Contacts of the strand formed by residues 470 - 475 (chain A) in PDB entry 1JXO
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 TRP 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A TYR* 3.5 26.2 - - - -
451A ALA* 5.2 6.1 - - + -
464A ASP 4.5 1.4 - - - +
467A ASP* 2.8 43.9 + - - +
469A GLU* 1.3 90.9 - - + +
471A TRP* 1.3 64.6 + - - +
472A GLN 4.1 0.5 + - - -
487A PHE* 3.9 35.4 - + + -
488A ILE* 3.5 20.6 - - - -
489A PRO* 3.7 15.5 - - + -
493A ARG* 3.4 39.4 - - - +
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Residues in contact with TRP 471 (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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431A PHE* 4.0 21.5 - + - -
433A ILE* 4.0 23.8 - - + -
462A VAL* 4.0 23.1 - - + -
464A ASP 3.6 4.3 - - - +
465A ALA* 3.5 30.9 + - + +
467A ASP 3.5 19.4 + - - -
468A GLU* 4.9 1.4 + - - +
470A TRP* 1.3 73.2 - - - +
472A GLN* 1.3 61.0 + - - +
487A PHE* 3.2 6.6 - - - -
488A ILE* 2.8 48.3 + - + +
490A SER* 3.4 25.5 - - - +
491A LYS* 3.7 34.1 - - + -
492A ARG 5.3 0.4 - - - -
523A TYR* 4.3 7.6 - + - -
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Residues in contact with GLN 472 (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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462A VAL* 3.5 4.0 - - - +
463A ILE* 3.0 49.3 + - + +
464A ASP* 2.8 35.1 + - + +
470A TRP 4.1 0.6 + - - -
471A TRP* 1.3 70.9 - - - +
473A ALA* 1.3 65.4 + - - +
485A ILE* 3.8 16.6 - - + +
486A GLY 3.3 11.7 - - - +
487A PHE* 3.9 28.9 - - + -
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Residues in contact with ALA 473 (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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452A LEU* 3.5 9.3 - - + +
460A LEU* 4.6 4.5 - - + -
461A HIS 2.9 28.7 - - - +
462A VAL* 3.7 12.6 - - + -
463A ILE* 4.3 2.5 - - - +
471A TRP 3.8 0.6 + - - -
472A GLN* 1.3 77.3 - - - +
474A ARG* 1.3 59.0 + - - +
485A ILE* 3.3 7.3 - - - +
486A GLY 2.7 40.6 + - - +
488A ILE* 4.2 16.8 - - + -
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Residues in contact with ARG 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 3.8 8.7 - - - -
460A LEU* 3.6 1.7 - - - -
461A HIS* 2.8 51.4 + - + +
463A ILE* 5.2 6.1 - - + -
473A ALA* 1.3 78.2 - - - +
475A ARG* 1.3 85.0 + - - +
476A VAL* 3.5 13.0 + - - +
485A ILE* 3.6 31.7 - - + +
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Residues in contact with ARG 475 (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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452A LEU* 4.1 11.2 - - + +
453A SER 3.7 21.9 + - - +
454A PHE* 4.0 3.1 - - - +
458A ASP* 3.5 39.9 + - - +
459A VAL 3.7 7.3 + - - +
460A LEU* 3.6 14.4 - - + -
474A ARG* 1.3 93.6 + - - +
476A VAL* 1.3 72.6 + - - +
485A ILE 5.4 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