Contacts of the helix formed by residues 485 - 496 (chain A) in PDB entry 1DCX
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 LYS 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A GLU* 3.1 31.9 + - - +
484A GLU* 1.3 84.2 - - - +
486A GLU* 1.3 60.7 + - - +
487A MET 3.5 1.3 - - - -
488A ALA* 3.7 0.6 - - - +
489A ALA* 2.9 33.7 + - + +
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Residues in contact with GLU 486 (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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438A ARG* 2.9 37.2 + - - +
484A GLU* 3.2 5.6 + - - +
485A LYS* 1.3 79.5 - - - +
487A MET* 1.3 64.9 + - - +
489A ALA* 3.3 4.1 + - - +
490A GLU* 3.1 27.5 + - + +
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Residues in contact with MET 487 (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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181A VAL* 3.6 21.7 - - + +
436A GLY 3.4 20.9 - - - +
437A GLY* 3.9 14.4 - - - -
438A ARG* 3.7 42.0 - - - +
482A THR* 4.4 6.7 - - + +
484A GLU* 2.7 35.4 + - + +
486A GLU* 1.3 72.4 - - + +
488A ALA* 1.3 59.0 + - - +
490A GLU* 3.0 6.8 + - - +
491A LEU* 2.8 34.8 + - + +
509A VAL* 3.9 23.3 - - + +
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Residues in contact with ALA 488 (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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478A PHE* 3.5 37.1 - - + +
479A GLU* 3.6 11.7 - - + +
482A THR* 3.5 6.4 + - - +
484A GLU* 2.8 36.7 + - - +
485A LYS 3.7 1.6 - - - +
487A MET* 1.3 72.5 - - - +
489A ALA* 1.3 52.3 + - - +
491A LEU* 3.2 4.7 + - - +
492A LYS* 2.8 35.4 + - - +
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Residues in contact with ALA 489 (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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479A GLU* 5.5 0.4 - - - +
485A LYS* 2.9 20.1 + - + +
486A GLU* 3.5 6.1 - - - +
488A ALA* 1.3 76.5 - - - +
490A GLU* 1.3 58.0 + - + +
492A LYS* 3.3 8.0 + - - +
493A ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 490 (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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180A LYS* 3.1 45.9 - - + +
181A VAL* 3.7 9.0 - - + +
438A ARG* 2.6 32.3 + - - -
486A GLU* 3.1 14.6 + - + +
487A MET* 3.0 8.4 + - - +
489A ALA* 1.3 77.4 - - + +
491A LEU* 1.3 63.0 + - - +
493A ALA* 3.3 8.9 + - - +
494A LEU* 3.1 29.4 + - - +
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Residues in contact with LEU 491 (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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177A VAL* 4.7 3.8 - - + -
181A VAL* 3.9 25.1 - - + -
478A PHE* 3.4 22.4 - - + -
481A LEU* 4.4 5.4 - - + -
482A THR* 3.8 14.6 - - + -
487A MET 2.8 18.8 + - - +
488A ALA* 3.4 6.3 - - - +
490A GLU* 1.3 73.6 - - - +
492A LYS* 1.3 61.7 + - - +
494A LEU* 3.0 5.5 + - + -
495A TYR* 2.8 49.1 + - + +
501A MET* 3.7 21.8 - - + -
505A PRO* 5.7 0.2 - - + -
509A VAL* 3.8 31.0 - - + -
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Residues in contact with LYS 492 (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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478A PHE* 3.7 27.9 - - + +
488A ALA 2.8 20.5 + - - +
489A ALA* 3.6 9.2 - - - +
491A LEU* 1.3 72.2 - - - +
493A ALA* 1.3 58.6 + - - +
496A SER* 2.7 58.8 + - - +
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Residues in contact with ALA 493 (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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489A ALA 2.9 13.4 + - - +
490A GLU* 3.4 11.9 - - - +
492A LYS* 1.3 80.3 - - - +
494A LEU* 1.3 61.5 + - + +
496A SER* 4.4 6.2 + - - -
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Residues in contact with LEU 494 (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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168A ASN* 5.9 0.9 + - - -
172A PRO* 3.4 39.1 - - + +
173A ASP* 5.1 1.1 - - + +
176A GLU* 3.7 34.3 - - + +
177A VAL* 4.1 29.6 - - + +
180A LYS* 4.4 16.6 - - + +
181A VAL* 5.7 0.9 - - + -
490A GLU* 3.1 19.6 + - + +
491A LEU* 3.0 9.2 + - + +
493A ALA* 1.3 83.5 - - + +
495A TYR* 1.3 62.7 + - + +
496A SER* 4.6 1.6 + - - -
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Residues in contact with TYR 495 (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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167A GLY* 5.5 2.8 - - - -
168A ASN* 5.3 4.2 + - - -
171A LEU* 4.7 1.1 - - + -
172A PRO* 3.4 31.2 - - + -
177A VAL* 3.7 26.5 - - + +
456A ARG* 4.0 0.2 + - - -
478A PHE* 3.6 19.1 - + + -
491A LEU* 2.8 34.0 + - + -
494A LEU* 1.3 75.9 - - + +
496A SER* 1.3 68.3 + - - +
497A ASP* 2.8 15.1 + - - +
500A VAL* 3.6 36.4 - - + +
501A MET* 3.5 26.9 - - + -
502A GLU* 2.6 37.1 + - + +
505A PRO* 4.0 7.3 - - - +
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Residues in contact with SER 496 (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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168A ASN* 4.7 11.4 + - - -
478A PHE* 4.1 5.1 - - - -
492A LYS* 2.7 56.0 + - - +
493A ALA 4.4 6.4 + - - -
494A LEU 4.6 2.1 + - - -
495A TYR* 1.3 75.1 + - - +
497A ASP* 1.3 58.0 + - - -
498A ILE 4.3 0.2 + - - -
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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