Contacts of the strand formed by residues 417 - 422 (chain B) in PDB entry 1U2Z
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 LEU 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ASP 3.4 1.8 + - - -
394B THR* 3.4 18.8 - - + +
395B PHE 2.8 26.0 + - - +
415B CYS* 3.0 4.0 - - - +
416B ALA* 1.3 82.1 - - + +
418B SER* 1.3 73.5 + - - +
419B PHE* 4.4 3.8 - - + -
451B ASN* 3.6 21.3 - - + +
453B GLU* 3.9 28.5 - - + +
465B ARG* 4.1 11.4 - - - +
469B LEU* 3.8 37.2 - - + -
472B GLN* 4.7 4.5 - - - +
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B PHE* 3.5 10.3 - - - -
406B VAL* 3.5 30.7 - - - +
409B ALA* 4.0 1.4 - - - +
410B ALA* 3.4 30.6 + - - +
415B CYS* 3.6 13.0 + - - +
417B LEU* 1.3 74.9 - - - +
419B PHE* 1.3 59.6 + - - +
451B ASN 3.0 12.5 + - - -
452B VAL* 3.4 2.9 - - - -
453B GLU 2.9 25.5 + - - +
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Residues in contact with PHE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B THR* 5.7 0.9 - - + -
395B PHE* 2.7 15.9 + - - +
396B MET* 3.2 30.5 - - + -
397B ASP 2.8 24.3 + - - -
406B VAL* 3.6 8.9 - - - +
417B LEU* 4.4 9.0 - - + -
418B SER* 1.3 74.9 - - - +
420B GLY* 1.3 70.6 + - - +
421B CYS* 4.2 2.5 - - + -
453B GLU* 3.2 44.9 - - + -
454B PHE 4.2 0.2 - - - -
455B SER* 3.5 34.5 - - - -
465B ARG* 3.9 18.2 - - + -
466B VAL* 3.9 23.8 - - + -
469B LEU* 3.7 20.2 - - + -
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Residues in contact with GLY 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ASP 3.4 9.2 - - - -
400B SER* 3.3 19.5 - - - -
406B VAL* 3.8 7.2 - - - +
419B PHE* 1.3 82.1 - - - +
421B CYS* 1.3 59.8 + - - +
453B GLU 3.0 8.9 + - - -
454B PHE* 3.1 9.7 - - - +
455B SER 2.8 24.1 + - - -
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Residues in contact with CYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ASP 3.2 8.2 + - - +
398B LEU* 5.2 1.8 - - + -
399B GLY* 2.8 30.5 + - - +
400B SER* 2.9 9.1 + - - -
419B PHE* 4.2 2.6 - - + -
420B GLY* 1.3 73.5 - - - -
422B GLU* 1.3 58.1 + - - +
455B SER* 3.2 13.9 - - - +
458B LYS 3.2 25.6 - - - -
460B PHE* 3.5 36.6 - - + -
463B ASN* 3.7 14.6 - - - -
466B VAL* 4.1 13.0 - - + -
802B SAH 3.9 1.4 + - - -
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B GLY 3.7 1.0 - - - -
400B SER* 3.5 12.3 + - - +
401B GLY* 2.8 42.4 + - - +
420B GLY 4.3 0.2 - - - -
421B CYS* 1.3 73.2 - - - +
423B ILE* 1.3 60.1 + - - +
424B MET* 2.9 25.8 + - - +
427B ALA* 3.9 11.7 - - + -
428B SER* 3.6 6.4 + - - +
455B SER 3.1 6.1 + - - +
456B LEU* 3.5 13.4 - - + +
457B LYS 2.9 24.1 + - - -
458B LYS 3.4 8.1 + - - +
802B SAH 2.7 49.1 + - - +
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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