Contacts of the helix formed by residues 526 - 533 (chain E) in PDB entry 1XMI
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 526 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502E ILE* 5.3 3.8 - - + -
506E ILE* 4.1 13.5 - - + -
521E ILE* 2.7 27.4 + - + +
524E CYS* 4.0 11.4 - - + +
525E GLN* 1.3 74.3 - - - +
527E GLU* 1.3 61.6 + - - +
528E GLU 3.5 2.2 - - - -
529E ASP* 3.3 28.7 + - + +
530E ILE* 3.1 31.7 + - + +
552E GLN* 4.5 3.1 - - - +
555E ARG* 3.8 24.2 - - + +
556E ILE* 3.8 25.8 - - + -
559E ALA* 3.7 29.8 - - + -
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Residues in contact with GLU 527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518E ARG* 3.6 8.2 - - - +
521E ILE* 3.4 31.5 + - + +
522E LYS* 3.4 54.9 + - - +
525E GLN* 3.5 2.9 - - - -
526E LEU* 1.3 77.4 - - - +
528E GLU* 1.3 57.5 + - - +
530E ILE* 3.4 2.8 + - - +
531E SER* 3.0 32.3 + - - -
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Residues in contact with GLU 528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E GLN 5.2 2.3 + - - +
526E LEU 3.5 0.2 - - - -
527E GLU* 1.3 75.6 - - - +
529E ASP* 1.3 65.5 + - - +
531E SER* 3.6 7.6 + - - -
532E LYS* 3.2 27.5 + - - +
667E ARG* 6.5 0.9 - - - -
671E LEU* 5.6 11.7 - - + -
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Residues in contact with ASP 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502E ILE* 5.5 3.6 - - + -
525E GLN 3.4 16.1 - - - +
526E LEU* 3.3 24.8 + - + +
527E GLU 3.3 0.6 - - - -
528E GLU* 1.3 78.8 - - - +
530E ILE* 1.3 60.9 + - + +
532E LYS* 4.0 5.4 - - - +
533E PHE* 3.2 29.9 - - + -
552E GLN* 2.7 38.0 + - - +
555E ARG* 2.8 26.2 + - - -
667E ARG* 5.0 6.7 - - - -
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Residues in contact with ILE 530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502E ILE* 4.4 20.6 - - + -
517E TYR* 3.8 2.7 - - + +
518E ARG* 4.9 8.5 - - - +
521E ILE* 3.8 38.8 - - + -
526E LEU* 3.1 26.6 + - + +
527E GLU* 4.0 3.1 - - - +
529E ASP* 1.3 79.0 - - + +
531E SER* 1.3 64.3 + - - +
532E LYS 3.2 1.3 + - - -
533E PHE* 3.5 7.5 + - - +
536E LYS* 3.3 44.2 - - + +
537E ASP* 3.4 35.7 - - - +
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Residues in contact with SER 531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D LYS* 3.1 33.5 + - - +
527E GLU 3.0 18.6 + - - -
528E GLU* 3.6 10.4 + - - -
530E ILE* 1.3 77.9 - - - +
532E LYS* 1.3 64.5 + - - +
533E PHE 3.4 5.9 - - - +
536E LYS* 5.4 7.2 - - - +
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Residues in contact with LYS 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B MET* 4.5 21.1 - - + -
499B PRO* 3.3 29.0 + - - +
500B GLY* 4.8 0.8 - - - -
504B GLU* 4.6 17.6 + - + +
528E GLU 3.2 18.6 + - - +
529E ASP* 4.0 8.5 - - - +
530E ILE 3.2 0.4 - - - -
531E SER* 1.3 80.1 - - - +
533E PHE* 1.3 93.1 + - + +
534E ALA 3.7 1.4 + - - -
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Residues in contact with PHE 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B PRO* 4.9 14.6 - - + -
612D LYS* 5.7 1.2 - - - +
502E ILE* 3.9 20.2 - - + -
529E ASP* 3.2 26.5 - - + -
530E ILE 3.5 4.0 + - - +
531E SER 3.4 5.3 - - - +
532E LYS* 1.3 109.7 - - - +
534E ALA* 1.3 60.6 + - - +
535E GLU* 3.1 2.9 - - + +
536E LYS* 2.9 40.6 + - - +
539E ILE* 3.6 30.7 - - + -
541E LEU* 6.2 1.6 - - + -
548E LEU* 5.5 6.5 - - + -
552E GLN* 4.8 14.1 - - - -
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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