Contacts of the helix formed by residues 522 - 532 (chain A) in PDB entry 4NAM
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 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A ASP* 4.1 5.1 + - + -
521A MET* 1.3 80.2 - - - +
523A LEU* 1.3 65.5 + - - +
524A LYS* 3.7 3.6 + - - +
525A GLU* 3.1 26.9 + - + +
526A ALA* 3.0 24.1 + - - +
578A LEU 3.8 4.7 - - - -
579A ASP* 3.1 28.8 + - - +
580A LYS* 5.0 0.7 - - - -
581A ILE 3.1 12.8 - - - +
582A LYS* 5.1 11.9 - - + +
583A LEU* 4.2 2.5 - - - -
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Residues in contact with LEU 523 (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 ILE* 4.2 20.6 - - + -
522A THR* 1.3 72.2 - - - +
524A LYS* 1.3 65.3 + - - +
526A ALA* 3.3 1.4 + - - +
527A LEU* 3.1 38.8 + - + +
552A PHE* 3.8 23.3 - - + -
554A PHE* 5.4 5.6 - - + -
562A ILE* 5.6 1.3 - - + -
574A ILE* 4.1 14.8 - - + -
578A LEU* 3.6 33.4 + - + +
581A ILE* 2.9 24.9 + - + +
583A LEU* 4.1 24.5 - - + +
589A ILE* 4.5 9.0 - - + -
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Residues in contact with LYS 524 (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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522A THR* 3.3 1.1 - - - +
523A LEU* 1.3 77.3 - - - +
525A GLU* 1.3 64.0 + - - +
527A LEU* 3.3 4.8 + - - +
528A LYS* 3.0 27.4 + - + +
535A GLU* 2.5 43.7 + - - -
538A GLY 4.9 4.4 + - - -
540A LEU* 4.1 33.9 - - + +
578A LEU* 3.1 32.1 + - + +
579A ASP* 3.8 26.4 - - + +
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Residues in contact with GLU 525 (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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218A LYS* 4.6 11.1 - - - +
253A HIS* 4.7 4.0 + - - -
255A LEU* 6.1 0.7 - - + -
521A MET* 4.0 19.5 - - + -
522A THR* 3.1 22.8 + - - +
524A LYS* 1.3 77.1 - - - +
526A ALA* 1.3 59.3 + - - +
528A LYS* 3.1 21.4 + - - +
529A ILE* 2.9 47.8 + - + +
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Residues in contact with ALA 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 4.0 12.6 - - + -
505A ILE* 4.2 10.5 - - + -
521A MET* 3.6 14.5 - - + -
522A THR 3.0 17.4 + - - +
523A LEU 3.7 4.7 - - - +
524A LYS 3.2 0.2 - - - -
525A GLU* 1.3 77.4 - - - +
527A LEU* 1.3 57.5 + - - +
529A ILE* 4.1 4.7 - - - -
530A ALA* 2.9 36.4 + - - +
583A LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 4.1 17.9 - - + -
493A PHE* 5.9 0.9 - - + -
523A LEU* 3.1 30.9 + - + +
524A LYS 3.3 5.6 + - - +
526A ALA* 1.3 72.3 - - - +
528A LYS* 1.3 66.7 + - - +
531A PHE* 3.1 24.0 + - + +
532A GLY 3.3 0.2 + - - -
533A PHE* 3.2 42.2 + - + -
540A LEU* 4.0 13.2 - - + -
547A ILE* 3.9 27.4 - - + -
552A PHE* 4.7 4.0 - - + -
578A LEU* 5.1 1.6 - - + -
591A ILE* 3.6 27.6 - - + -
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Residues in contact with LYS 528 (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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524A LYS* 3.0 21.8 + - + +
525A GLU* 3.5 22.4 - - - +
527A LEU* 1.3 76.4 - - - +
529A ILE* 1.3 63.5 + - + +
532A GLY* 3.0 25.5 + - - -
533A PHE 3.4 23.4 - - - +
534A ASN* 5.1 2.9 - - - +
535A GLU* 4.0 28.5 - - + +
540A LEU* 3.9 20.0 - - + -
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Residues in contact with ILE 529 (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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217A THR* 5.9 2.2 - - + -
250A GLU* 3.3 22.5 - - - +
253A HIS* 3.8 44.6 - - + +
255A LEU* 4.0 4.3 - - + -
256A VAL* 3.8 24.2 - - + +
505A ILE* 4.4 3.8 - - + -
521A MET* 3.9 25.8 - - + -
525A GLU* 2.9 41.6 + - + +
526A ALA* 3.9 6.3 - - - +
528A LYS* 1.3 76.9 - - + +
530A ALA* 1.3 64.1 + - + +
532A GLY 4.7 0.7 + - - -
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Residues in contact with ALA 530 (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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250A GLU* 3.7 22.4 - - - +
256A VAL* 4.2 9.2 - - + -
503A ARG* 3.7 28.1 + - + +
505A ILE* 3.7 30.7 - - + -
526A ALA 2.9 18.8 + - - +
529A ILE* 1.3 82.0 - - - +
531A PHE* 1.3 64.0 + - + +
532A GLY 3.8 0.2 - - - -
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Residues in contact with PHE 531 (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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250A GLU* 6.3 0.2 - - - -
491A ILE* 3.6 38.8 - - + -
493A PHE* 3.6 35.9 - + + -
501A VAL* 3.6 34.1 - - + -
503A ARG* 3.4 32.5 - - + -
527A LEU* 3.1 23.8 + - + +
530A ALA* 1.3 85.4 - - + +
532A GLY* 1.3 64.7 + - - +
533A PHE* 3.3 14.8 - - + -
542A TYR* 3.4 20.5 - + - -
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Residues in contact with GLY 532 (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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250A GLU* 6.0 1.0 - - - +
528A LYS 3.0 14.9 + - - -
529A ILE 4.5 0.8 + - - -
530A ALA 3.8 1.0 - - - -
531A PHE* 1.3 80.0 - - - +
533A PHE* 1.3 67.2 + - - +
534A ASN* 3.6 5.7 + - - +
541A GLN 4.6 0.5 - - - +
542A TYR* 4.5 7.8 - - - -
543A GLN* 5.3 2.6 + - - +
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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