Contacts of the strand formed by residues 479 - 484 (chain A) in PDB entry 1UPX
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 ILE 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LYS* 3.9 0.8 - - - +
393A PHE* 3.3 27.4 - - + +
395A VAL* 3.8 16.4 - - + -
423A LEU* 5.3 5.2 - - + -
462A ALA* 4.1 14.1 - - + -
465A LEU* 5.0 6.1 - - + -
474A VAL 5.4 0.4 - - - +
475A ASN 5.5 1.4 - - - +
477A LEU* 2.9 44.8 + - + +
478A PRO* 1.3 79.3 - - + +
480A VAL* 1.3 74.7 + - - +
481A TYR* 3.5 44.4 - - + +
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Residues in contact with VAL 480 (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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392A LYS* 4.1 10.1 - - + -
393A PHE 2.9 9.7 + - - +
394A VAL* 3.2 17.4 - - + +
395A VAL 2.8 31.4 + - - -
412A PHE* 5.3 0.4 - - + -
479A ILE* 1.3 79.5 - - - +
481A TYR* 1.3 61.3 + - - +
482A ASN* 4.6 0.7 - - + +
506A HIS* 4.1 20.4 - - + +
542A PHE* 3.6 37.9 - - + +
543A PHE* 3.8 26.9 - - + -
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Residues in contact with TYR 481 (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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395A VAL* 3.7 35.2 - - + -
462A ALA* 4.4 10.9 - - + +
474A VAL* 4.9 8.9 + - - +
475A ASN* 5.0 6.7 - - - -
479A ILE* 3.5 41.0 - - + +
480A VAL* 1.3 75.1 - - - +
482A ASN* 1.3 59.5 + - - +
483A ILE* 3.8 12.6 - - + -
497A LEU* 5.0 9.6 - - + -
502A VAL* 3.6 41.1 - - + +
503A LYS 4.2 11.0 - - - -
504A ASN* 4.8 3.7 + - + -
505A ILE* 3.9 21.5 - - + -
506A HIS* 2.9 36.9 + - - -
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Residues in contact with ASN 482 (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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394A VAL* 4.2 15.0 - - + -
395A VAL 2.8 12.8 + - - +
396A MET* 3.3 24.2 - - + +
408A TYR* 3.0 30.0 + - - -
409A TYR* 4.0 12.1 + - - -
412A PHE* 3.4 29.6 - - + -
480A VAL* 4.0 1.7 + - + -
481A TYR* 1.3 71.3 - - - +
483A ILE* 1.3 59.5 + - - +
484A ALA 4.0 0.2 + - - -
506A HIS* 3.5 8.7 - - - +
532A ILE* 3.6 23.4 - - - +
542A PHE* 3.6 12.8 - - + -
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Residues in contact with ILE 483 (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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395A VAL* 4.0 24.9 - - + +
397A ALA* 3.4 22.4 - - + +
398A GLY* 4.6 2.0 - - - -
409A TYR* 3.7 3.9 + - - -
481A TYR* 4.4 8.1 - - + -
482A ASN* 1.3 78.3 - - - +
484A ALA* 1.3 71.6 + - - +
485A TRP* 5.2 1.3 - - + -
490A ALA* 6.1 2.2 - - + +
493A VAL* 5.8 5.8 - - + -
494A LEU* 5.9 4.9 - - + -
497A LEU* 3.7 29.4 - - + -
505A ILE* 4.1 20.0 - - + -
506A HIS 2.9 10.4 + - - +
507A LEU* 3.4 18.2 - - + +
508A GLY 3.0 23.9 + - - -
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Residues in contact with ALA 484 (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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396A MET 4.8 1.1 + - - +
397A ALA 3.3 4.8 + - - -
398A GLY* 3.1 8.7 - - - -
399A CYS 2.9 36.1 + - - +
406A ARG* 3.8 9.2 - - - +
409A TYR* 3.8 27.6 - - + -
428A ALA* 4.2 12.6 - - + -
482A ASN 4.0 1.4 + - - -
483A ILE* 1.3 78.7 - - - +
485A TRP* 1.3 60.5 + - - +
490A ALA* 4.8 0.3 - - - +
508A GLY 3.2 5.6 - - - +
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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