Contacts of the helix formed by residues 372 - 387 (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 SER 372 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309Y ASP* 4.0 17.3 + - - -
339Y ALA* 4.5 6.4 - - - +
340Y GLU* 5.5 3.4 - - - -
343Y VAL* 4.7 1.6 - - - +
369Y ASN* 3.7 24.0 + - - +
370Y SER 3.5 3.8 - - - +
371Y ASN* 1.3 78.7 - - - +
373Y VAL* 1.3 66.0 + - - +
374Y GLN 3.2 0.4 - - - -
375Y ALA* 3.0 34.3 + - - +
376Y LEU* 3.7 4.9 + - - +
402Y LEU* 5.2 0.4 - - - -
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Residues in contact with VAL 373 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371Y ASN 3.3 5.1 + - - +
372Y SER* 1.3 71.3 - - - +
374Y GLN* 1.3 74.1 + - + +
376Y LEU* 3.0 10.6 + - - +
377Y LEU* 3.0 32.8 + - + +
399Y ALA* 4.0 10.5 - - + +
402Y LEU* 3.4 33.2 - - + +
403Y ALA* 3.2 37.2 - - + +
406Y ARG* 5.4 9.0 - - + +
409Y CYS* 5.8 3.1 - - + -
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Residues in contact with GLN 374 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Y PHE* 4.8 11.9 - - - -
309Y ASP* 3.0 46.0 + - - +
310Y VAL* 4.1 17.8 - - + +
313Y TYR* 3.6 41.2 - - + +
343Y VAL* 3.9 7.2 - - + -
347Y CYS* 5.3 2.6 - - - -
373Y VAL* 1.3 88.0 - - + +
375Y ALA* 1.3 54.0 + - - +
377Y LEU* 3.6 27.1 - - - +
378Y LEU* 2.9 33.4 + - + +
408Y ASP* 5.2 2.2 + - - -
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Residues in contact with ALA 375 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343Y VAL* 4.2 10.3 - - + +
362Y GLY 4.1 7.4 - - - +
365Y ALA* 3.9 34.3 - - + +
366Y ILE* 4.1 7.9 - - + +
369Y ASN 4.7 0.9 - - - +
372Y SER* 3.0 25.9 + - - +
374Y GLN* 1.3 77.7 - - - +
376Y LEU* 1.3 59.4 - - + +
378Y LEU* 3.3 8.1 - - - +
379Y LYS* 3.0 27.2 + - - +
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Residues in contact with LEU 376 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366Y ILE* 5.2 19.1 - - + -
370Y SER 5.7 0.9 - - - +
372Y SER 3.7 3.8 + - - +
373Y VAL* 3.0 11.8 + - - +
375Y ALA* 1.3 77.1 - - + +
377Y LEU* 1.3 61.5 + - - +
379Y LYS* 3.2 9.6 + - + +
380Y GLY 3.0 21.5 + - - -
395Y HIS* 3.3 37.5 - - + +
398Y GLU* 3.0 45.8 - - + +
399Y ALA* 3.6 15.0 - - + +
402Y LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 377 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313Y TYR* 4.7 15.0 - - + -
350Y PHE* 5.4 4.0 - - + -
373Y VAL* 3.0 22.4 + - + +
374Y GLN* 3.6 37.2 - - - +
376Y LEU* 1.3 74.8 - - - +
378Y LEU* 1.3 67.0 - - + +
380Y GLY* 3.2 1.6 + - - -
381Y ALA* 3.0 29.0 + - + +
395Y HIS* 5.6 0.2 - - - -
396Y PHE* 3.7 28.7 - - + -
399Y ALA* 4.5 9.8 - - + +
408Y ASP* 5.1 13.7 - - + +
409Y CYS* 4.8 24.2 - - + +
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Residues in contact with LEU 378 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313Y TYR* 6.2 0.7 - - + -
343Y VAL* 3.6 42.6 - - + +
346Y GLY* 3.6 28.7 - - - +
347Y CYS* 3.9 11.4 - - - +
350Y PHE* 3.0 58.3 - - + -
358Y ALA 5.0 3.6 - - - +
362Y GLY* 4.2 18.2 - - - -
374Y GLN* 2.9 19.6 + - + +
375Y ALA* 3.3 5.4 - - - +
377Y LEU* 1.3 79.6 - - + +
379Y LYS* 1.3 65.1 + - - +
382Y ALA* 3.5 2.4 + - - +
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Residues in contact with LYS 379 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358Y ALA 5.3 2.2 - - - -
359Y LEU* 4.8 15.7 - - + +
362Y GLY* 4.5 11.7 - - - +
363Y ALA* 3.6 24.2 - - - +
366Y ILE* 3.1 38.9 - - + +
375Y ALA 3.0 10.9 + - - +
376Y LEU* 3.3 11.7 - - + +
378Y LEU* 1.3 79.7 - - - +
380Y GLY* 1.3 65.5 + - - +
382Y ALA* 3.2 14.6 + - - +
383Y LEU* 3.3 17.4 + - + +
395Y HIS* 3.6 29.8 - - + +
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Residues in contact with GLY 380 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376Y LEU 3.0 10.1 + - - -
377Y LEU 3.2 4.4 + - - -
379Y LYS* 1.3 80.5 - - - +
381Y ALA* 1.3 58.7 + - - +
383Y LEU* 3.0 22.2 + - - +
384Y ARG* 3.0 10.0 + - - +
392Y ALA* 3.5 5.8 - - - +
395Y HIS* 4.2 19.5 - - - +
396Y PHE* 3.6 18.6 - - - -
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Residues in contact with ALA 381 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350Y PHE* 3.5 26.9 - - + -
377Y LEU* 3.0 14.6 + - + +
378Y LEU 3.7 0.2 + - - -
379Y LYS 3.4 0.4 - - - -
380Y GLY* 1.3 75.3 - - - +
382Y ALA* 1.3 60.9 + - - +
384Y ARG* 3.5 15.8 - - + +
385Y ASN* 3.3 27.6 + - - +
396Y PHE* 3.4 11.5 - - + -
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Residues in contact with ALA 382 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350Y PHE* 3.4 22.2 - - + -
355Y TYR* 3.8 16.8 - - - +
358Y ALA* 4.2 5.2 - - + -
359Y LEU* 3.7 32.9 - - + +
378Y LEU 4.2 1.3 - - - +
379Y LYS 3.2 9.2 + - - +
380Y GLY 3.2 1.2 - - - -
381Y ALA* 1.3 74.6 - - - +
383Y LEU* 1.3 64.9 + - - +
385Y ASN* 3.9 6.0 + - - +
386Y MET* 3.3 22.0 + - - +
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Residues in contact with LEU 383 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359Y LEU* 3.8 28.5 - - + -
379Y LYS* 3.3 16.5 + - + +
380Y GLY* 3.0 7.5 + - - +
382Y ALA* 1.3 76.0 - - - +
384Y ARG* 1.3 59.1 + - - +
386Y MET* 3.5 4.4 + - + +
387Y GLY 2.9 25.3 + - - -
388Y ARG* 3.0 25.6 + - + +
391Y GLU* 3.9 24.7 - - + +
392Y ALA* 3.5 20.4 - - + +
395Y HIS* 3.3 39.5 - - + +
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Residues in contact with ARG 384 (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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380Y GLY 3.0 11.2 + - - +
381Y ALA* 3.5 20.4 - - - +
383Y LEU* 1.3 74.8 - - - +
385Y ASN* 1.3 65.2 + - - +
387Y GLY* 3.1 15.3 + - - -
388Y ARG 5.0 2.0 - - - +
389Y VAL* 5.5 6.6 - - + +
392Y ALA* 3.9 6.4 - - + +
396Y PHE* 5.5 0.4 - - - -
412Y GLY* 4.5 5.3 + - - -
415Y GLU* 2.8 66.9 + - - +
416Y CYS* 3.5 29.9 - - - +
418Y LEU* 5.2 4.4 - - - +
419Y ALA* 4.4 13.9 - - + +
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Residues in contact with ASN 385 (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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350Y PHE* 4.6 6.9 - - - +
355Y TYR* 2.8 64.2 + - + -
381Y ALA* 3.3 14.7 + - - +
382Y ALA 4.0 3.1 - - - +
384Y ARG* 1.3 75.6 - - - +
386Y MET* 1.3 66.2 + - - +
387Y GLY* 3.2 1.4 + - - -
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Residues in contact with MET 386 (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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355Y TYR* 4.5 12.6 - - + +
359Y LEU* 6.3 5.8 - - + -
382Y ALA 3.3 17.8 + - - +
383Y LEU* 3.5 4.9 + - + +
385Y ASN* 1.3 73.8 - - - +
387Y GLY* 1.3 58.7 + - - +
388Y ARG* 3.7 33.4 - - + +
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Residues in contact with GLY 387 (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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383Y LEU 2.9 4.8 + - - -
384Y ARG 3.1 13.3 + - - -
385Y ASN 4.1 1.3 - - - -
386Y MET* 1.3 78.5 - - - +
388Y ARG* 1.3 62.5 + - - +
389Y VAL* 3.0 14.6 + - - +
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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
------------------------------------------------------------
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