Contacts of the helix formed by residues 484 - 500 (chain A) in PDB entry 5E8W
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 THR 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A GLU* 5.2 9.6 - - - +
397A LYS* 6.2 3.6 - - - +
401A ILE* 4.0 5.4 - - - -
482A ARG 4.9 3.6 - - - +
483A LEU* 1.3 77.2 - - - +
485A ALA* 1.4 63.9 + - - +
486A LEU* 3.6 8.8 + - - +
487A ARG* 3.1 26.2 + - + +
488A ILE* 3.2 22.1 + - - +
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Residues in contact with ALA 485 (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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310A ALA* 4.1 5.0 - - - +
313A LEU* 4.0 10.1 - - + -
314A ALA* 3.7 31.0 - - - +
317A HIS* 4.0 16.3 + - + +
401A ILE* 3.4 24.2 - - + +
404A MET* 4.7 2.9 - - + -
484A THR* 1.4 71.4 - - - +
486A LEU* 1.4 57.4 + - - +
488A ILE* 3.4 8.3 + - - +
489A LYS* 2.9 29.8 + - - +
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA* 4.1 18.0 - - + +
484A THR* 3.2 8.3 + - - +
485A ALA* 1.4 75.8 - - - +
487A ARG* 1.4 65.3 + - - +
489A LYS* 3.3 17.3 + - + +
490A LYS* 3.0 53.7 + - + +
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 3.7 25.4 - - + -
484A THR* 3.1 26.6 + - + +
486A LEU* 1.4 76.1 - - - +
488A ILE* 1.3 56.7 + - - +
490A LYS* 3.2 43.7 + - - +
491A THR* 2.9 41.1 + - - +
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Residues in contact with ILE 488 (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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310A ALA* 3.8 10.1 - - + -
401A ILE* 4.3 5.2 - - + -
404A MET* 3.7 16.2 - - + -
408A PHE* 3.8 28.3 - - + -
470A ILE* 4.0 9.2 - - + -
474A CYS* 3.7 29.6 - - - -
483A LEU* 3.8 28.3 - - + -
484A THR 3.2 19.7 + - - +
485A ALA 3.7 6.1 - - - +
486A LEU 3.3 0.2 - - - -
487A ARG* 1.3 71.7 - - - +
489A LYS* 1.4 60.7 + - - +
491A THR* 3.3 7.0 + - - +
492A LEU* 2.9 38.1 + - + +
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Residues in contact with LYS 489 (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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256A HIS* 5.0 8.3 + - - -
307A LEU* 3.6 9.8 - - + +
310A ALA* 4.1 16.5 - - + +
311A SER* 3.4 40.3 + - - +
314A ALA* 4.5 10.6 - - + +
485A ALA 2.9 17.4 + - - +
486A LEU* 3.5 17.2 - - + +
488A ILE* 1.4 75.2 - - - +
490A LYS* 1.3 52.8 + - + +
492A LEU 3.4 0.2 + - - -
493A SER* 2.8 47.0 + - - +
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Residues in contact with LYS 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU* 3.0 49.6 + - + +
487A ARG* 3.4 40.4 - - - +
489A LYS* 1.3 76.8 - - + +
491A THR* 1.4 61.9 + - - +
493A SER* 3.3 7.0 + - - -
494A GLN* 3.1 33.8 + - + +
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Residues in contact with THR 491 (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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466A VAL* 3.7 27.1 - - + -
470A ILE* 4.0 15.5 - - + -
483A LEU* 6.1 0.9 - - - +
487A ARG* 2.9 25.4 + - - +
488A ILE* 3.3 8.4 + - - -
490A LYS* 1.4 75.6 - - - +
492A LEU* 1.4 57.8 + - - +
494A GLN* 3.5 11.4 + - - +
495A LEU* 3.1 25.1 + - - +
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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
----------------------------------------------------------
303A ILE* 4.1 9.0 - - + +
306A ALA* 3.7 31.6 - - + +
307A LEU* 3.8 21.4 - - + +
310A ALA* 4.3 2.7 - - + -
408A PHE* 3.7 23.3 - - + -
466A VAL* 4.9 1.1 - - + -
467A MET* 3.9 19.1 - - + -
470A ILE* 3.8 21.5 - - + -
488A ILE* 2.9 25.0 + - + +
491A THR* 1.4 72.7 - - - +
493A SER* 1.3 59.2 + - - +
495A LEU* 3.4 21.4 + - + +
496A SER* 2.9 30.1 + - - -
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Residues in contact with SER 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.4 17.4 - - - +
489A LYS* 2.8 32.6 + - - +
490A LYS* 3.3 8.0 + - - -
492A LEU* 1.3 77.1 - - - +
494A GLN* 1.3 56.7 + - - +
496A SER* 2.7 22.5 + - - -
497A GLN* 3.0 17.4 + - - +
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Residues in contact with GLN 494 (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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490A LYS* 3.1 23.1 + - + +
491A THR* 3.7 11.7 + - - +
493A SER* 1.3 72.3 - - - +
495A LEU* 1.4 64.4 + - - +
497A GLN* 3.3 9.1 + - - +
498A GLN* 3.1 23.4 + - - +
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Residues in contact with LEU 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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303A ILE* 3.8 30.3 - - + -
462A GLU* 4.7 7.6 - - + +
463A ALA* 3.9 26.0 - - + +
466A VAL* 4.2 31.9 - - + -
467A MET* 5.3 1.8 - - + -
491A THR 3.1 17.6 + - - +
492A LEU* 3.7 16.6 - - + +
493A SER 3.4 0.2 - - - -
494A GLN* 1.4 75.0 - - - +
496A SER* 1.4 61.9 + - - +
498A GLN* 3.4 8.1 + - + +
499A GLU* 3.1 45.6 + - + +
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Residues in contact with SER 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 3.8 20.8 - - - +
307A LEU* 3.9 13.4 - - - +
492A LEU 2.9 18.1 + - - -
493A SER* 2.7 24.3 + - - -
495A LEU* 1.4 71.8 - - - +
497A GLN* 1.3 55.2 + - - +
499A GLU* 3.5 3.9 + - - -
500A GLY* 3.1 22.5 + - - -
501A ILE* 3.2 27.0 + - - +
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Residues in contact with GLN 497 (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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493A SER 3.0 13.8 + - - +
494A GLN* 3.5 11.9 - - - +
495A LEU 3.2 0.2 - - - -
496A SER* 1.3 76.7 + - - +
498A GLN* 1.3 60.8 + - - +
500A GLY* 3.3 14.0 + - - -
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Residues in contact with GLN 498 (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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494A GLN 3.1 15.6 + - - +
495A LEU* 3.8 9.2 - - + +
497A GLN* 1.3 74.5 - - - +
499A GLU* 1.4 62.2 + - + +
500A GLY 3.7 0.5 + - - -
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Residues in contact with GLU 499 (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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299A VAL* 4.0 20.6 - - + +
300A GLU* 6.3 1.3 - - - -
303A ILE* 3.9 19.1 - - + -
461A CYS* 6.0 0.2 - - - -
462A GLU* 4.9 6.4 - - - +
463A ALA* 4.0 12.3 + - - +
495A LEU* 3.1 33.6 + - + +
496A SER* 3.9 5.8 - - - +
497A GLN 3.3 0.2 - - - -
498A GLN* 1.4 75.6 - - + +
500A GLY* 1.3 61.6 + - - +
501A ILE* 3.5 6.5 + - + +
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Residues in contact with GLY 500 (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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300A GLU* 4.7 1.6 - - - +
496A SER 3.1 4.6 + - - -
497A GLN* 3.3 13.6 + - - -
498A GLN 3.3 1.0 + - - -
499A GLU* 1.3 78.4 - - - +
501A ILE* 1.3 63.7 + - - +
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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
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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