Contacts of the helix formed by residues 525 - 535 (chain B) in PDB entry 2I91
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 GLY 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ARG* 3.3 24.4 + - - +
362B LYS* 3.9 19.7 - - - -
523B ASP* 2.8 6.3 + - - -
524B SER* 1.3 77.8 + - - +
526B ALA* 1.3 66.2 + - - +
527B LEU 3.1 3.6 - - - -
528B ASP* 3.0 20.7 + - - +
529B VAL* 3.2 9.7 + - - +
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Residues in contact with ALA 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 5.6 1.1 - - + -
399B MET* 3.6 26.0 - - + -
519B ILE* 4.6 9.6 - - + -
520B CYS 4.2 7.4 - - - +
523B ASP* 2.6 28.8 + - + +
524B SER 3.4 0.4 - - - -
525B GLY* 1.3 77.6 - - - +
527B LEU* 1.3 64.7 + - + +
529B VAL* 3.1 13.9 - - - +
530B ILE* 3.0 30.2 + - + +
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 4.2 6.0 - - + -
362B LYS 3.4 26.5 - - - +
363B LEU* 4.1 14.4 - - + -
364B VAL* 4.1 20.3 - - + +
399B MET* 6.0 0.9 - - + -
402B LEU* 3.4 50.4 - - + +
403B VAL* 4.1 24.9 - - + -
406B THR* 4.5 12.1 - - + +
524B SER 4.8 2.0 + - - +
525B GLY 3.0 1.0 + - - -
526B ALA* 1.3 80.7 - - + +
528B ASP* 1.3 60.6 + - - +
530B ILE* 3.6 7.2 + - + +
531B ARG* 3.1 23.4 + - - +
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Residues in contact with ASP 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLN* 2.5 34.6 + - - +
113A ARG* 5.2 4.0 + - - -
362B LYS* 4.8 8.0 + - + +
364B VAL* 2.9 24.8 - - + +
525B GLY* 3.0 12.0 + - - +
527B LEU* 1.3 76.0 - - - +
529B VAL* 1.3 60.9 + - + +
531B ARG* 3.3 8.0 + - - +
532B ASN* 2.8 40.9 + - - +
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Residues in contact with VAL 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ARG* 4.6 8.7 - - - +
517B LEU* 4.3 7.9 - - + +
519B ILE* 4.6 21.5 - - + -
523B ASP* 4.6 3.4 - - - +
525B GLY 3.2 13.9 - - - +
526B ALA* 3.1 22.4 - - - +
528B ASP* 1.3 72.7 - - + +
530B ILE* 1.3 64.1 + - - +
532B ASN* 3.4 10.2 + - + +
533B PHE* 3.1 24.1 + - - +
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Residues in contact with ILE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B PHE* 4.5 9.4 - - + -
399B MET* 5.7 3.1 - - + -
403B VAL* 4.0 18.8 - - + -
465B ILE* 3.8 30.3 - - + -
467B PHE* 5.8 2.5 - - + -
497B ILE* 3.5 27.0 - - + +
517B LEU* 5.4 1.1 - - - -
519B ILE* 3.6 30.3 - - + -
526B ALA* 3.0 23.1 + - + +
527B LEU* 3.9 7.6 - - + +
529B VAL* 1.3 76.2 - - - +
531B ARG* 1.3 58.3 + - - +
533B PHE* 3.7 2.4 - - - +
534B THR* 2.9 39.2 + - - +
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Residues in contact with ARG 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLN* 4.7 11.7 - - - +
364B VAL* 3.8 19.9 - - + +
365B GLU* 3.2 43.3 + - - +
366B PRO 5.0 1.0 + - - -
367B THR* 3.9 16.5 - - + +
407B GLU* 5.6 1.3 - - - +
527B LEU 3.1 18.4 + - - +
528B ASP* 3.5 9.2 + - - +
530B ILE* 1.3 76.0 - - - +
532B ASN* 1.3 76.9 + - - +
534B THR* 2.9 17.5 + - - -
535B LEU* 3.0 37.3 + - + +
537B LEU* 5.5 2.4 - - - +
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Residues in contact with ASN 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LYS* 3.8 25.9 - - - +
109A GLN* 3.5 26.2 + - - +
528B ASP* 2.8 35.0 + - - +
529B VAL* 3.8 9.5 - - + +
531B ARG* 1.3 80.7 + - - +
533B PHE* 1.3 59.1 + - - +
536B ASP 3.5 1.0 + - - -
537B LEU* 2.8 59.8 + - + +
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Residues in contact with PHE 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ILE* 5.2 0.2 - - + -
495B LYS* 3.8 30.5 + - + -
497B ILE* 4.0 22.7 - - + -
514B ARG 3.4 26.2 - - - -
515B GLY* 3.7 25.1 - - - -
516B MET 3.9 1.6 - - - -
517B LEU* 3.5 45.1 - - + -
529B VAL 3.1 16.5 + - - +
530B ILE 3.7 4.3 - - - +
531B ARG 3.0 0.6 - - - -
532B ASN* 1.3 76.9 - - - +
534B THR* 1.3 67.2 + - - +
536B ASP* 3.0 13.9 + - - +
537B LEU 4.6 4.9 - - - +
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Residues in contact with THR 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B THR* 3.9 18.8 - - - +
369B LYS* 3.6 38.8 - - + -
371B PHE* 3.8 13.1 - - + -
463B ILE* 3.6 33.0 - - + +
495B LYS* 3.0 21.3 + - - -
497B ILE* 4.9 0.7 - - - +
530B ILE* 2.9 22.2 + - - +
531B ARG* 2.9 10.5 + - - -
533B PHE* 1.3 76.0 - - - +
535B LEU* 1.3 58.3 + - - +
536B ASP* 3.2 0.9 + - - +
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Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B THR* 4.0 25.6 - - + +
369B LYS* 4.6 15.0 - - - +
531B ARG* 3.0 55.9 + - + +
533B PHE 3.1 0.2 - - - -
534B THR* 1.3 77.7 - - - +
536B ASP* 1.3 69.4 - - - +
537B LEU* 3.3 28.0 - - + +
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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