Contacts of the helix formed by residues 461 - 482 (chain A) in PDB entry 1U9J
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 TRP 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A GLU 4.8 1.1 - - - -
437A GLY* 3.8 23.8 - - - -
438A MET* 3.7 41.7 - - + +
452A ILE 4.5 1.6 - - - -
453A VAL* 4.0 21.1 - - + -
454A GLY* 3.0 38.6 - - - +
455A PRO 4.5 0.9 - - - +
458A LYS* 3.3 33.2 - - + +
459A PRO 3.1 0.6 - - - -
460A ARG* 1.3 114.3 - - + +
462A ILE* 1.3 64.4 + - - +
463A TYR 3.2 3.4 - - - -
464A SER* 3.1 16.8 + - - -
465A VAL* 3.0 28.2 + - + +
616A VAL* 5.4 6.5 - - + -
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Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A TYR* 3.9 25.8 - - + +
402A PRO* 4.5 26.0 - - + +
403A LEU* 6.4 1.6 - - + -
405A VAL* 5.5 4.3 - - + -
406A PHE* 4.9 12.1 - - + -
459A PRO* 3.3 21.2 + - + +
460A ARG 3.3 0.2 - - - -
461A TRP* 1.3 77.0 - - - +
463A TYR* 1.3 63.5 + - - +
465A VAL* 4.4 5.3 - - + +
466A SER* 3.0 39.1 + - - +
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Residues in contact with TYR 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA* 5.5 1.1 - - + -
392A ILE 3.6 12.8 - - - -
393A ALA* 4.0 18.4 - - + +
398A TYR* 3.4 51.8 - + + -
405A VAL* 4.4 7.6 - - + -
409A ASP* 3.4 27.6 - - + -
432A THR* 3.7 34.2 + - + -
434A GLU* 3.7 15.9 - - - +
460A ARG 4.0 1.5 + - - +
461A TRP 3.2 0.6 - - - -
462A ILE* 1.3 81.2 - - + +
464A SER* 1.3 67.7 + - - +
466A SER* 3.1 6.1 + - - -
467A LYS* 3.0 51.5 + - + +
506A ILE* 4.8 9.0 - - - +
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Residues in contact with SER 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A THR* 5.0 0.4 - - - -
434A GLU* 2.7 40.6 + - - -
435A VAL* 3.6 13.2 + - - +
453A VAL* 4.0 11.1 - - - +
461A TRP* 3.1 25.4 + - - -
463A TYR* 1.3 86.4 - - - +
465A VAL* 1.3 59.5 + - - +
467A LYS* 3.4 4.0 + - - +
468A GLN* 2.9 28.1 + - - +
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Residues in contact with VAL 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A VAL* 4.2 32.1 - - + -
461A TRP* 3.0 20.2 + - + +
462A ILE* 4.4 4.7 - - + +
464A SER* 1.3 72.6 - - - +
466A SER* 1.3 66.2 + - - +
468A GLN* 3.6 15.4 - - + +
469A LEU* 2.9 26.0 + - + +
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A VAL* 5.8 2.0 - - - -
406A PHE* 3.7 27.0 - - - +
409A ASP* 5.5 6.3 - - - -
410A PHE* 3.4 29.3 - - - -
462A ILE* 3.0 29.8 + - - +
463A TYR* 3.1 6.7 + - - -
465A VAL* 1.3 75.5 - - - +
467A LYS* 1.3 65.3 + - - +
469A LEU* 3.2 3.1 + - - -
470A LEU* 3.1 19.4 + - - +
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Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA* 4.9 3.4 - - - +
409A ASP* 4.7 20.2 + - + +
413A ASN* 6.1 0.6 - - - -
429A PHE* 3.7 19.1 - - - -
430A PRO* 2.6 29.6 + - - +
431A SER* 4.2 14.6 - - - +
432A THR* 3.6 18.6 - - + +
435A VAL* 4.5 0.7 - - + -
463A TYR* 3.0 56.6 + - + +
464A SER 3.8 1.3 - - - +
466A SER* 1.3 78.5 - - - +
468A GLN* 1.3 62.8 + - - +
470A LEU* 3.4 9.0 + - + +
471A ASP* 3.0 28.0 + - - +
506A ILE* 3.7 18.4 - - + +
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Residues in contact with GLN 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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435A VAL* 3.2 29.6 - - + +
451A LEU* 3.4 27.1 - - + +
453A VAL* 5.3 5.2 - - - +
464A SER* 2.9 13.8 + - - +
465A VAL* 3.6 18.9 - - - +
466A SER 3.2 0.2 - - - -
467A LYS* 1.3 74.7 - - - +
469A LEU* 1.3 66.6 + - - +
471A ASP* 3.1 8.5 + - + +
472A ARG* 2.7 62.2 + - + +
489A ARG* 6.0 0.7 - - - +
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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
----------------------------------------------------------
406A PHE* 6.4 0.4 - - + -
410A PHE* 3.6 34.1 - - + -
465A VAL* 2.9 19.5 + - + +
466A SER* 3.2 2.0 + - - +
468A GLN* 1.3 76.0 - - - +
470A LEU* 1.3 65.0 + - - +
472A ARG* 3.1 19.8 + - + +
473A VAL* 2.9 36.7 + - + +
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Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASP 3.3 26.5 - - - +
410A PHE* 3.7 34.3 - - + +
413A ASN* 4.0 4.7 - - + -
414A LEU* 4.1 15.9 - - + -
417A ILE* 3.5 22.7 - - + -
429A PHE* 3.5 34.1 - - + -
466A SER 3.1 7.0 + - - +
467A LYS* 3.6 15.5 - - + +
469A LEU* 1.3 80.8 - - - +
471A ASP* 1.3 62.4 + - - +
473A VAL* 3.1 5.2 + - + +
474A ILE* 2.9 28.6 + - - +
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PHE* 4.5 6.8 - - - -
431A SER* 2.4 39.0 + - - -
435A VAL* 4.1 6.4 - - - +
467A LYS 3.0 18.3 + - - +
468A GLN* 3.1 9.8 + - + +
470A LEU* 1.3 76.5 - - - +
472A ARG* 1.3 58.9 + - + +
474A ILE* 3.3 6.4 + - - +
475A TRP* 2.9 28.3 + - - +
487A LEU* 3.4 30.5 - - + +
489A ARG* 2.9 18.8 + - - +
562A ILE* 5.9 0.7 - - + -
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Residues in contact with ARG 472 (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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451A LEU* 3.9 15.8 - - - +
468A GLN* 2.7 44.7 + - + +
469A LEU* 3.1 22.6 + - + +
471A ASP* 1.3 74.6 - - + +
473A VAL* 1.3 59.2 + - - +
475A TRP* 3.3 10.1 + - - +
476A ALA* 2.8 28.4 + - - +
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Residues in contact with VAL 473 (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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410A PHE* 5.0 11.4 - - + -
414A LEU* 3.8 22.7 - - + -
417A ILE* 5.1 1.6 - - + -
418A ARG* 5.8 2.2 - - - +
469A LEU* 2.9 34.0 + - + +
470A LEU* 3.6 8.3 - - + +
472A ARG* 1.3 72.8 - - - +
474A ILE* 1.3 67.7 + - - +
476A ALA* 3.2 7.9 + - + +
477A TYR* 3.0 47.1 + - + -
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Residues in contact with ILE 474 (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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417A ILE* 3.7 33.2 - - + -
427A ILE* 4.8 4.3 - - + -
429A PHE* 3.6 41.3 - - + -
470A LEU 2.9 17.9 + - - +
471A ASP 3.5 6.5 - - - +
473A VAL* 1.3 78.1 - - - +
475A TRP* 1.3 64.0 + - - +
477A TYR* 3.0 6.5 + - - +
478A GLY* 2.9 19.8 + - - -
483A LEU* 4.0 12.0 - - + +
485A PHE* 3.5 40.2 - - + -
487A LEU* 3.8 13.0 - - + -
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Residues in contact with TRP 475 (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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447A ASP* 6.0 1.6 - - - -
471A ASP 2.9 17.6 + - - +
472A ARG* 3.4 11.0 - - - +
473A VAL 3.2 0.2 - - - -
474A ILE* 1.3 77.5 - - - +
476A ALA* 1.3 60.4 + - + +
478A GLY* 3.2 2.3 + - - -
479A GLU* 2.9 55.2 + - + +
485A PHE* 3.9 26.5 - + + -
487A LEU* 6.0 1.1 - - + -
560A GLY* 3.6 22.7 - - - -
562A ILE* 4.5 22.0 - - + -
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Residues in contact with ALA 476 (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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472A ARG 2.8 20.3 + - - +
473A VAL* 3.6 8.5 - - + +
475A TRP* 1.3 72.2 - - - +
477A TYR* 1.3 62.8 + - + +
479A GLU* 3.3 6.7 + - - +
480A LYS* 2.9 38.5 + - + +
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Residues in contact with TYR 477 (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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414A LEU* 4.8 0.2 - - + -
417A ILE* 4.2 15.3 - - + -
418A ARG* 3.0 47.1 + - + +
421A VAL* 3.9 17.7 - - + -
473A VAL* 3.0 44.6 + - + -
474A ILE 3.0 6.0 + - - +
476A ALA* 1.3 77.0 - - + +
478A GLY* 1.3 57.8 + - - +
480A LYS* 5.3 0.2 - - - -
481A GLU* 2.8 64.7 + - + +
483A LEU* 3.3 29.5 + - + -
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Residues in contact with GLY 478 (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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474A ILE 2.9 13.4 + - - -
475A TRP 3.2 4.5 + - - -
476A ALA 3.1 0.4 - - - -
477A TYR* 1.3 79.4 - - - +
479A GLU* 1.3 58.9 + - - +
482A GLY* 3.8 12.8 + - - -
483A LEU* 3.5 24.0 + - - +
485A PHE* 3.9 11.7 - - - -
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Residues in contact with GLU 479 (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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475A TRP* 2.9 48.6 + - + +
476A ALA* 3.8 6.4 - - - +
478A GLY* 1.3 78.2 - - - +
480A LYS* 1.3 89.3 + - + +
482A GLY 5.2 0.3 + - - -
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Residues in contact with LYS 480 (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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476A ALA* 2.9 19.8 + - + +
479A GLU* 1.3 104.4 + - + +
481A GLU* 1.3 73.7 + - + +
482A GLY 3.8 0.9 - - - -
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Residues in contact with GLU 481 (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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421A VAL* 3.6 30.7 - - + +
424A ARG* 6.0 1.9 - - - +
477A TYR* 2.8 41.8 + - + +
480A LYS* 1.3 86.2 - - + +
482A GLY* 1.3 64.6 + - - +
483A LEU* 3.3 4.4 + - - +
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Residues in contact with GLY 482 (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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424A ARG* 6.0 3.3 - - - +
477A TYR 3.3 2.0 + - - -
478A GLY 3.8 10.1 + - - -
479A GLU 5.0 0.4 + - - -
480A LYS 3.8 0.8 - - - -
481A GLU* 1.3 76.7 - - - +
483A LEU* 1.3 64.5 + - - +
484A GLN* 3.3 5.2 + - - +
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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