Contacts of the helix formed by residues 489 - 500 (chain A) in PDB entry 3RC3
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 GLU 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A ASN* 3.3 31.1 + - - +
488A HIS* 1.3 82.0 + - + +
490A ASP* 1.3 72.3 + - - +
491A LEU 3.3 0.6 + - - -
492A SER* 4.5 10.5 + - - -
493A LEU* 4.5 5.9 + - - +
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Residues in contact with ASP 490 (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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441A TYR 4.5 3.6 - - - +
442A SER* 4.3 16.8 - - - -
443A LEU* 3.4 24.5 - - + +
485A THR* 3.8 17.1 - - + +
487A ASN* 3.3 21.5 + - - +
488A HIS 3.0 1.0 + - - -
489A GLU* 1.3 93.1 + - - +
491A LEU* 1.3 58.7 + - - +
492A SER 3.5 0.4 - - - -
493A LEU* 3.4 10.6 + - - +
494A LEU* 2.9 26.0 + - - +
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Residues in contact with LEU 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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353A VAL* 4.0 15.5 - - + -
354A LEU 3.4 23.6 - - - +
355A ASP 3.3 29.4 - - - +
356A HIS 3.8 9.0 - - - +
357A ALA 4.1 2.2 - - - +
484A THR* 3.5 21.3 - - - +
485A THR* 3.6 20.7 + - + +
487A ASN 4.7 0.2 - - - +
488A HIS* 3.0 23.8 + - + +
489A GLU 3.3 0.2 - - - -
490A ASP* 1.3 78.1 - - - +
492A SER* 1.3 57.9 + - - +
494A LEU* 3.4 5.6 + - + +
495A LYS* 3.0 35.8 + - + +
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Residues in contact with SER 492 (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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488A HIS 4.7 1.0 + - - -
489A GLU 4.5 6.9 + - - -
491A LEU* 1.3 74.3 - - - +
493A LEU* 1.3 63.6 + - - +
495A LYS* 3.7 12.1 - - - +
496A GLU* 2.8 34.2 + - - +
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Residues in contact with LEU 493 (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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443A LEU* 3.8 22.2 - - + -
458A PRO* 5.6 7.4 - - + -
489A GLU 4.5 4.6 + - - +
490A ASP* 3.4 21.1 + - - +
492A SER* 1.3 81.7 + - - +
494A LEU* 1.3 57.4 + - - +
496A GLU* 3.3 22.1 + - - +
497A ILE* 2.9 44.8 + - + +
500A ARG* 5.6 1.3 - - - +
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Residues in contact with LEU 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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353A VAL* 4.4 9.9 - - + -
440A PHE* 3.9 34.5 - - + -
443A LEU* 3.7 17.6 - - + +
459A ILE* 5.0 0.7 - - + -
464A ALA* 4.6 7.4 - - + -
483A VAL* 3.9 18.6 - - + -
484A THR* 4.1 9.6 - - - -
485A THR* 3.7 22.9 - - + +
490A ASP 2.9 14.6 + - - +
491A LEU* 3.6 8.5 - - + +
492A SER 3.2 0.2 - - - -
493A LEU* 1.3 73.1 - - - +
495A LYS* 1.3 59.2 + - - +
497A ILE* 3.3 4.7 + - + -
498A LEU* 2.9 50.8 + - + +
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Residues in contact with LYS 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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353A VAL* 3.9 25.8 - - + -
354A LEU 3.0 28.3 + - - -
355A ASP* 3.4 18.6 + - - +
491A LEU* 3.0 30.3 + - + +
492A SER* 3.7 14.4 - - - +
494A LEU* 1.3 75.3 - - - +
496A GLU* 1.3 62.3 + - - +
498A LEU* 3.4 7.0 + - - +
499A LYS* 3.1 29.8 + - - +
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Residues in contact with GLU 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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492A SER 2.8 22.3 + - - +
493A LEU* 3.4 21.8 - - + +
495A LYS* 1.3 70.7 - - - +
497A ILE* 1.3 66.3 + - - +
499A LYS* 3.4 24.1 + - - +
500A ARG* 3.2 43.2 + - + +
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Residues in contact with ILE 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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443A LEU* 4.4 10.1 - - + -
458A PRO* 4.6 12.3 - - + -
459A ILE* 4.0 29.8 - - + +
461A THR* 2.7 54.4 + - - +
464A ALA* 3.9 17.5 - - + -
493A LEU* 2.9 46.9 + - + +
494A LEU* 3.3 6.5 + - + +
496A GLU* 1.3 76.4 - - - +
498A LEU* 1.3 62.7 + - - +
499A LYS 3.3 0.9 + - - -
500A ARG* 3.5 21.1 + - - +
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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
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353A VAL* 3.6 30.3 - - + -
461A THR* 4.2 3.2 - - - +
464A ALA* 3.6 34.5 - - + +
465A LEU* 3.7 46.5 - - + +
468A ALA* 4.3 8.1 - - + -
483A VAL* 4.7 7.0 - - + -
494A LEU* 2.9 46.0 + - + +
495A LYS* 3.9 5.8 - - - +
496A GLU 3.2 0.4 - - - -
497A ILE* 1.3 79.2 - - - +
499A LYS* 1.3 59.0 + - + +
500A ARG 4.7 0.2 - - - +
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Residues in contact with LYS 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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495A LYS* 3.1 16.1 + - - +
496A GLU* 3.4 32.4 + - - +
498A LEU* 1.3 78.7 - - + +
500A ARG* 1.3 65.1 + - - +
501A PRO* 3.5 7.1 - - - +
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Residues in contact with ARG 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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459A ILE 5.0 3.4 + - - -
460A THR* 5.3 1.8 - - - +
461A THR* 3.4 45.3 + - - +
493A LEU* 5.6 1.6 - - - +
496A GLU* 3.2 37.0 + - + +
497A ILE* 4.3 26.3 - - - +
498A LEU 3.5 1.5 - - - +
499A LYS* 1.3 78.8 - - - +
501A PRO* 1.4 86.0 + - + +
502A VAL* 3.5 1.0 + - - +
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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