Contacts of the helix formed by residues 457 - 468 (chain J) in PDB entry 4XLN
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 457 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126J VAL* 3.2 28.6 + - - +
127J LEU* 4.1 2.2 - - - -
129J PHE* 3.4 20.6 - - - -
456J MET* 1.3 75.7 - - - +
458J ALA* 1.3 65.6 + - - -
459J GLU 3.2 2.9 - - - -
460J ALA* 3.2 11.8 + - - +
461J ILE* 3.5 14.4 + - - +
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Residues in contact with ALA 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J THR* 5.5 0.2 - - - +
98J PRO 3.2 19.5 - - - +
99J ALA* 3.8 5.8 - - - -
100J ALA 4.0 3.1 - - - +
127J LEU* 3.7 30.4 + - + +
129J PHE* 4.0 7.9 - - + -
457J GLY* 1.3 70.4 - - - -
459J GLU* 1.3 59.6 + - - +
461J ILE* 3.3 2.5 + - - +
462J GLN 2.9 23.9 + - - -
513J ILE* 3.4 10.2 - - + +
575J GLN* 3.5 23.8 - - - +
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Residues in contact with GLU 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J THR* 4.3 17.1 + - - +
98J PRO* 3.7 22.7 + - + +
129J PHE* 5.3 1.8 - - + -
455J ARG* 4.6 26.0 + - - +
456J MET 5.0 8.0 - - - +
457J GLY 3.2 1.1 - - - -
458J ALA* 1.3 78.7 - - - +
460J ALA* 1.3 57.9 + - - +
462J GLN* 3.2 13.9 - - - +
463J GLU* 2.9 27.6 + - + +
571J LYS* 5.7 1.2 + - - -
155L ARG* 4.6 16.8 + - - +
159L ILE* 3.8 23.6 - - - +
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Residues in contact with ALA 460 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J ILE* 3.6 15.9 - - + -
135J LEU* 4.3 6.7 - - + -
455J ARG* 3.1 38.6 - - + +
456J MET 4.2 2.8 + - - -
457J GLY 3.2 11.7 + - - +
459J GLU* 1.3 78.1 + - - +
461J ILE* 1.3 60.1 + - + +
463J GLU* 2.8 24.4 + - - +
464J LEU* 2.9 19.5 + - - +
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Residues in contact with ILE 461 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ILE* 4.3 6.3 - - + -
116J LEU* 3.8 13.2 - - + -
118J LEU* 6.2 0.9 - - + -
123J LEU* 3.7 21.3 - - + -
126J VAL* 3.6 24.0 - - + -
127J LEU* 3.6 24.2 - - + -
133J ILE* 4.8 2.9 - - + -
457J GLY 3.5 13.5 - - - +
458J ALA 3.3 6.0 + - - +
460J ALA* 1.3 75.8 - - - +
462J GLN* 1.3 56.9 + - - +
464J LEU* 3.8 19.9 - - + +
465J LEU* 2.9 51.0 + - + +
513J ILE* 3.9 9.4 - - + -
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Residues in contact with GLN 462 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J PRO* 3.4 24.4 - - - +
458J ALA 2.9 13.8 + - - +
459J GLU* 3.2 16.2 - - - +
460J ALA 3.1 0.2 - - - -
461J ILE* 1.3 76.5 - - - +
463J GLU* 1.3 65.0 + - - +
465J LEU* 3.8 2.2 - - - +
466J LYS* 2.9 42.7 + - + +
510J GLU* 4.2 13.0 - - + +
513J ILE* 3.6 31.3 + - + +
515J GLU* 3.2 30.5 + - - +
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Residues in contact with GLU 463 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 3.6 26.2 - - + +
455J ARG* 3.5 27.1 + - - +
459J GLU* 2.9 12.4 + - + +
460J ALA* 2.8 15.1 + - - +
462J GLN* 1.3 83.5 + - - +
464J LEU* 1.3 64.0 + - - +
466J LYS* 3.0 21.4 + - - +
467J GLU* 3.0 32.4 + - - +
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Residues in contact with LEU 464 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J LEU* 4.0 23.8 - - + -
118J LEU* 5.4 6.5 - - + -
133J ILE* 3.7 24.7 - - + -
134J VAL 5.1 3.6 - - - +
135J LEU* 3.8 22.7 - - + -
150J ARG* 6.2 5.8 - - + -
460J ALA 2.9 21.3 + - - +
461J ILE* 3.8 30.5 - - + -
463J GLU* 1.3 72.5 - - - +
465J LEU* 1.3 61.5 + - - +
467J GLU* 3.1 21.3 + - - +
468J LEU* 3.2 18.7 + - + +
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Residues in contact with LEU 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ILE* 3.5 29.2 - - + -
115J LEU* 5.2 4.3 - - + -
116J LEU* 3.7 21.5 - - + -
461J ILE* 2.9 27.3 + - + +
462J GLN 3.8 3.4 - - - +
464J LEU* 1.3 77.0 - - - +
466J LYS* 1.3 61.5 + - - +
468J LEU* 3.4 40.1 + - + +
509J PRO* 4.0 25.8 - - + +
510J GLU* 3.4 23.0 - - - +
512J MET* 4.9 2.2 - - + -
513J ILE* 3.5 26.2 - - + -
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Residues in contact with LYS 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462J GLN* 2.9 31.3 + - - +
463J GLU* 3.0 11.8 + - - +
465J LEU* 1.3 77.1 - - - +
467J GLU* 1.3 61.4 + - + +
468J LEU 3.2 4.3 + - - +
510J GLU* 3.8 32.4 - - + +
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Residues in contact with GLU 467 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 4.2 14.3 - - - +
463J GLU* 3.0 40.7 + - + +
464J LEU* 3.1 12.0 + - - +
466J LYS* 1.3 77.8 - - + +
468J LEU* 1.3 65.5 + - - +
469J ASP* 3.6 3.3 + - - +
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Residues in contact with LEU 468 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU* 3.6 30.7 - - + -
116J LEU* 3.6 17.5 - - + -
150J ARG* 5.4 13.2 - - - +
464J LEU* 3.2 16.8 - - + +
465J LEU* 3.4 37.6 - - + +
466J LYS 3.2 5.7 - - - +
467J GLU* 1.3 79.8 - - - +
469J ASP* 1.3 62.0 + - - +
470J LEU* 4.0 20.3 + - + +
473J LEU* 5.9 4.0 - - + -
509J PRO* 4.3 6.3 - - + -
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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