Contacts of the helix formed by residues 526 - 533 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502D ILE* 5.3 3.6 - - + -
506D ILE* 4.3 10.8 - - + -
521D ILE* 2.6 28.0 + - + +
524D CYS* 3.9 12.8 - - + +
525D GLN* 1.3 72.2 - - - +
527D GLU* 1.3 56.3 - - - +
528D GLU 3.3 2.5 - - - -
529D ASP* 3.2 27.8 + - + +
530D ILE* 2.9 40.3 + - + +
552D GLN* 4.6 2.7 - - + +
555D ARG* 3.6 35.9 - - + +
556D ILE* 3.9 26.7 - - + -
559D ALA* 3.6 19.1 - - + -
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Residues in contact with GLU 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ARG* 4.4 5.4 - - - +
521D ILE* 3.4 26.5 + - + +
522D LYS* 3.1 54.7 + - - +
525D GLN* 3.6 1.7 - - - -
526D LEU* 1.3 76.9 - - - +
528D GLU* 1.3 58.1 + - + +
530D ILE* 3.9 2.6 - - - +
531D SER* 3.0 33.1 + - - -
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Residues in contact with GLU 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ASP* 5.3 2.2 - - - +
525D GLN 4.9 3.9 + - - +
526D LEU* 3.3 0.8 - - - +
527D GLU* 1.3 77.9 - - + +
529D ASP* 1.3 67.7 + - - +
531D SER* 3.4 10.2 + - - -
532D LYS* 3.3 24.4 + - - +
667D ARG* 6.2 3.4 - - - +
671D LEU* 4.3 13.3 - - + +
672D GLU* 3.4 50.5 + - + +
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Residues in contact with ASP 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D ILE* 5.7 1.8 - - + -
525D GLN 3.4 10.9 - - - +
526D LEU* 3.2 20.7 + - + +
528D GLU* 1.3 80.0 - - - +
530D ILE* 1.3 62.9 + - + +
532D LYS* 3.6 10.3 + - - +
533D PHE* 3.1 27.9 - - + -
552D GLN* 3.0 36.7 + - - +
555D ARG* 3.0 34.2 + - - -
667D ARG* 4.9 7.6 - - - -
671D LEU* 6.0 1.4 - - - +
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Residues in contact with ILE 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D ILE* 4.4 18.8 - - + -
517D TYR* 3.9 10.5 - - - +
518D ARG* 4.9 7.4 - - - +
521D ILE* 3.8 39.5 - - + -
526D LEU* 2.9 27.6 + - + +
527D GLU* 3.9 4.3 - - - +
529D ASP* 1.3 79.6 - - + +
531D SER* 1.3 62.1 + - - +
532D LYS 3.4 0.3 + - - -
533D PHE* 3.7 8.6 + - - -
536D LYS* 3.3 29.2 - - + +
537D ASP* 3.4 40.4 - - + +
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Residues in contact with SER 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D GLU 3.0 18.1 + - - -
528D GLU* 3.4 17.8 + - - -
530D ILE* 1.3 77.7 - - - +
532D LYS* 1.3 65.2 + - - +
533D PHE 3.6 7.1 - - - +
536D LYS* 3.7 23.4 + - - +
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Residues in contact with LYS 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A MET* 3.5 36.4 - - + +
499A PRO* 2.9 32.3 + - - +
504A GLU* 5.8 2.4 + - - -
528D GLU 3.3 16.1 + - - +
529D ASP* 3.8 6.7 - - - +
530D ILE 3.3 0.6 - - - -
531D SER* 1.3 81.0 + - - +
533D PHE* 1.3 93.6 + - + +
534D ALA* 3.7 1.2 + - - -
552D GLN* 6.3 0.4 - - - +
671D LEU* 4.7 13.0 - - + -
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Residues in contact with PHE 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A PRO* 4.8 16.8 - - + -
502D ILE* 3.6 24.7 - - + -
529D ASP* 3.1 26.7 - - + -
530D ILE* 3.7 1.9 + - - +
531D SER 3.4 8.7 - - - +
532D LYS* 1.3 104.5 - - + +
534D ALA* 1.3 66.3 + - - +
535D GLU 4.3 1.6 - - - +
536D LYS* 3.1 33.2 + - - +
539D ILE* 3.8 34.1 - - + -
541D LEU* 6.0 1.3 - - + -
548D LEU* 4.9 8.7 - - + -
552D GLN* 3.9 24.2 - - - -
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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