Contacts of the helix formed by residues 492 - 502 (chain A) in PDB entry 4N78
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 LEU 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A PHE* 2.9 53.3 + - + +
488A SER* 3.9 22.9 - - - +
490A VAL 3.2 1.2 - - - +
491A THR* 1.3 76.0 - - + +
493A ARG* 1.3 62.9 + - - +
494A GLU 3.4 0.7 - - - -
495A PRO* 3.5 12.4 - - + +
496A LEU* 3.1 26.7 + - - +
511A LEU* 3.9 27.4 - - + +
514A ILE* 4.0 23.1 - - + -
515A ARG* 4.3 17.9 - - + +
566A LEU* 4.7 3.4 - - + -
592A ILE* 4.7 6.7 - - + -
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Residues in contact with ARG 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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489A GLN 3.2 27.6 + - - +
490A VAL* 3.1 21.9 + - - +
492A LEU* 1.3 75.6 - - - +
494A GLU* 1.3 60.7 + - - +
496A LEU* 3.4 6.0 + - - +
497A ARG* 2.8 31.2 + - - +
515A ARG* 3.8 12.3 - - - +
530A ASP* 2.6 38.2 + - - +
531A PRO* 3.9 2.8 - - - +
532A ALA* 3.8 14.1 - - + +
538A ASP* 3.1 40.2 + - - -
543A PHE* 3.5 22.3 + - - +
545A ILE* 3.7 15.9 - - - +
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Residues in contact with GLU 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 VAL 4.5 1.0 + - - -
491A THR 4.0 3.7 + - - +
493A ARG* 1.3 78.5 - - - +
495A PRO* 1.3 70.9 - - + +
497A ARG* 3.1 40.1 + - - +
498A GLN* 3.1 42.5 + - - +
537A LYS* 6.0 0.2 - - - -
588A THR* 4.3 11.2 - - + -
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Residues in contact with PRO 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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491A THR* 3.2 18.8 - - + +
492A LEU* 3.5 18.4 - - + +
494A GLU* 1.3 96.9 - - + +
496A LEU* 1.3 60.4 + - - +
498A GLN* 3.3 12.7 + - - +
499A ALA* 3.1 22.5 + - - +
507A ILE* 5.2 0.5 - - - +
511A LEU* 3.6 21.1 - - + +
584A LEU* 5.2 12.1 - - + +
588A THR* 3.9 28.3 - - + +
591A ASP* 6.4 0.9 - - + -
592A ILE* 5.3 7.2 - - + -
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Residues in contact with LEU 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 LEU 3.1 17.2 + - - +
493A ARG* 3.7 5.2 - - - +
495A PRO* 1.3 78.6 - - - +
497A ARG* 1.3 63.4 + - - +
499A ALA* 3.3 0.9 + - - +
500A ILE* 3.1 36.6 + - + +
508A GLN* 3.9 19.5 - - + +
511A LEU* 3.4 24.6 - - + +
512A GLN* 3.8 30.1 - - + +
515A ARG* 3.9 35.0 - - - +
532A ALA* 5.1 3.4 - - + +
533A LEU* 5.4 11.7 - - + -
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Residues in contact with ARG 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 ARG 2.8 15.6 + - - +
494A GLU* 3.2 36.5 + - - +
496A LEU* 1.3 77.5 - - - +
498A GLN* 1.3 89.0 + - - +
501A LYS* 3.1 56.7 + - - +
532A ALA* 3.5 23.8 + - + -
535A GLY* 3.7 19.6 + - - +
536A GLU 4.0 13.5 + - - +
537A LYS* 3.1 50.8 - - - +
538A ASP* 6.6 0.2 - - - -
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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 GLU* 3.1 39.3 + - - +
495A PRO* 3.8 9.2 - - - +
496A LEU 3.3 0.2 - - - -
497A ARG* 1.3 96.6 - - - +
499A ALA* 1.3 61.3 + - - +
501A LYS* 3.7 4.2 - - - +
502A LYS* 2.8 55.5 + - - +
504A LYS* 5.1 0.4 - - - -
584A LEU* 5.3 3.8 - - - +
585A GLU* 3.0 47.2 + - - +
588A THR* 4.6 4.4 + - - +
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Residues in contact with ALA 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 PRO 3.1 15.3 + - - +
496A LEU* 3.3 6.9 + - - +
498A GLN* 1.3 76.6 - - - +
500A ILE* 1.3 58.4 + - - +
503A LYS 3.1 5.0 + - - -
504A LYS* 2.5 50.8 + - + +
507A ILE* 3.9 12.1 - - + -
508A GLN* 3.8 32.3 - - - +
584A LEU* 6.3 0.2 - - + -
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Residues in contact with ILE 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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496A LEU* 3.1 29.3 + - + +
497A ARG 3.9 2.9 - - - +
499A ALA* 1.3 74.2 - - - +
501A LYS* 1.3 66.5 + - - +
503A LYS* 3.2 16.6 + - - +
508A GLN* 3.4 41.7 - - + +
512A GLN* 4.4 3.6 - - - +
532A ALA 3.9 4.7 - - - +
533A LEU* 3.1 39.0 - - + +
534A ARG 4.1 16.4 - - - +
535A GLY* 4.3 1.3 - - - -
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Residues in contact with LYS 501 (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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497A ARG* 3.1 53.1 + - - +
498A GLN* 3.7 3.6 - - - +
500A ILE* 1.3 80.3 - - - +
502A LYS* 1.3 76.7 + - + +
503A LYS* 3.3 9.2 + - - +
534A ARG 5.8 0.2 - - - -
535A GLY* 3.9 17.9 - - - +
537A LYS* 5.6 1.0 - - - +
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Residues in contact with LYS 502 (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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498A GLN* 2.8 47.3 + - - +
501A LYS* 1.3 91.3 - - + +
503A LYS* 1.3 70.8 + - - +
504A LYS* 3.2 28.8 + - + +
583A SER 4.6 14.0 + - - -
584A LEU 6.0 0.2 - - - -
585A GLU* 4.0 20.0 + - - +
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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