VAL* 4.4 9.2 - - + -
264A MET* 3.5 25.3 - - + +
265A GLY 5.6 0.7 - - - +
266A ILE* 4.3 23.8 - - + -
267A PRO* 4.3 3.8 - - - +
324A VAL* 4.1 10.1 - - + -
337A ASP* 2.7 35.4 + - - +
341A SER 3.0 15.6 + - - +
342A MET* 3.2 8.0 + - - +
344A THR* 1.3 74.8 - - - +
346A VAL* 1.3 59.1 + - - +
348A PHE* 3.3 8.6 + - - +
349A LEU 3.0 22.9 + - - -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 4.8 3.6 - - + -
342A MET 2.9 18.2 + - - +
343A GLU 3.7 6.5 - - - +
344A THR 3.2 0.2 - - - -
345A LYS* 1.3 75.2 - - - +
347A GLN* 1.3 70.0 + - - +
349A LEU* 3.3 14.8 + - + +
350A LYS* 3.1 28.1 + - + +
383A VAL* 4.1 30.5 - - + +
386A SER* 3.5 42.4 - - - +
387A LEU* 3.9 16.6 - - + +
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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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343A GLU* 3.0 30.6 + - + +
344A THR* 3.1 10.7 + - + +
346A VAL* 1.3 87.5 - - - +
348A PHE* 1.3 58.2 + - - +
350A LYS* 3.5 14.0 + - - +
351A ASN* 3.0 29.9 + - - +
386A SER* 4.2 15.2 + - - +
389A SER* 5.5 2.2 + - - -
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Residues in contact with PHE 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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230A LEU* 3.8 28.0 - - + -
245A VAL* 4.2 4.5 - - + -
246A GLU* 3.7 42.8 - - + -
249A VAL* 3.9 20.2 - - + -
264A MET* 3.6 28.5 - - - -
344A THR 3.0 12.1 + - - +
345A LYS 3.5 6.3 - - - +
347A GLN* 1.3 77.0 - - - +
349A LEU* 1.3 65.6 + - - +
351A ASN* 3.1 7.3 + - - +
352A LEU* 2.9 56.7 + - + +
354A LEU* 4.4 4.0 - - + -
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Residues in contact with LEU 349 (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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27A TYR* 3.9 27.6 - - + -
264A MET* 3.9 14.6 - - + -
345A LYS 3.0 10.0 + - - +
346A VAL* 3.5 24.7 - - + +
348A PHE* 1.3 77.0 - - - +
350A LYS* 1.3 67.6 + - + +
352A LEU 3.4 1.2 + - - -
353A ASN 3.1 3.3 + - - -
354A LEU* 3.0 53.7 + - + +
356A GLY* 3.7 28.3 - - - +
357A ALA* 3.7 21.8 - - + +
387A LEU* 4.1 12.3 - - + -
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Residues in contact with LYS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.5 39.0 + - + +
346A VAL* 3.1 24.2 + - + +
347A GLN* 3.8 15.1 + - - +
349A LEU* 1.3 80.2 - - + +
351A ASN* 1.3 63.8 + - - +
353A ASN* 3.0 21.7 + - - -
386A SER 2.9 25.8 + - - -
387A LEU* 3.3 27.5 + - - +
389A SER* 3.7 19.6 + - - -
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Residues in contact with ASN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A GLN 3.0 19.1 + - - +
348A PHE* 3.1 7.8 + - - +
350A LYS* 1.3 79.0 - - - +
352A LEU* 1.3 72.5 + - + +
353A ASN* 3.5 8.7 + - - +
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Residues in contact with LEU 352 (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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246A GLU 5.6 0.7 - - - +
249A VAL* 3.8 16.4 - - + -
250A GLY* 5.2 6.3 - - - +
253A ILE* 4.6 9.2 - - + +
259A SER* 3.5 13.7 - - - -
348A PHE* 2.9 56.3 + - + +
349A LEU 3.4 0.2 + - - -
350A LYS 3.1 0.2 - - - -
351A ASN* 1.3 90.8 - - - +
353A ASN* 1.3 72.4 + - - +
354A LEU* 3.3 16.4 + - + +
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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