Contacts of the strand formed by residues 963 - 966 (chain A) in PDB entry 1WZ2
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 ALA 963 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862A TYR* 3.2 2.8 - - - +
863A ILE* 3.1 30.3 + - + +
952A GLY 5.6 0.2 - - - +
953A LYS* 4.3 16.6 - - - +
956A GLN* 3.6 18.8 - - + +
957A ALA* 3.0 26.8 - - + +
961A LYS 4.6 0.2 - - - -
962A PRO* 1.3 74.6 - - - +
964A ILE* 1.3 60.0 + - - +
954C G 3.0 10.8 - - - +
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Residues in contact with ILE 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A VAL* 4.7 7.4 - - + -
845A ASP* 5.2 2.0 - - + -
846A ILE* 4.3 20.6 - - + -
849A ILE* 3.1 32.5 - - + -
860A ARG* 4.4 5.4 - - + +
861A ALA 3.5 0.2 - - - -
862A TYR* 3.4 31.4 - - + -
953A LYS* 5.7 1.6 - - - -
962A PRO* 4.1 5.6 - - + +
963A ALA* 1.3 78.0 - - - +
965A PHE* 1.3 67.7 - - - +
966A ILE* 3.3 33.2 - - + +
953C A 3.8 8.4 - - + -
954C G 2.6 36.0 + - + +
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Residues in contact with PHE 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A ARG* 3.3 0.3 - - - -
861A ALA 2.5 44.0 + - - +
950A LYS* 3.8 30.5 - - + -
951A GLY* 3.9 33.9 - - - +
953A LYS* 5.2 7.0 - - + -
964A ILE* 1.3 78.4 - - - +
966A ILE* 1.3 68.9 + - - +
967A GLU* 3.6 30.7 - - + -
953C A 3.4 27.6 - + - -
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Residues in contact with ILE 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A ILE* 3.9 12.6 - - + -
849A ILE* 3.9 14.8 - - + +
850A ILE* 4.0 29.2 - - + -
854A LYS* 3.6 33.4 - - + -
857A ASN* 4.6 3.4 - - + -
859A LYS 4.3 2.2 - - - +
860A ARG* 3.2 26.7 - - + -
940A ILE* 6.3 0.2 - - + -
964A ILE* 3.3 17.7 - - + -
965A PHE* 1.3 74.3 - - - +
967A GLU* 1.3 70.1 + - + +
953C A 2.6 54.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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