Contacts of the helix formed by residues 525 - 532 (chain A) in PDB entry 1IGN
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 PHE 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A LEU* 4.5 1.8 - - + -
460A ALA* 3.8 39.9 - - + -
461A VAL* 3.8 21.3 - - + -
464A GLN* 3.6 34.3 - - + -
467A ARG* 5.5 1.8 - - - -
521A ILE* 3.5 16.4 - - + -
522A ALA* 3.1 21.8 + - + +
523A ARG 3.2 2.4 + - - -
524A GLU* 1.3 76.1 - - - +
526A PHE* 1.3 92.4 + + - +
528A HIS* 3.8 2.3 - - - +
529A PHE* 2.8 42.2 + + - +
21D C 4.4 1.2 + - - -
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Residues in contact with PHE 526 (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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457A LEU* 4.1 8.7 - - + -
521A ILE* 3.8 27.1 - - + -
524A GLU* 3.4 0.4 - - - +
525A PHE* 1.3 100.0 - + - +
527A LYS* 1.3 60.1 + - - +
529A PHE* 3.8 3.4 - - + +
530A ALA* 2.9 31.2 + - - +
538A GLU* 3.6 28.1 - - + +
541A TRP* 3.9 11.8 - - + -
542A ARG* 3.6 49.8 - - + -
545A PHE* 3.4 43.5 - + + -
21D C 4.9 8.1 + - - +
22D T 4.9 3.4 - - - -
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Residues in contact with LYS 527 (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 GLU* 3.4 37.2 + - + +
525A PHE 3.3 0.4 - - - -
526A PHE* 1.3 78.7 - - - +
528A HIS* 1.3 65.6 + - + +
530A ALA* 3.5 3.5 + - - +
531A GLU* 3.2 40.1 + - + +
538A GLU* 3.5 30.9 + - + +
20D C 4.1 18.0 + - - +
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Residues in contact with HIS 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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523A ARG* 5.4 2.4 + - - -
524A GLU* 2.9 52.1 + - + +
525A PHE* 4.2 2.7 - - - +
527A LYS* 1.3 82.6 - - + +
529A PHE* 1.3 64.9 + - - +
531A GLU* 3.3 33.3 + - - +
532A GLU* 3.1 26.1 + - - +
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Residues in contact with PHE 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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456A THR* 3.6 14.1 - - + -
457A LEU* 3.5 27.4 - - + -
460A ALA* 3.3 34.5 - - + -
525A PHE* 2.8 31.4 + + + +
526A PHE* 3.3 10.1 + - + +
528A HIS* 1.3 75.2 - - - +
530A ALA* 1.3 58.6 + - - +
532A GLU* 3.3 1.5 + - - -
533A HIS* 2.9 62.3 + + - +
541A TRP* 3.6 50.0 - + + -
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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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526A PHE 2.9 18.4 + - - +
527A LYS 3.6 4.7 - - - +
529A PHE* 1.3 78.1 - - - +
531A GLU* 1.3 56.4 + - - +
533A HIS 3.9 1.8 - - - -
534A ALA* 3.0 34.8 + - - +
536A HIS 3.9 2.5 - - - +
537A THR* 3.9 6.5 - - - -
538A GLU* 3.5 29.8 - - + +
541A TRP* 3.8 11.8 - - + -
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Residues in contact with GLU 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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527A LYS* 3.2 35.7 + - + +
528A HIS* 3.3 34.5 + - + +
529A PHE 3.3 0.2 - - - -
530A ALA* 1.3 79.6 - - + +
532A GLU* 1.3 62.8 + - - +
534A ALA* 4.2 9.2 + - - +
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Residues in contact with GLU 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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528A HIS 3.1 13.8 + - - +
529A PHE* 3.8 4.2 - - - +
531A GLU* 1.3 78.6 - - - +
533A HIS* 1.3 84.6 + - + +
534A ALA 3.9 0.9 - - - -
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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