Contacts of the helix formed by residues 483 - 498 (chain A) in PDB entry 5ID6
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 ASP 483 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A TYR* 3.6 8.4 - - - +
332A SER* 2.8 38.8 + - - -
335A GLY* 2.9 25.2 + - - +
336A ILE* 3.8 12.6 - - + -
482A ARG* 1.3 70.6 - - - +
484A GLU* 1.3 55.3 + - - +
485A SER* 3.4 23.0 - - - -
486A PHE* 3.0 11.9 + - - +
487A TYR* 2.8 28.4 + - - -
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Residues in contact with GLU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 3.3 17.4 + - - +
189A ILE* 4.3 14.4 - - + -
192A LYS* 5.9 2.0 - - - +
271A PRO* 3.6 25.4 - - + +
272A LYS 4.3 0.2 + - - -
274A LYS* 3.0 30.8 + - - -
482A ARG* 2.9 44.7 + - - +
483A ASP* 1.3 69.3 + - - +
485A SER* 1.3 56.0 + - - +
486A PHE 3.3 0.2 - - - -
487A TYR* 3.7 6.0 - - - +
488A GLY* 2.8 29.3 + - - -
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA* 2.8 49.3 + - - +
270A LEU 4.8 0.2 - - - -
271A PRO* 3.7 17.6 - - - +
272A LYS 5.6 0.5 + - - -
331A TYR* 3.6 12.6 + - - -
483A ASP* 3.4 12.8 - - - -
484A GLU* 1.3 77.9 - - - +
486A PHE* 1.3 57.5 + - - +
488A GLY* 4.8 0.3 - - - -
489A ASP* 3.0 26.0 + - - +
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Residues in contact with PHE 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.9 20.6 - - + +
325A PHE* 3.8 23.3 - + - -
328A PHE* 3.4 27.8 - + - -
331A TYR* 3.7 37.2 - + + -
336A ILE* 3.4 31.9 - - + -
473A PHE* 4.8 4.9 - - + -
483A ASP* 3.0 11.5 + - + +
485A SER* 1.3 76.4 - - - +
487A TYR* 1.3 91.1 + + - +
488A GLY 3.2 4.9 + - - -
489A ASP* 3.6 1.9 + - - +
490A PHE* 3.0 46.8 + + - +
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Residues in contact with TYR 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 3.6 17.4 - - - -
335A GLY 3.5 20.4 - - - -
336A ILE* 3.9 3.6 - - + +
337A PHE* 3.1 35.1 + + - +
473A PHE 3.1 24.0 + - - -
474A PHE* 3.7 6.2 + + - -
482A ARG* 3.1 44.6 - - + +
483A ASP 2.8 32.8 + - - +
484A GLU* 3.7 6.1 - - - +
486A PHE* 1.3 96.1 - + - +
488A GLY* 1.3 65.7 + - - +
490A PHE* 4.0 15.7 - + - -
491A VAL* 3.2 26.9 + - + +
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 4.0 21.1 - - - -
274A LYS* 4.4 8.8 - - - +
484A GLU 2.8 18.9 + - - -
485A SER 4.8 0.7 - - - -
486A PHE 3.2 0.2 - - - -
487A TYR* 1.3 79.6 - - - +
489A ASP* 1.3 63.3 + - - +
491A VAL* 3.9 1.0 - - - +
492A LEU* 3.0 34.9 + - - +
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Residues in contact with ASP 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 2.3 34.0 + - - +
320A LYS* 5.8 0.7 - - - +
321A LEU* 4.8 0.2 - - - +
324A LEU* 3.9 26.5 - - + -
331A TYR* 4.1 6.9 + - - -
485A SER 3.0 21.2 + - - +
486A PHE 3.6 2.0 + - - +
488A GLY* 1.3 73.0 - - - +
490A PHE* 1.3 62.1 + - - +
492A LEU* 3.4 9.1 + - - +
493A ALA* 3.2 25.3 + - - +
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.1 12.6 - - + +
324A LEU* 3.6 11.6 - - + +
325A PHE* 3.9 21.3 - + - -
470A ILE* 3.5 39.9 - - + -
471A LYS* 5.0 0.7 - - - -
473A PHE* 3.5 17.0 - - + -
474A PHE* 3.2 41.1 - + - -
486A PHE* 3.0 39.4 + + + +
487A TYR* 4.0 14.4 - + - -
489A ASP* 1.3 76.6 - - - +
491A VAL* 1.3 61.7 + - - +
493A ALA* 3.9 1.2 - - - +
494A TYR* 2.9 40.0 + + + +
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Residues in contact with VAL 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 3.2 39.9 - - - +
274A LYS* 4.0 22.2 - - + -
275A PRO* 5.1 2.2 - - + -
474A PHE* 4.3 15.3 - - + -
482A ARG* 5.7 1.6 - - - +
487A TYR* 3.2 25.2 + - + +
488A GLY 3.2 2.9 + - - +
490A PHE* 1.3 89.9 - - + +
492A LEU* 1.3 70.0 + - - +
494A TYR* 4.5 2.9 - - - +
495A ASP* 2.8 32.6 + - - +
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ILE* 5.9 1.6 - - + -
256A ASN* 3.7 20.4 - - - +
272A LYS* 4.5 15.5 - - + +
273A PHE 4.1 8.7 - - - +
274A LYS* 5.5 0.7 - - - -
275A PRO* 3.5 34.8 - - + -
320A LYS* 6.3 2.0 - - + -
488A GLY 3.0 28.3 + - - +
489A ASP* 3.7 9.2 - - - +
491A VAL* 1.3 81.5 - - + +
493A ALA* 1.3 60.9 + - + +
495A ASP* 3.9 6.2 + - - +
496A ILE* 3.9 16.1 + - - +
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Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 3.2 29.3 + - - +
320A LYS* 4.3 17.9 - - + +
321A LEU* 3.5 28.9 - - + -
489A ASP 3.2 14.3 + - - +
492A LEU* 1.3 78.9 - - + +
494A TYR* 1.3 63.7 + - - +
496A ILE* 3.3 4.2 + - - +
497A LEU 3.2 16.6 + - - -
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.5 5.6 - - + +
467A GLU* 2.4 55.2 + - + -
470A ILE* 3.7 22.7 - - + -
471A LYS* 3.2 28.4 - - + +
474A PHE* 4.3 21.3 - + + -
490A PHE* 2.9 34.4 + + + +
491A VAL* 4.4 3.1 - - - +
493A ALA* 1.3 74.4 - - - +
495A ASP* 1.3 72.2 + - - +
497A LEU* 3.6 11.3 - - + +
498A LEU* 3.0 42.5 + - + +
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Residues in contact with ASP 495 (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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182A ARG* 2.9 23.9 + - - -
275A PRO* 5.6 3.0 - - + +
277A TYR* 2.2 40.2 + - + -
491A VAL* 2.8 24.9 + - - +
492A LEU* 4.1 4.7 - - - +
493A ALA 3.3 0.2 - - - -
494A TYR* 1.3 83.4 - - - +
496A ILE* 1.3 66.5 + - + +
498A LEU* 3.8 24.0 - - - +
499A LYS* 4.3 8.4 + - - +
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Residues in contact with ILE 496 (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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313A GLU* 3.3 59.7 - - + +
314A ILE* 3.9 7.3 - - + +
317A SER* 3.9 5.6 - - - -
492A LEU 3.9 14.6 - - - +
493A ALA* 3.3 7.8 + - - +
494A TYR 3.1 0.4 - - - -
495A ASP* 1.3 75.6 - - + +
497A LEU* 1.3 68.5 + - - +
498A LEU 2.7 3.5 + - - -
499A LYS* 2.7 47.5 + - - +
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 4.1 10.3 - - + -
317A SER* 3.6 13.6 + - - +
318A ILE* 3.8 27.1 - - + -
321A LEU* 4.1 10.1 - - + -
463A VAL* 4.0 20.9 - - + -
466A PHE* 3.8 20.2 - - + -
467A GLU* 3.6 34.7 - - + +
470A ILE* 4.7 1.6 - - + -
493A ALA 3.2 6.6 + - - +
494A TYR* 3.6 18.8 - - + +
496A ILE* 1.3 80.0 - - - +
498A LEU* 1.3 60.9 + - - +
499A LYS 3.1 0.2 - - - -
500A VAL* 3.1 27.4 + - + +
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 6.0 0.4 - - - +
467A GLU* 4.5 13.2 - - - +
494A TYR* 3.0 40.5 + - + +
495A ASP* 3.8 18.6 - - - +
496A ILE 2.7 4.2 + - - -
497A LEU* 1.3 68.5 - - - +
499A LYS* 1.3 71.2 + - + +
500A VAL 3.0 2.5 - - - -
501A ASP* 3.0 23.4 + - + +
502A HIS 4.5 0.3 + - - -
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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