Contacts of the helix formed by residues 338 - 352 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C TYR* 4.6 10.3 - - + +
318C ARG* 2.3 39.2 + - - -
325C PRO* 3.6 11.3 - - - +
336C TYR* 3.9 15.9 + - + -
337C ASP* 1.3 74.2 - - - +
339C VAL* 1.3 66.7 + - - +
340C LYS 3.4 3.0 + - - -
341C SER* 2.9 28.3 + - - -
342C MET* 3.1 23.6 + - - +
379C LEU* 3.6 11.2 - - - -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C TYR* 5.0 0.8 + - - -
338C ASP* 1.3 75.9 - - - +
340C LYS* 1.3 60.8 + - + +
342C MET* 3.4 4.2 + - - +
343C GLU* 3.0 47.3 + - - +
374C GLN* 3.8 26.6 - - - +
378C PRO* 3.9 24.2 - - + +
379C LEU* 3.6 12.8 - - + +
382C ALA* 3.9 16.6 - - + +
385C ARG* 5.3 3.6 - - - +
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Residues in contact with LYS 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ARG* 3.8 30.7 - - - +
338C ASP* 3.2 8.1 + - - +
339C VAL* 1.3 78.6 - - + +
341C SER* 1.3 66.4 + - - +
343C GLU* 3.3 18.6 + - - +
344C THR* 3.2 23.2 + - - -
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Residues in contact with SER 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ARG* 4.0 3.2 - - - +
323C GLN 3.6 23.4 - - - +
324C VAL* 3.9 3.1 - - - -
325C PRO* 3.9 14.1 - - - -
337C ASP* 3.0 24.5 + - - -
338C ASP* 2.9 38.8 + - - -
340C LYS* 1.3 73.8 - - - +
342C MET* 1.3 57.9 + - - +
344C THR* 3.4 5.4 + - - -
345C LYS* 2.9 31.9 + - - +
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Residues in contact with MET 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ILE* 3.6 26.6 - - + +
267C PRO 3.3 27.8 - - - +
268C THR* 4.7 2.7 - - + -
337C ASP* 3.7 12.8 - - + +
338C ASP 3.1 13.6 + - - +
339C VAL* 3.7 4.7 - - - +
341C SER* 1.3 79.6 - - - +
343C GLU* 1.3 60.8 + - + +
345C LYS* 3.2 7.0 + - - +
346C VAL* 2.8 34.6 + - - +
359C ILE* 5.3 2.5 - - + -
379C LEU* 3.5 47.6 - - + +
382C ALA* 5.5 1.6 - - + -
383C VAL* 3.7 28.5 - - + +
386C SER* 5.4 0.2 - - - -
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C VAL* 3.0 36.2 + - + +
340C LYS* 3.3 22.6 + - - +
342C MET* 1.3 75.9 - - - +
344C THR* 1.3 62.0 + - - +
346C VAL* 3.2 3.5 + - - +
347C GLN* 2.9 36.9 + - - +
382C ALA* 5.0 4.5 - - + -
385C ARG* 3.8 16.3 + - - -
386C SER* 3.7 24.1 + - - +
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Residues in contact with THR 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C LEU* 3.6 22.7 - - + -
323C GLN* 4.3 25.0 + - + +
340C LYS 3.2 11.1 + - - -
341C SER* 3.6 10.8 - - - -
343C GLU* 1.3 79.1 - - - +
345C LYS* 1.3 61.4 + - - +
347C GLN* 3.2 21.8 + - - +
348C PHE* 3.0 21.3 + - - +
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Residues in contact with LYS 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C SER* 2.8 42.5 + - - -
230C LEU* 4.4 20.6 - - + +
245C VAL* 4.3 11.4 - - + -
264C MET* 3.5 30.4 - - + +
265C GLY 5.7 0.4 - - - +
266C ILE* 4.4 19.3 - - + -
267C PRO* 4.3 4.4 - - - +
323C GLN 6.0 0.2 - - - +
324C VAL* 4.1 10.1 - - + -
337C ASP* 2.5 34.8 + - - +
341C SER 2.9 18.5 + - - +
342C MET* 3.2 6.5 + - - +
344C THR* 1.3 77.1 - - - +
346C VAL* 1.3 57.0 + - - +
348C PHE* 3.3 8.2 + - - +
349C LEU* 2.9 22.7 + - - +
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Residues in contact with VAL 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ILE* 4.8 4.0 - - + -
342C MET 2.8 24.7 + - - +
343C GLU 3.7 4.3 - - - +
345C LYS* 1.3 70.1 - - - +
347C GLN* 1.3 68.1 + - - +
349C LEU* 3.3 14.1 + - + +
350C LYS* 3.1 28.9 + - - +
383C VAL* 4.0 29.4 - - + +
386C SER* 3.5 43.5 - - - +
387C LEU* 3.9 17.0 - - + +
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Residues in contact with GLN 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C GLU* 2.9 35.2 + - - +
344C THR* 3.2 20.4 + - - +
346C VAL* 1.3 76.0 - - - +
348C PHE* 1.3 63.0 + - - +
350C LYS* 3.5 7.6 + - - +
351C ASN* 3.0 33.5 + - - +
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Residues in contact with PHE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C LEU* 3.9 25.1 - - + -
245C VAL* 4.5 1.6 - - + -
246C GLU* 3.5 46.0 - - + -
249C VAL* 4.0 15.9 - - + -
264C MET* 3.7 26.7 - - - -
344C THR 3.0 13.1 + - - +
345C LYS 3.4 7.4 - - - +
346C VAL 3.1 0.2 - - - -
347C GLN* 1.3 74.8 - - - +
349C LEU* 1.3 68.1 + - - +
351C ASN* 3.0 9.9 + - + +
352C LEU* 3.0 60.9 + - + +
354C LEU* 4.3 6.1 - - + -
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Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TYR* 4.1 13.7 - - + -
264C MET* 4.1 14.8 - - + -
266C ILE* 5.1 0.2 - - + -
345C LYS 2.9 14.0 + - - +
346C VAL* 3.3 25.1 + - + +
348C PHE* 1.3 74.6 - - - +
350C LYS* 1.3 64.4 + - + +
352C LEU 3.4 0.5 + - - -
353C ASN 3.3 3.5 + - - -
354C LEU* 3.0 55.9 + - + +
356C GLY* 3.8 37.2 - - - +
357C ALA* 3.9 20.6 - - + -
387C LEU* 4.0 17.3 - - + -
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Residues in contact with LYS 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TYR* 3.6 36.0 + - + +
346C VAL* 3.1 28.7 + - + +
347C GLN* 3.7 6.7 - - - +
349C LEU* 1.3 78.8 - - + +
351C ASN* 1.3 70.3 + - - +
353C ASN* 3.1 23.0 + - - -
386C SER 2.6 29.7 + - - -
387C LEU* 3.8 20.3 + - - +
389C SER* 2.9 23.0 + - - -
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Residues in contact with ASN 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C GLN* 3.0 22.4 + - - +
348C PHE* 3.0 8.7 + - + +
350C LYS* 1.3 80.6 - - - +
352C LEU* 1.3 68.5 + - + +
353C ASN* 3.3 9.0 + - - +
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Residues in contact with LEU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU 5.5 1.1 - - - +
249C VAL* 3.9 16.2 - - + -
250C GLY* 5.3 5.4 - - - +
253C ILE* 4.6 7.9 - - + +
259C SER* 3.6 8.3 - - - -
348C PHE* 3.0 57.0 + - + +
349C LEU 3.4 0.2 + - - -
350C LYS 3.1 0.4 - - - -
351C ASN* 1.3 85.7 - - + +
353C ASN* 1.3 70.3 + - - +
354C LEU* 3.1 24.4 + - + +
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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