Contacts of the helix formed by residues 452 - 472 (chain A) in PDB entry 1U2X
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 GLY 452 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.1 13.6 - - - +
391A ARG* 3.3 4.1 + - - -
450A THR 3.2 1.8 + - - -
451A VAL* 1.3 73.5 - - - +
453A LEU* 1.3 62.8 + - - +
454A GLY 3.5 2.2 - - - -
455A ASP* 3.5 24.8 + - - +
456A THR* 2.9 27.0 + - - -
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Residues in contact with LEU 453 (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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388A ALA* 4.0 14.0 - - + +
391A ARG* 3.6 20.6 - - + +
392A ALA* 4.0 29.2 - - + +
444A VAL* 4.7 6.3 - - + -
447A PRO* 4.2 9.0 - - + -
449A LEU* 3.4 27.4 - - + +
450A THR* 3.2 21.3 + - + +
451A VAL 4.2 0.4 - - - +
452A GLY* 1.3 73.2 - - - +
454A GLY* 1.3 61.3 + - - +
456A THR* 3.0 7.2 + - - +
457A ILE* 2.9 37.2 + - + +
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 4.2 1.6 - - - -
357A HIS* 3.6 33.1 - - - -
452A GLY 3.5 0.2 - - - -
453A LEU* 1.3 78.2 - - - +
455A ASP* 1.3 60.6 + - - +
457A ILE* 3.3 9.0 + - - +
458A SER* 3.1 26.3 + - - -
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.2 49.0 + - + +
122A ILE* 4.5 10.3 - - + +
123A ILE* 3.8 24.2 - - + +
282A GLU* 3.5 14.3 - - - +
452A GLY* 3.5 23.2 + - - +
453A LEU 3.2 0.6 - - - -
454A GLY* 1.3 75.5 - - - +
456A THR* 1.3 58.7 + - - +
458A SER* 3.4 1.2 + - - -
459A ALA* 3.0 28.2 + - - +
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Residues in contact with THR 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.2 3.6 - - - +
123A ILE* 5.5 0.9 - - - +
126A THR* 4.1 12.8 + - + -
384A GLY 4.4 0.7 - - - +
387A LEU* 3.7 32.5 - - + +
388A ALA* 3.7 18.4 - - - -
391A ARG* 3.3 32.5 + - - -
452A GLY 2.9 13.3 + - - -
453A LEU* 3.0 10.4 + - - -
455A ASP* 1.3 74.1 - - - +
457A ILE* 1.3 66.7 + - - +
459A ALA* 3.4 7.2 + - - +
460A GLY* 3.2 17.5 + - - -
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Residues in contact with ILE 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLN* 4.1 19.1 - - - +
357A HIS* 4.0 19.3 - - + +
358A THR 5.9 1.1 - - - +
362A LEU* 3.6 35.4 - - + -
384A GLY* 3.5 18.2 - - - +
385A THR* 4.6 4.3 - - - +
388A ALA* 3.5 18.1 - - + +
441A THR* 5.8 2.0 - - + -
453A LEU* 2.9 23.6 + - + +
454A GLY* 3.5 12.6 - - - +
456A THR* 1.3 75.9 - - - +
458A SER* 1.3 57.4 + - - +
460A GLY 3.3 1.6 + - - -
461A ALA* 2.9 29.2 + - + +
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Residues in contact with SER 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 5.8 2.2 - - - -
241A ILE* 5.5 0.9 - - - -
280A HIS* 3.6 13.1 + - - -
282A GLU* 2.7 42.7 + - - -
355A GLN* 3.1 22.7 + - - -
357A HIS* 3.4 5.9 - - - -
454A GLY 3.1 8.6 + - - -
455A ASP 3.9 2.7 - - - -
456A THR 3.3 0.2 - - - -
457A ILE* 1.3 78.0 - - - +
459A ALA* 1.3 57.0 + - - +
461A ALA* 3.9 0.4 - - - +
462A PHE* 2.8 35.3 + - - +
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Residues in contact with ALA 459 (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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123A ILE* 4.0 28.4 - - + +
126A THR* 5.2 4.3 - - + -
127A LEU* 4.4 18.3 - - + +
241A ILE* 4.4 12.7 - - + +
387A LEU* 4.8 4.3 - - + -
455A ASP 3.0 17.8 + - - +
456A THR* 3.7 8.3 - - - +
457A ILE 3.4 0.2 - - - -
458A SER* 1.3 77.5 - - - +
460A GLY* 1.3 57.3 + - - +
462A PHE* 4.1 0.9 - - - +
463A LEU* 3.1 29.1 + - - +
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Residues in contact with GLY 460 (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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127A LEU* 6.0 0.2 - - - -
383A PHE* 3.5 34.2 - - - -
384A GLY* 4.2 4.3 - - - -
387A LEU* 3.8 11.5 - - - +
456A THR 3.2 8.5 + - - -
457A ILE 3.8 2.0 - - - -
459A ALA* 1.3 75.4 - - - +
461A ALA* 1.3 64.3 + - - +
463A LEU* 3.5 3.5 + - - +
464A THR* 3.0 24.1 + - - -
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Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLN* 4.0 15.5 - - - +
364A TYR* 3.2 21.2 + - + +
380A SER* 2.6 38.4 + - - +
381A LEU* 4.6 7.2 - - + -
384A GLY* 3.9 4.1 - - - -
457A ILE* 2.9 18.8 + - + +
458A SER 3.9 2.7 - - - +
460A GLY* 1.3 76.3 - - - +
462A PHE* 1.3 56.4 + - - +
464A THR* 3.1 1.2 + - - -
465A TYR 2.9 15.4 + - - -
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Residues in contact with PHE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 4.8 3.1 - - + -
239A GLY* 4.3 4.7 - - - -
240A ALA 3.8 11.2 - - - -
241A ILE* 3.7 19.1 - - + -
278A LYS* 3.5 27.8 - - + -
279A ILE 4.5 0.7 - - - -
280A HIS* 3.7 42.4 - - + -
304A ASP* 5.7 0.7 - - + -
305A SER* 3.8 21.8 - - - -
364A TYR* 4.7 1.1 - - - -
458A SER 2.8 18.6 + - - +
459A ALA* 4.2 2.7 - - - +
461A ALA* 1.3 76.3 - - - +
463A LEU* 1.3 59.8 + - - +
465A TYR* 3.2 17.4 + + + +
466A LEU* 2.9 62.7 + - + +
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 5.0 0.2 - - + -
25A PRO* 3.7 28.9 - - + -
28A LEU* 3.2 33.6 - - + +
30A ILE* 4.1 26.0 - - + -
127A LEU* 4.3 13.7 - - + -
130A LEU* 4.3 13.5 - - + -
132A ILE* 4.2 27.6 - - + -
383A PHE* 4.6 7.6 - - + -
459A ALA 3.1 20.6 + - - +
460A GLY* 3.7 4.5 - - - +
462A PHE* 1.3 79.0 - - - +
464A THR* 1.3 57.7 + - - +
466A LEU* 3.4 5.7 + - - +
467A GLU* 3.2 19.8 + - - +
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Residues in contact with THR 464 (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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23A MSE 5.2 0.7 - - - +
25A PRO* 4.4 4.3 - - + -
379A LYS 5.3 0.2 - - - +
380A SER* 3.0 36.1 + - - -
383A PHE* 3.4 41.7 - - + -
460A GLY 3.0 11.0 + - - +
463A LEU* 1.3 73.7 - - - +
465A TYR* 1.3 59.8 + - - +
467A GLU* 3.3 22.4 + - - +
468A PHE* 2.9 43.0 + - + -
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Residues in contact with TYR 465 (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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278A LYS* 5.3 2.0 - - - -
304A ASP* 6.1 1.3 - - + -
305A SER* 5.1 1.8 - - - -
352A GLU* 2.6 27.8 + - - +
353A ILE* 3.4 40.4 - - + +
364A TYR* 3.8 11.2 - + - +
370A ASN* 2.9 22.4 + - - -
372A LEU* 3.8 34.3 - - + -
377A LEU* 4.5 1.3 - - + -
380A SER* 3.7 5.5 + - - -
461A ALA 2.9 18.7 + - - +
462A PHE* 3.2 30.3 + + - +
464A THR* 1.3 74.6 - - - +
466A LEU* 1.3 63.9 + - + +
468A PHE* 3.3 2.3 + - - +
469A LEU* 3.0 49.0 + - + +
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Residues in contact with LEU 466 (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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28A LEU* 3.9 12.8 - - + -
30A ILE* 3.4 33.2 - - + -
238A ASP* 4.1 14.1 - - + +
239A GLY* 4.0 12.8 - - - +
278A LYS* 3.6 38.4 - - + -
462A PHE* 2.9 35.8 + - + +
463A LEU* 3.4 9.4 - - - +
464A THR 3.2 0.2 - - - -
465A TYR* 1.3 76.8 - - - +
467A GLU* 1.3 56.0 + - - +
469A LEU* 3.2 9.0 + - + +
470A LYS* 2.9 33.1 + - - +
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Residues in contact with GLU 467 (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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23A MSE 4.0 11.7 - - - +
25A PRO* 3.3 42.6 - - + +
27A HIS* 4.6 11.6 + - + +
28A LEU* 3.7 7.6 - - + +
463A LEU 3.2 6.2 + - - +
464A THR* 3.3 23.6 + - - +
466A LEU* 1.3 77.6 - - - +
468A PHE* 1.3 72.3 + - - +
470A LYS* 3.4 5.4 + - - +
471A ARG* 3.0 65.7 + - + +
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Residues in contact with PHE 468 (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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372A LEU* 3.8 25.6 - - + -
376A GLU* 3.5 48.9 - - + +
379A LYS* 3.9 40.4 - - + -
380A SER* 4.3 6.7 - - - -
464A THR* 2.9 36.7 + - + +
465A TYR 4.0 0.2 - - - +
467A GLU* 1.3 85.5 - - + +
469A LEU* 1.3 62.3 + - - +
471A ARG* 3.2 40.5 + - + +
472A HIS* 3.0 28.9 + - - -
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Residues in contact with LEU 469 (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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278A LYS* 4.2 25.1 - - + +
352A GLU* 4.1 9.0 - - - +
371A PRO* 3.8 24.2 - - + -
372A LEU* 3.8 20.4 - - + +
465A TYR* 3.0 51.7 + - + +
466A LEU* 3.6 9.4 - - + +
468A PHE* 1.3 73.7 - - - +
470A LYS* 1.3 60.7 + - - +
472A HIS* 2.9 33.9 + - - +
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Residues in contact with LYS 470 (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 HIS* 4.2 26.6 + - - +
28A LEU* 4.2 14.5 - - + +
133A ARG* 5.4 4.6 - - - +
238A ASP* 3.1 32.9 + - + +
466A LEU 2.9 18.4 + - - +
467A GLU* 3.6 6.7 - - - +
469A LEU* 1.3 73.5 - - - +
471A ARG* 1.3 64.9 + - + +
472A HIS 3.1 10.0 + - - +
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Residues in contact with ARG 471 (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 HIS* 5.9 2.7 - - - +
376A GLU* 5.7 1.9 + - - +
379A LYS* 5.0 4.0 - - - +
467A GLU* 3.0 44.0 + - + +
468A PHE* 3.2 42.5 - - + +
469A LEU 3.2 0.2 - - - -
470A LYS* 1.3 76.8 - - + +
472A HIS* 1.3 61.3 + - - +
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Residues in contact with HIS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO* 3.2 42.4 + - + -
372A LEU* 4.6 2.0 + - - +
373A SER* 4.7 1.3 + - - -
376A GLU* 2.9 39.8 + - - -
468A PHE 3.0 19.6 + - - +
469A LEU* 2.9 22.6 + - - +
470A LYS 3.1 9.0 - - - +
471A ARG* 1.3 81.2 - - - +
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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