Contacts of the strand formed by residues 824 - 828 (chain Z) in PDB entry 5WTI
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 824 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523Z VAL* 5.4 4.5 - - + -
568Z LEU* 4.0 19.3 - - + -
569Z ARG 3.7 2.2 + - - -
570Z VAL* 3.6 26.1 - - + -
571Z MET 3.0 26.1 + - - -
822Z CYS* 3.9 3.6 - - - +
823Z GLN* 1.3 87.0 - - + +
825Z ILE* 1.3 69.3 + - - +
826Z LEU* 3.7 28.5 - - + -
869Z GLN* 3.2 19.5 - - + +
871Z GLY* 5.1 2.0 - - - +
963Z PHE* 4.2 17.9 - - + -
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Residues in contact with ILE 825 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571Z MET* 3.2 10.1 - - + +
573Z ILE* 4.1 14.8 - - + -
799Z ILE* 4.5 5.8 - - + -
800Z ILE* 4.3 4.3 - - + -
803Z ALA* 3.6 31.6 - - + -
822Z CYS* 5.3 1.3 - - + +
824Z ILE* 1.3 78.2 - - - +
826Z LEU* 1.3 62.8 + - - +
827Z PHE* 3.6 27.8 - - + -
859Z VAL* 3.8 21.3 - - + -
868Z LEU* 4.1 21.5 - - + -
869Z GLN 2.8 13.8 + - - +
870Z VAL* 3.2 12.6 - - + +
871Z GLY 2.9 26.5 + - - +
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Residues in contact with LEU 826 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570Z VAL* 3.6 27.4 - - + -
571Z MET 2.7 10.8 + - - +
572Z SER* 3.3 13.5 - - - -
573Z ILE* 2.6 35.3 + - - +
824Z ILE* 3.7 21.1 - - + -
825Z ILE* 1.3 74.8 - - - +
827Z PHE* 1.3 57.8 + - - +
871Z GLY* 3.3 13.9 - - - +
873Z VAL* 4.2 20.0 - - + -
959Z LEU* 4.4 9.4 - - + +
960Z GLN* 4.9 3.1 - - - -
963Z PHE* 3.7 43.3 - - + -
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Residues in contact with PHE 827 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573Z ILE* 3.6 33.9 - - + -
575Z LEU* 4.3 10.8 - - + -
799Z ILE* 4.2 5.8 - - + -
825Z ILE* 3.6 19.3 - - + -
826Z LEU* 1.3 77.0 - - - +
828Z GLU* 1.3 66.5 + - - +
855Z ILE* 4.1 17.0 - - + -
856Z PRO* 3.7 31.0 - - + -
859Z VAL* 3.8 30.7 - - + -
870Z VAL* 3.6 32.8 - - + -
871Z GLY 2.9 9.4 + - - +
872Z GLU* 3.2 8.9 - - + -
873Z VAL* 2.9 26.5 + - - +
959Z LEU* 4.1 3.8 - - - -
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Residues in contact with GLU 828 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573Z ILE 3.3 13.1 + - - +
574Z ASP* 3.1 17.8 - - - +
575Z LEU* 3.1 28.6 + - + +
827Z PHE* 1.3 77.0 - - - +
829Z ASP* 1.3 60.0 + - - +
830Z LEU* 2.9 41.5 + - + +
850Z TRP* 5.4 0.5 - - - -
856Z PRO* 5.8 0.9 - - - +
872Z GLU* 4.3 2.4 - - - +
873Z VAL 3.7 5.8 - - - -
875Z ALA* 3.7 25.7 - - + +
878Z SER* 4.6 1.2 + - - -
959Z LEU* 3.7 11.4 - - + +
1202Z MG 2.6 22.9 - - - -
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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