Contacts of the strand formed by residues 454 - 463 (chain A) in PDB entry 1UUR
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 ASN 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A THR 3.7 0.2 - - - +
408A MET* 3.6 2.3 - - - -
409A ILE* 2.8 41.5 + - + +
411A ASP* 4.1 7.1 - - - +
453A VAL* 1.3 79.5 + - - +
455A LEU* 1.3 61.7 + - - +
456A LYS* 6.0 0.2 - - + -
475A ALA* 3.7 25.2 - - + +
476A SER* 2.8 28.7 + - - +
477A ASN 4.4 0.2 - - - -
478A PRO* 3.5 21.0 - - - +
479A PHE* 4.1 5.8 - - - -
498A LYS* 3.8 21.8 + - - +
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Residues in contact with LEU 455 (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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371A PHE* 4.1 8.3 - - + -
386A LEU* 3.7 16.8 - - + -
406A ALA* 4.6 2.2 - - + -
407A THR 3.5 2.9 - - - +
408A MET* 3.8 25.1 - - + +
424A LEU* 3.9 19.1 - - + -
442A LEU* 3.1 32.1 - - + -
454A ASN* 1.3 73.9 - - - +
456A LYS* 1.3 61.0 + - - +
457A PHE* 3.8 23.1 - - + -
474A ASP 4.1 1.4 - - - +
475A ALA* 3.5 5.9 - - - -
476A SER* 2.8 36.7 + - - +
479A PHE* 3.8 26.6 - - + -
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Residues in contact with LYS 456 (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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405A LYS 3.4 2.4 - - - +
406A ALA* 3.5 1.0 - - - -
407A THR* 2.8 38.6 + - - +
409A ILE* 3.3 33.9 - - + -
455A LEU* 1.3 77.6 - - - +
457A PHE* 1.3 62.9 + - - +
472A GLU* 4.6 25.5 + - + +
473A SER* 2.9 33.2 + - - +
474A ASP* 4.1 6.8 + - - +
475A ALA* 3.7 22.2 - - + +
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Residues in contact with PHE 457 (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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364A LEU* 3.8 14.4 - - + -
366A LEU* 3.6 26.9 - - + -
386A LEU* 4.0 14.4 - - + -
388A VAL* 3.4 29.6 - - + -
404A VAL* 4.1 2.5 - - + -
405A LYS 3.0 8.3 - - - +
406A ALA* 3.8 7.4 - - + -
440A PHE* 3.6 43.1 - + - -
455A LEU* 3.8 38.6 - - + -
456A LYS* 1.3 76.9 - - - +
458A GLY* 1.3 59.0 + - - +
472A GLU* 3.2 8.5 - - - +
473A SER* 2.9 46.8 + - - +
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Residues in contact with GLY 458 (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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364A LEU* 3.7 2.6 - - - +
403A PRO 4.1 1.0 - - - +
405A LYS* 2.9 35.6 + - - +
457A PHE* 1.3 77.0 - - - +
459A VAL* 1.3 64.7 + - - +
470A THR* 4.7 4.7 - - - -
471A VAL 3.1 12.8 - - - -
472A GLU* 4.1 9.6 - - - -
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Residues in contact with VAL 459 (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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362A VAL* 6.0 0.4 - - + -
364A LEU* 3.4 26.7 - - + -
390A VAL* 5.9 0.7 - - + -
400A ILE* 4.7 15.7 - - + -
401A ASN 5.2 0.4 - - - +
403A PRO 4.2 6.3 - - - +
404A VAL* 3.1 45.5 - - + +
431A ILE* 4.9 4.7 - - + -
458A GLY* 1.3 78.8 - - - +
460A ASN* 1.3 65.7 + - - +
461A ILE* 3.1 22.1 - - + +
470A THR* 3.4 4.3 - - - +
471A VAL 2.9 27.8 + - - +
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Residues in contact with ASN 460 (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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400A ILE* 3.7 4.0 - - - +
401A ASN* 2.8 49.8 + - + +
402A GLY* 6.0 0.8 - - - -
403A PRO 5.2 0.4 + - - -
459A VAL* 1.3 72.9 - - - +
461A ILE* 1.3 63.9 + - - +
468A THR* 4.3 17.8 - - + +
469A THR 3.7 2.5 - - - +
470A THR* 2.5 32.6 + - - +
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Residues in contact with ILE 461 (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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360A PRO* 3.9 22.0 - - + -
362A VAL* 4.1 18.6 - - + -
398A PHE* 3.5 34.8 - - + -
399A HIS 3.5 2.9 - - - -
400A ILE* 4.3 13.9 - - + -
401A ASN* 4.5 0.4 - - - -
459A VAL* 3.1 43.7 - - + +
460A ASN* 1.3 76.7 - - - +
462A ARG* 1.3 64.0 + - - +
467A VAL 3.7 1.4 - - - +
468A THR* 3.4 5.3 - - - +
469A THR* 2.9 34.4 + - - +
471A VAL* 3.9 15.9 - - + -
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Residues in contact with ARG 462 (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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398A PHE* 3.5 1.4 - - - +
399A HIS* 2.8 39.4 + - + +
401A ASN* 3.1 31.8 - - - +
461A ILE* 1.3 74.9 - - - +
463A ASP* 1.3 78.4 + - - +
466A ASN* 2.9 49.3 + - - +
467A VAL 3.6 2.5 - - - -
468A THR* 3.4 21.0 + - - +
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Residues in contact with ASP 463 (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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360A PRO* 4.5 18.5 - - + +
397A ASN 4.2 7.4 - - - +
398A PHE* 4.4 7.8 - - - +
399A HIS* 5.9 0.9 + - - -
461A ILE* 3.9 3.7 + - - +
462A ARG* 1.3 85.7 - - - +
464A LEU* 1.3 67.8 + - - +
465A ASP* 3.0 40.5 + - - +
466A ASN* 3.3 8.5 + - - +
467A VAL* 2.7 39.1 + - + +
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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