Contacts of the strand formed by residues 441 - 447 (chain D) in PDB entry 2UZ1
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 ARG 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386D GLY 2.8 11.6 + - - +
387D VAL* 3.2 14.0 - - + +
388D THR 2.9 21.6 + - - -
432D GLN* 3.8 10.1 + - - -
435D ASP* 4.3 0.7 - - - -
439D GLY 4.2 0.2 + - - -
440D ARG* 1.3 74.1 - - - +
442D THR* 1.3 66.5 + - - +
443D ILE* 5.0 0.9 - - + -
467D PRO* 2.8 41.0 + - - +
469D ILE* 3.4 14.6 - - + +
531D ALA 3.3 10.9 + - - -
532D LEU* 3.2 41.2 + - + +
534D HIS 3.0 29.5 + - - -
535D ASN* 4.7 1.5 - - - +
536D ARG 3.2 15.0 + - - -
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Residues in contact with THR 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D THR* 3.4 10.3 - - - +
390D VAL* 4.0 20.4 - - + -
428D ALA 3.6 19.1 - - - +
431D ALA* 4.0 7.6 - - + -
432D GLN* 2.9 37.5 + - - +
435D ASP* 2.7 21.7 + - - +
441D ARG* 1.3 76.7 - - - +
443D ILE* 1.3 66.7 + - - +
468D LEU* 3.5 15.1 - - + +
469D ILE* 3.3 22.0 + - - +
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Residues in contact with ILE 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ILE* 4.9 13.5 - - + -
382D HIS* 5.1 6.7 - - + -
383D VAL* 5.6 1.1 - - + -
387D VAL* 3.9 25.4 - - + -
388D THR 2.8 10.2 + - - +
389D VAL* 3.4 6.5 - - + +
390D VAL* 2.9 25.1 + - - +
441D ARG* 4.7 1.6 - - + +
442D THR* 1.3 80.1 - - - +
444D LEU* 1.3 64.0 + - - +
445D VAL* 3.9 10.5 + - + -
468D LEU* 4.4 1.1 - - - -
469D ILE* 3.5 14.1 - - + +
471D ILE* 3.6 29.6 - - + -
528D LEU* 4.7 10.3 - - + -
532D LEU* 4.0 30.1 - - + -
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Residues in contact with LEU 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D VAL* 3.4 20.9 - - + +
392D ASP* 4.3 3.1 - - + -
424D GLY* 3.5 25.6 - - - +
425D PHE* 3.7 31.0 - - + +
428D ALA* 3.8 14.4 - - + -
443D ILE* 1.3 71.2 - - - +
445D VAL* 1.3 66.4 + - - +
446D THR* 4.1 23.8 - - + -
468D LEU* 3.9 5.5 - - + +
469D ILE 2.8 13.6 + - - +
470D VAL* 3.9 28.7 - - + -
471D ILE* 2.8 35.9 + - - +
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Residues in contact with VAL 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ILE* 3.9 33.4 - - + -
389D VAL* 4.2 8.7 - - + -
390D VAL 2.7 13.5 + - - +
391D ALA* 3.3 3.3 - - - +
392D ASP 2.9 25.8 + - - +
396D THR* 3.9 19.2 - - + +
400D LEU* 3.9 30.3 - - + -
443D ILE* 4.1 14.6 - - + -
444D LEU* 1.3 76.8 - - - +
446D THR* 1.3 60.4 + - - +
471D ILE* 3.6 5.8 - - + +
473D MET* 4.1 13.5 - - + -
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Residues in contact with THR 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D ASP* 3.3 28.3 + - - +
396D THR* 3.8 5.3 - - - +
444D LEU* 4.1 13.5 - - + -
445D VAL* 1.3 74.1 - - - +
447D GLY* 1.3 66.7 + - - +
450D SER* 3.4 14.0 - - - -
451D VAL* 3.9 30.7 + - + -
470D VAL* 4.1 14.1 - - + -
471D ILE 2.9 16.3 + - - +
472D ILE* 3.5 4.6 - - + -
473D MET* 2.7 28.4 + - - +
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Residues in contact with GLY 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D GLY* 3.9 9.1 - - - -
396D THR* 3.8 10.3 - - - -
446D THR* 1.3 81.4 + - - +
448D ASP* 1.3 66.3 + - - -
449D GLY 3.2 2.9 - - - -
450D SER 3.3 0.3 + - - -
451D VAL* 3.0 24.3 + - - +
472D ILE* 3.9 2.9 - - - -
473D MET 3.5 8.5 - - - -
1556D TPP 3.6 17.3 - - - -
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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