Contacts of the helix formed by residues 338 - 353 (chain Y) in PDB entry 5A31
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 HIS 338 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90X ASP 4.9 6.3 - - - -
91X LYS* 4.2 17.5 + - + -
92X GLU* 4.4 16.7 - - + +
305Y ILE* 3.7 32.2 - - + +
335Y SER* 3.3 24.0 - - - -
336Y ASP* 3.2 26.1 + - - +
337Y GLN* 1.3 85.2 + - + +
339Y ALA* 1.3 66.9 + - - +
340Y GLU* 3.2 1.2 + - - +
341Y PRO* 3.3 24.7 - - + +
342Y TRP* 3.1 18.7 - - - -
368Y LEU* 3.6 2.9 - - - +
369Y ASN* 5.6 1.3 - - - +
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Residues in contact with ALA 339 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338Y HIS* 1.3 73.3 - - - +
340Y GLU* 1.3 61.9 + - + +
342Y TRP* 3.1 7.3 + - - +
343Y VAL* 2.9 33.0 + - + +
365Y ALA* 3.8 14.5 - - - +
368Y LEU* 4.0 11.1 - - - +
369Y ASN* 3.3 45.7 - - + +
372Y SER* 4.5 9.9 - - - +
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Residues in contact with GLU 340 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Y ILE* 2.1 66.5 - - + +
306Y LYS* 3.9 7.5 + - - +
309Y ASP* 3.5 35.3 - - + +
331Y LEU* 3.9 6.2 - - + +
338Y HIS* 3.1 1.2 + - - +
339Y ALA* 1.3 83.6 - - + +
341Y PRO* 1.3 64.8 - - + +
343Y VAL* 3.7 6.8 - - - +
344Y VAL* 2.9 30.5 + - - +
369Y ASN* 3.7 18.5 + - - -
372Y SER* 5.5 2.6 - - - -
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Residues in contact with PRO 341 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Y ILE* 4.6 0.9 - - + -
331Y LEU* 3.8 39.3 - - + +
332Y PHE* 3.6 35.8 - - + +
335Y SER* 4.2 9.0 - - - +
336Y ASP* 5.1 1.1 - - - -
338Y HIS* 3.3 29.2 - - + +
340Y GLU* 1.3 94.7 - - + +
342Y TRP* 1.3 61.4 + - + +
344Y VAL* 3.1 25.7 - - + +
345Y SER 3.3 5.0 + - - -
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Residues in contact with TRP 342 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E VAL* 4.0 15.3 - - + -
64E ALA* 5.7 0.4 - - - -
67E LEU* 3.4 44.2 - - + -
332Y PHE* 3.8 10.9 - + - -
336Y ASP* 3.2 36.5 + - - -
338Y HIS 3.1 24.4 + - - -
339Y ALA 3.1 6.8 + - - +
341Y PRO* 1.3 74.3 - - + +
343Y VAL* 1.3 67.0 + - - +
345Y SER* 3.4 2.2 + - - -
346Y GLY* 3.0 19.2 + - - -
361Y LEU* 3.7 55.3 - - + +
364Y LYS* 3.8 29.8 - - + +
365Y ALA* 3.7 8.7 - - + -
368Y LEU* 3.5 18.8 - - + +
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Residues in contact with VAL 343 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309Y ASP* 3.1 34.5 - - - +
339Y ALA* 2.9 29.9 + - + +
340Y GLU* 3.7 5.6 - - - +
342Y TRP* 1.3 75.7 - - - +
344Y VAL* 1.3 58.5 + - - +
346Y GLY* 3.0 4.2 + - - -
347Y CYS* 2.8 31.9 + - - +
365Y ALA* 3.6 16.4 - - + -
372Y SER* 4.7 0.9 - - - +
374Y GLN* 3.9 15.7 - - + -
375Y ALA* 4.2 14.6 - - + +
378Y LEU* 3.6 21.6 - - + +
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Residues in contact with VAL 344 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308Y MET 5.1 3.8 - - - +
309Y ASP* 5.7 1.7 - - - +
312Y GLY* 4.5 9.6 - - - -
324Y VAL* 3.7 32.2 - - + +
327Y LEU* 3.9 24.5 - - + -
328Y GLY* 3.7 15.7 - - - +
331Y LEU* 3.5 22.0 - - + -
340Y GLU 2.9 17.4 + - - +
341Y PRO* 3.1 21.3 - - + +
343Y VAL* 1.3 75.5 - - - +
345Y SER* 1.3 61.5 + - - +
347Y CYS* 3.1 9.1 + - - +
348Y HIS 3.1 17.7 + - - -
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Residues in contact with SER 345 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E VAL* 4.7 9.8 - - - +
74E GLN* 5.2 4.2 + - - -
324Y VAL* 5.6 0.2 - - - -
328Y GLY* 4.5 6.2 - - - -
332Y PHE* 3.2 28.5 - - - -
341Y PRO 3.3 8.3 + - - -
342Y TRP 4.0 1.6 - - - -
343Y VAL 3.2 0.8 - - - -
344Y VAL* 1.3 82.3 - - - +
346Y GLY* 1.3 62.2 + - - +
348Y HIS* 3.3 9.2 + - - +
349Y SER* 3.1 26.0 + - - -
361Y LEU* 3.4 23.6 - - - -
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Residues in contact with GLY 346 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342Y TRP 3.0 11.5 + - - -
343Y VAL 3.0 7.9 + - - -
345Y SER* 1.3 74.5 - - - +
347Y CYS* 1.3 61.7 + - - +
349Y SER 3.3 7.4 + - - -
350Y PHE* 3.5 5.2 + - - -
358Y ALA* 3.4 28.6 - - - +
361Y LEU* 4.1 10.4 - - - +
378Y LEU* 3.6 22.8 - - - +
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Residues in contact with CYS 347 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309Y ASP 4.7 2.7 - - - -
312Y GLY* 3.8 14.1 - - - +
313Y TYR* 3.5 42.8 - - - -
316Y ALA* 4.4 5.5 - - + +
321Y LEU* 5.5 0.2 - - - +
324Y VAL* 4.6 4.5 - - + -
343Y VAL* 2.8 28.1 + - - +
344Y VAL* 3.1 12.8 + - - +
346Y GLY* 1.3 69.4 - - - +
348Y HIS* 1.3 66.3 + - - +
349Y SER 3.4 0.2 + - - -
350Y PHE* 3.9 4.7 + - - +
351Y TYR* 3.2 27.1 - - - +
374Y GLN* 5.3 2.2 - - - -
378Y LEU* 3.9 14.3 - - - +
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Residues in contact with HIS 348 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASP* 5.8 1.3 - - - -
321Y LEU* 3.6 37.7 + - + +
324Y VAL* 3.5 21.4 - - + +
325Y GLU* 3.0 48.4 + - + +
344Y VAL 3.1 6.7 + - - +
345Y SER* 3.3 13.9 + - - +
347Y CYS* 1.3 77.6 - - - +
349Y SER* 1.3 61.6 + - - +
351Y TYR* 3.2 4.9 + - - +
352Y SER* 2.9 48.8 + - - -
354Y ARG* 5.8 0.9 - - - -
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Residues in contact with SER 349 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E VAL* 5.2 1.2 - - - +
345Y SER 3.1 15.5 + - - -
346Y GLY 3.3 0.4 + - - -
347Y CYS 3.2 0.6 - - - -
348Y HIS* 1.3 78.6 + - - +
350Y PHE* 1.3 65.6 + - - +
352Y SER* 3.1 11.3 + - - -
353Y LYS 3.0 17.5 + - - -
354Y ARG* 3.1 18.4 + - - +
357Y ARG* 3.8 21.2 - - - +
358Y ALA* 3.4 33.4 - - - -
361Y LEU* 4.6 2.1 - - - +
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Residues in contact with PHE 350 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313Y TYR* 5.1 13.9 - + - -
346Y GLY 3.5 6.6 + - - -
347Y CYS* 4.5 4.0 - - - -
349Y SER* 1.3 74.0 - - - +
351Y TYR* 1.3 87.3 + + + +
353Y LYS* 3.1 21.8 + - - +
355Y TYR* 3.8 19.7 + + + -
358Y ALA* 4.0 7.1 - - + +
377Y LEU* 5.4 2.7 - - + -
378Y LEU* 3.0 56.1 - - + -
381Y ALA* 3.5 25.6 - - + -
382Y ALA* 3.4 25.8 - - + -
385Y ASN* 4.6 8.1 - - - +
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Residues in contact with TYR 351 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313Y TYR* 4.1 23.5 + + - -
316Y ALA* 3.2 50.2 - - + +
317Y ARG* 4.2 5.7 + - - +
319Y GLY* 5.8 2.0 - - - -
321Y LEU* 3.4 32.7 - - + +
347Y CYS* 3.2 16.4 - - - -
348Y HIS 3.2 2.1 + - - +
349Y SER 3.1 0.4 - - - -
350Y PHE* 1.3 106.6 - + + +
352Y SER* 1.3 59.8 + - - +
353Y LYS* 3.2 9.8 + - - +
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Residues in contact with SER 352 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321Y LEU* 4.4 8.9 - - - +
348Y HIS* 2.9 30.0 + - - -
349Y SER* 3.1 25.3 + - - -
351Y TYR* 1.3 75.0 - - - +
353Y LYS* 1.3 67.0 - - - +
354Y ARG* 3.4 34.3 + - - -
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Residues in contact with LYS 353 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349Y SER 3.0 4.2 + - - -
350Y PHE 3.1 12.9 + - - +
351Y TYR 4.0 8.7 - - - +
352Y SER* 1.3 81.8 - - - +
354Y ARG* 1.3 57.0 + - - +
355Y TYR* 3.3 39.6 + - + +
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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