Contacts of the helix formed by residues 469 - 482 (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 ASP 469 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467J GLU 3.6 3.9 + - - +
468J LEU* 1.3 74.1 - - - +
470J LEU* 1.3 65.9 + - - +
471J GLU* 3.5 26.6 + - - +
472J LYS* 3.2 31.2 + - + +
473J LEU* 3.3 22.9 + - - +
475J ARG* 5.7 1.0 + - - -
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Residues in contact with LEU 470 (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* 4.2 23.6 - - + -
468J LEU* 4.0 18.8 - - + +
469J ASP* 1.3 74.4 + - - +
471J GLU* 1.3 61.3 + - + +
473J LEU* 4.6 3.4 - - + -
474J GLU* 2.9 28.1 + - - +
499J VAL* 3.4 23.7 - - + +
502J PHE* 4.6 20.6 - - + -
503J LEU* 3.6 26.1 - - + +
507J ASN 5.9 0.2 - - - +
508J ARG* 5.2 10.3 - - - +
509J PRO* 4.3 27.6 - - + -
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Residues in contact with GLU 471 (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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469J ASP* 3.3 16.8 - - - +
470J LEU* 1.3 76.1 - - + +
472J LYS* 1.3 65.7 + - - +
474J GLU* 3.0 17.5 + - - +
475J ARG* 3.0 28.9 + - - +
503J LEU* 4.5 14.8 - - + -
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Residues in contact with LYS 472 (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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469J ASP* 3.2 32.0 + - + +
471J GLU* 1.3 79.7 - - - +
473J LEU* 1.3 60.7 + - + +
475J ARG* 3.2 28.0 - - + +
476J GLU* 2.9 45.4 + - + +
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Residues in contact with LEU 473 (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* 4.1 16.4 - - + -
468J LEU* 5.9 4.5 - - + -
469J ASP 3.3 15.3 + - - +
470J LEU* 4.0 6.5 - - + +
471J GLU 3.2 0.2 - - - -
472J LYS* 1.3 80.7 - - + +
474J GLU* 1.3 61.3 + - - +
476J GLU* 4.2 19.3 - - - +
477J LEU* 2.9 57.0 + - + +
495J ARG* 3.7 37.9 - - - +
499J VAL* 3.7 23.1 - - + -
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Residues in contact with GLU 474 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470J LEU 2.9 17.0 + - - +
471J GLU* 3.0 18.9 + - - +
473J LEU* 1.3 78.6 - - - +
475J ARG* 1.3 60.4 + - - +
478J LEU* 2.9 36.7 + - + +
496J LEU* 3.7 15.6 - - + +
499J VAL* 4.3 2.2 - - + +
500J ARG* 3.0 43.9 + - - +
503J LEU* 3.8 18.2 - - + +
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Residues in contact with ARG 475 (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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469J ASP* 5.7 1.2 + - - -
471J GLU* 3.0 12.9 + - - +
472J LYS* 3.2 38.0 - - + +
474J GLU* 1.3 79.3 - - - +
476J GLU* 1.3 63.1 + - - +
478J LEU* 3.1 17.2 + - + +
479J GLU* 2.9 28.3 + - + +
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Residues in contact with GLU 476 (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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472J LYS* 2.9 35.0 + - + +
473J LEU* 3.9 22.9 - - + +
475J ARG* 1.3 77.5 - - + +
477J LEU* 1.3 60.6 + - + +
479J GLU* 3.5 6.0 + - - +
480J GLU* 2.9 37.2 + - + +
495J ARG* 5.7 1.7 + - - -
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Residues in contact with LEU 477 (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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473J LEU* 2.9 41.7 + - + +
474J GLU 3.8 2.7 - - - +
476J GLU* 1.3 76.9 - - + +
478J LEU* 1.3 60.8 + - - +
480J GLU* 3.5 21.4 - - + +
481J MET* 2.9 28.4 + - - +
492J ALA* 4.3 18.2 - - - +
495J ARG* 3.6 47.8 - - + +
496J LEU* 3.7 34.6 - - + +
499J VAL* 4.0 4.5 - - + -
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Residues in contact with LEU 478 (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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474J GLU* 2.9 29.9 + - + +
475J ARG* 3.1 19.2 + - + +
477J LEU* 1.3 77.4 - - - +
479J GLU* 1.3 64.7 + - + +
481J MET* 3.1 15.7 + - + +
482J LYS* 3.2 18.7 + - - +
496J LEU* 3.7 16.6 - - + -
500J ARG* 3.7 28.0 - - - +
1390J LEU* 3.9 13.9 - - + -
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Residues in contact with GLU 479 (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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475J ARG* 2.9 17.6 + - + +
476J GLU* 3.9 5.4 - - - +
478J LEU* 1.3 79.0 - - + +
480J GLU* 1.3 59.8 + - - +
481J MET 3.3 0.2 - - - -
482J LYS* 3.4 44.5 + - - +
483J HIS* 4.0 3.8 + - - +
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Residues in contact with GLU 480 (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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476J GLU* 2.9 28.5 + - + +
477J LEU* 3.6 22.9 - - + +
478J LEU 3.1 0.4 - - - -
479J GLU* 1.3 74.9 - - - +
481J MET* 1.3 63.7 + - - +
483J HIS* 3.3 20.4 - - - +
488J ARG* 3.2 45.8 + - - +
489J ARG* 4.7 0.7 - - - -
492J ALA* 3.8 15.6 - - + +
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Residues in contact with MET 481 (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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477J LEU 2.9 14.2 + - - +
478J LEU* 3.1 8.5 + - + +
480J GLU* 1.3 74.4 - - - +
482J LYS* 1.3 57.3 + - + +
483J HIS 3.0 17.9 + - - +
489J ARG* 3.3 41.8 + - + +
492J ALA* 4.2 7.2 - - + +
493J ARG* 3.6 26.2 - - + +
496J LEU* 3.7 28.9 - - + -
1390J LEU* 4.0 24.2 - - + -
1391J GLU* 4.3 23.1 - - + +
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Residues in contact with LYS 482 (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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478J LEU* 3.2 15.9 - - + +
479J GLU* 3.4 42.8 + - - +
480J GLU 3.3 0.6 - - - -
481J MET* 1.3 74.1 - - + +
483J HIS* 1.3 64.9 + - - +
484J PRO* 3.5 5.4 - - - +
489J ARG* 5.1 1.7 + - - -
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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