Contacts of the strand formed by residues 75 - 83 (chain 8) in PDB entry 4UOW
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 GLY 75 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408 CYS* 4.4 6.1 - - - -
738 ASP 3.4 4.5 + - - -
748 GLY* 1.3 74.2 - - - -
768 LEU* 1.3 59.4 + - - -
778 TYR* 3.4 11.9 - - - -
938 ASN* 3.6 8.5 - - - +
948 ILE 2.9 34.5 + - - -
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Residues in contact with LEU 76 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128 SER 5.6 0.2 - - - +
398 SER 4.0 0.2 - - - +
408 CYS* 3.8 19.4 - - - -
418 GLY 4.1 4.2 + - - -
758 GLY* 1.3 69.3 - - - -
778 TYR* 1.3 61.0 + - - +
788 THR* 3.9 7.2 + - - +
918 THR* 3.9 37.0 - - + +
928 VAL 3.8 0.9 - - - -
938 ASN* 3.8 35.0 - - + +
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Residues in contact with TYR 77 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388 TRP* 4.4 8.5 - + + -
398 SER 3.4 5.4 - - - -
408 CYS* 3.8 22.9 - - + -
458 ILE* 3.9 28.5 - - + -
538 PHE* 3.4 27.7 - + - -
648 LEU* 3.9 15.3 - - + -
668 ILE* 3.8 12.6 - - + +
738 ASP* 2.6 33.7 + - - -
758 GLY 3.4 17.0 - - - -
768 LEU* 1.3 72.1 - - - +
788 THR* 1.3 59.7 + - - +
798 LEU 4.2 0.4 + - - -
908 ALA 3.9 0.2 - - - +
918 THR* 3.2 4.9 - - - -
928 VAL* 2.8 51.0 + - + +
948 ILE* 3.5 22.0 - - + -
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Residues in contact with THR 78 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378 THR 3.2 6.4 - - - +
388 TRP* 3.5 3.1 - - - -
398 SER* 2.7 49.2 + - - +
768 LEU* 4.0 8.1 + - - +
778 TYR* 1.3 73.3 - - - +
798 LEU* 1.3 63.1 + - - +
808 SER* 3.7 6.5 + - - +
898 SER* 4.3 15.0 - - - -
908 ALA 3.4 14.1 - - - +
918 THR* 3.4 21.6 - - + +
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Residues in contact with LEU 79 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78 ILE* 3.4 23.8 - - + +
108 LEU* 4.1 9.8 - - + +
268 CYS* 3.7 26.2 - - + -
288 PHE* 5.9 0.9 - - + -
368 VAL* 3.8 15.7 - - + -
378 THR 3.8 2.7 - - - +
388 TRP* 3.7 43.8 - - + +
628 THR* 3.7 26.9 - - + -
778 TYR 4.2 1.2 + - - -
788 THR* 1.3 71.1 - - - +
808 SER* 1.3 62.3 + - - +
818 LEU* 4.4 9.2 - - + -
898 SER* 3.3 4.0 - - - -
908 ALA 2.9 34.3 + - - +
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Residues in contact with SER 80 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358 GLU 3.2 4.2 - - - +
378 THR* 2.9 54.9 + - - +
398 SER* 4.4 6.2 + - - -
788 THR* 3.8 9.1 + - - +
798 LEU* 1.3 77.3 - - - +
818 LEU* 1.3 64.0 + - - +
888 ASP 3.4 7.6 - - - -
898 SER* 4.2 11.4 - - - -
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Residues in contact with LEU 81 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58 PRO* 3.8 14.4 - - + -
68 LYS* 3.7 22.9 - - - +
78 ILE* 3.5 30.1 - - + +
288 PHE* 3.6 36.1 - - + -
298 THR 4.6 0.2 - - - +
348 PRO* 3.9 5.2 - - + -
358 GLU 3.4 4.9 - - - -
368 VAL* 3.8 28.9 - - + -
798 LEU* 4.4 11.9 - - + -
808 SER* 1.3 77.8 - - - +
828 GLY* 1.3 57.8 + - - +
878 SER* 3.3 7.4 - - - -
888 ASP* 2.9 30.2 + - + +
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Residues in contact with GLY 82 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58 PRO* 3.8 2.9 - - - -
348 PRO* 3.4 5.2 - - - +
358 GLU* 2.8 37.7 + - - +
818 LEU* 1.3 77.8 - - - +
838 ASN* 1.3 61.7 + - - -
868 GLY 3.5 11.0 - - - -
878 SER* 4.2 3.8 - - - -
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Residues in contact with ASN 83 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38 ILE 3.0 24.4 + - - -
58 PRO* 3.3 24.2 - - - +
308 GLY* 4.1 2.4 - - - -
318 GLU 3.8 6.7 + - - +
328 PRO* 3.0 35.8 + - + +
338 THR 4.8 1.1 - - - +
348 PRO* 4.2 5.3 - - + +
828 GLY* 1.3 75.9 - - - +
848 GLU* 1.3 62.7 + - - +
858 PHE* 2.9 29.6 + - - +
868 GLY 3.2 13.7 + - - +
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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