Contacts of the helix formed by residues 373 - 392 (chain O) 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 LEU 373 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338O VAL* 4.3 20.4 - - + +
341O GLN* 3.3 41.7 - - + -
342O HIS* 3.9 24.5 - - + +
368O ALA* 3.3 17.1 - - - +
371O PHE* 2.8 23.0 + - + +
372O GLY* 1.3 69.5 - - - +
374O PRO* 1.3 74.6 - - + +
375O TYR* 3.2 3.1 - - + -
376O LEU* 3.1 23.6 + - + -
377O ALA* 3.1 9.2 + - - +
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Residues in contact with PRO 374 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372O GLY* 3.2 7.6 - - - +
373O LEU* 1.3 90.4 - - - +
375O TYR* 1.3 67.1 + - + +
377O ALA* 3.5 6.1 + - + +
378O SER* 3.1 23.0 + - - -
408O LEU* 3.6 7.7 - - + +
412O HIS* 3.5 52.0 - - + +
414O LEU* 4.3 4.9 - - + -
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Residues in contact with TYR 375 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE 4.9 0.2 + - - -
10D PRO* 3.9 5.3 - - + +
11D ARG* 3.2 48.8 + - + +
14D GLU* 3.6 22.4 - - - -
342O HIS* 5.3 0.7 - + - -
373O LEU* 3.2 1.8 - - + -
374O PRO* 1.3 84.0 - - + +
376O LEU* 1.3 81.3 + - + +
378O SER* 3.2 3.3 + - - -
379O LEU* 2.9 39.9 + - + +
414O LEU* 3.7 18.1 - - + +
416O GLU* 2.8 34.3 + - + -
417O LEU* 3.4 30.4 - - + +
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Residues in contact with LEU 376 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PRO* 5.1 3.4 - - + -
14D GLU* 4.7 1.1 - - - +
341O GLN* 3.4 50.0 - - + +
342O HIS* 3.7 28.0 - - + +
345O SER* 3.9 23.3 + - - +
364O SER* 4.9 4.7 + - - +
368O ALA* 4.1 5.1 - - + +
373O LEU* 3.1 22.9 + - + +
375O TYR* 1.3 100.0 - - + +
377O ALA* 1.3 66.1 + - - +
379O LEU* 3.4 8.1 + - + +
380O GLY* 3.0 19.2 + - - -
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Residues in contact with ALA 377 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364O SER 5.5 0.2 - - - -
365O VAL* 3.5 9.6 - - + +
368O ALA* 3.4 24.7 - - + +
369O VAL* 4.1 24.7 - - + +
373O LEU 3.1 6.8 + - - +
374O PRO* 3.6 10.8 - - + +
376O LEU* 1.3 77.8 - - - +
378O SER* 1.3 62.8 + - - +
380O GLY* 3.1 11.4 + - - -
381O ILE* 3.1 20.4 + - + +
408O LEU* 5.0 7.6 - - + -
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Residues in contact with SER 378 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374O PRO 3.1 15.1 + - - -
375O TYR* 3.2 7.2 + - - -
377O ALA* 1.3 80.7 - - - +
379O LEU* 1.3 61.8 + - - +
381O ILE* 3.1 15.8 + - - +
382O GLN* 3.0 23.7 + - - +
405O SER* 3.8 0.2 + - - -
408O LEU* 3.7 16.4 - - - -
409O HIS* 2.7 35.8 + - - -
414O LEU* 4.7 2.7 - - - -
417O LEU* 3.2 10.6 - - - +
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Residues in contact with LEU 379 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.7 39.0 - - + +
9D PHE 5.2 0.4 - - - +
10D PRO* 3.8 36.6 - - + -
345O SER* 4.4 15.7 - - - +
375O TYR* 2.9 39.4 + - + +
376O LEU* 3.6 5.6 - - + +
378O SER* 1.3 73.4 + - - +
380O GLY* 1.3 67.6 + - - +
382O GLN* 3.2 3.9 + - + +
383O SER* 3.2 18.7 + - - -
416O GLU* 5.5 1.1 - - - +
417O LEU* 3.7 19.0 - - + +
420O ILE* 4.9 2.0 - - + -
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Residues in contact with GLY 380 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345O SER* 5.4 2.9 + - - -
361O LEU* 4.5 13.0 - - - +
364O SER* 4.9 8.7 - - - -
365O VAL* 3.9 13.0 - - - -
376O LEU 3.0 15.0 + - - -
377O ALA 3.1 5.1 + - - -
379O LEU* 1.3 77.4 - - - +
381O ILE* 1.3 62.5 + - - +
383O SER* 2.9 18.7 + - - -
384O LEU* 2.9 13.8 + - - +
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Residues in contact with ILE 381 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365O VAL* 3.6 19.0 - - + +
377O ALA* 3.1 18.0 + - + +
378O SER* 3.1 4.7 + - - +
380O GLY* 1.3 74.8 - - - +
382O GLN* 1.3 64.0 - - - +
384O LEU* 3.4 14.2 + - + +
385O VAL* 3.0 29.3 + - + +
401O ALA* 3.9 25.6 - - + +
404O ASP* 4.2 16.6 - - - +
405O SER* 3.9 18.4 - - - -
408O LEU* 3.8 27.6 - - + -
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Residues in contact with GLN 382 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.3 24.2 - - + -
378O SER 3.0 8.8 + - - +
379O LEU 3.5 4.5 - - - +
380O GLY 3.2 0.2 - - - -
381O ILE* 1.3 78.4 - - - +
383O SER* 1.3 56.9 + - - +
385O VAL* 3.5 1.9 - - - +
386O GLN* 3.1 17.7 + - - +
402O LEU* 3.5 12.7 - - - +
405O SER* 2.3 35.0 + - - -
409O HIS* 3.6 1.6 + - - -
417O LEU* 3.2 31.0 - - + -
420O ILE* 4.8 4.6 - - + +
421O SER* 3.0 36.7 - - - +
424O GLN* 3.0 32.5 + - - +
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Residues in contact with SER 383 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.9 28.6 + - - +
348O TYR* 3.5 25.7 + - - -
361O LEU* 4.0 16.3 - - - +
379O LEU* 3.2 9.8 + - - -
380O GLY* 2.9 10.2 + - - -
382O GLN* 1.3 75.0 - - - +
384O LEU* 1.3 61.6 + - - +
386O GLN* 3.2 5.0 + - - +
387O GLN* 2.9 29.1 + - - +
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Residues in contact with LEU 384 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358O TYR* 4.6 3.8 - - + +
361O LEU* 3.7 30.8 - - + +
362O GLU* 3.2 28.0 - - - +
365O VAL* 5.7 6.7 - - + -
380O GLY 2.9 12.0 + - - +
381O ILE* 3.4 22.4 - - + +
383O SER* 1.3 77.0 - - - +
385O VAL* 1.3 57.6 + - - +
387O GLN* 3.1 17.9 + - - +
388O ARG* 2.9 67.3 + - - +
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Residues in contact with VAL 385 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381O ILE* 3.0 12.4 + - + +
382O GLN 3.5 9.4 - - - +
384O LEU* 1.3 75.9 - - - +
386O GLN* 1.3 69.0 + - - +
388O ARG* 3.3 12.2 + - - +
389O ALA* 3.1 21.0 + - - +
398O LEU* 4.0 15.5 - - + +
401O ALA* 3.6 31.4 - - + -
402O LEU* 3.7 41.7 - - + +
424O GLN* 4.4 2.5 - - - +
428O ILE* 3.9 15.3 - - + -
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Residues in contact with GLN 386 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.0 34.3 - - + +
6D PRO 4.0 2.2 + - - +
7D SER 5.5 1.4 + - - -
8D LEU* 3.1 20.9 - - + +
382O GLN 3.1 6.4 + - - +
383O SER* 3.2 9.3 + - - +
385O VAL* 1.3 81.2 - - - +
387O GLN* 1.3 63.4 + - - +
389O ALA* 3.2 15.6 + - - +
390O PHE* 3.2 35.9 + - + -
424O GLN* 2.7 33.5 + - - +
428O ILE* 5.0 0.9 - - - -
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Residues in contact with GLN 387 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348O TYR* 3.7 13.9 + - - +
356O ASP* 2.9 34.9 - - - +
358O TYR* 3.1 32.3 - - - +
361O LEU* 3.6 21.3 - - - +
383O SER 2.9 13.9 + - - +
384O LEU* 3.1 16.6 + - - +
386O GLN* 1.3 78.5 - - - +
388O ARG* 1.3 69.0 + - + +
390O PHE* 3.3 10.9 + - - +
391O ALA* 3.1 20.3 + - + +
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Residues in contact with ARG 388 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362O GLU* 4.6 11.5 + - - -
384O LEU* 2.9 51.2 + - + +
385O VAL* 3.8 3.8 - - - +
387O GLN* 1.3 82.2 - - + +
389O ALA* 1.3 56.5 + - - +
391O ALA* 3.2 9.1 + - - +
392O GLY 2.9 30.3 + - - +
393O LYS* 3.4 39.4 + - + +
397O LYS 5.3 2.6 + - - -
398O LEU* 3.6 21.9 - - + +
401O ALA* 3.7 26.9 - - - +
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Residues in contact with ALA 389 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 4.2 7.6 - - - +
385O VAL 3.1 12.1 + - - +
386O GLN 3.4 9.6 - - - +
388O ARG* 1.3 76.0 - - - +
390O PHE* 1.3 63.9 + - - +
392O GLY* 3.3 4.9 + - - -
398O LEU* 3.7 16.7 - - + +
428O ILE* 3.9 25.1 - - + -
431O LEU* 4.2 4.4 - - + +
432O TYR* 3.1 33.0 + - + +
614O TYR 4.7 1.6 - - - +
616O LEU* 5.5 0.9 - - - +
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Residues in contact with PHE 390 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 4.8 2.7 - - - -
5D TYR* 3.2 35.4 - + - -
386O GLN* 3.2 49.1 + - + -
387O GLN* 3.8 9.0 - - - +
388O ARG 3.2 0.4 - - - -
389O ALA* 1.3 78.4 - - - +
391O ALA* 1.3 61.3 + - - +
392O GLY 3.5 0.3 + - - -
431O LEU* 3.9 17.3 - - + -
576O ASN* 6.5 1.6 - - + -
577O THR* 5.3 2.6 - - - -
578O GLU* 4.7 13.7 - - + -
614O TYR* 3.5 20.1 - - - +
616O LEU* 5.6 3.3 - - + +
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Residues in contact with ALA 391 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387O GLN* 3.1 13.5 + - + +
388O ARG* 3.2 12.8 + - - +
390O PHE* 1.3 78.2 - - - +
392O GLY* 1.3 63.0 + - - +
393O LYS* 5.7 0.9 - - + -
613O GLU 4.0 6.9 - - - +
614O TYR* 3.5 21.7 - - - -
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Residues in contact with GLY 392 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388O ARG 2.9 6.8 + - - +
389O ALA 3.3 8.2 + - - -
390O PHE 3.3 3.6 - - - -
391O ALA* 1.3 82.9 - - - +
393O LYS* 1.3 70.1 + - - +
432O TYR* 4.0 1.8 - - - -
613O GLU 4.6 2.2 - - - +
614O TYR* 4.0 22.4 - - - -
615O ARG* 4.3 9.9 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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