Contacts of the strand formed by residues 94 - 98 (chain D) in PDB entry 2ZOT
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 THR 94 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 4.7 2.7 - - + -
93D PHE* 1.3 78.5 + - - +
95D LEU* 1.3 64.6 + - - +
96D ILE* 4.8 2.7 - - + -
125D MET* 3.2 31.0 - - + -
131D ALA* 4.9 0.4 - - + -
132D VAL 3.3 3.8 - - - +
133D THR* 3.6 8.1 - - + +
134D GLU* 5.3 0.2 + - - -
161D ALA* 3.2 4.5 - - - +
162D SER 2.7 38.6 + - - -
164D VAL 5.4 0.3 + - - -
165D GLN* 4.6 6.6 + - - -
169D ILE* 3.8 31.5 - - + +
171D PHE* 3.6 20.2 - - + -
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU* 3.6 33.2 - - + -
80D VAL* 4.4 8.5 - - + -
82D LEU* 5.6 1.1 - - + -
93D PHE* 4.4 11.7 - - + -
94D THR* 1.3 78.2 - - - +
96D ILE* 1.3 67.5 + - - +
114D PHE* 3.8 20.0 - - + -
131D ALA* 3.7 2.8 - - - -
132D VAL* 2.9 46.6 + - + +
143D ILE* 4.8 8.3 - - + -
145D VAL* 3.6 34.5 - - + -
159D LEU* 5.9 0.9 - - + -
160D LYS 3.3 14.1 - - - +
161D ALA* 4.2 5.6 - - + -
171D PHE* 4.7 0.2 - - - -
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.7 34.5 - - + -
94D THR* 4.8 0.2 - - + -
95D LEU* 1.3 79.8 - - - +
97D ALA* 1.3 61.9 + - - +
98D LEU* 3.6 31.0 - - + -
110D HIS* 4.0 14.6 - - + +
114D PHE* 3.8 11.0 - - - -
130D VAL 5.3 0.2 - - - -
131D ALA* 4.1 5.4 - - + -
159D LEU* 3.5 4.3 - - - +
160D LYS* 2.7 55.0 + - + +
171D PHE* 3.8 40.6 - - + -
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Residues in contact with ALA 97 (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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96D ILE* 1.3 76.2 - - - +
98D LEU* 1.3 61.5 + - - +
110D HIS* 3.4 11.9 - - + +
111D ALA* 2.8 46.0 + - - +
114D PHE* 3.8 13.2 - - + -
130D VAL* 5.9 1.1 - - + +
147D TRP* 3.5 23.6 - - + +
157D VAL* 5.6 2.0 - - + -
158D ILE 3.8 4.7 - - - -
159D LEU* 3.7 10.8 - - + -
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Residues in contact with LEU 98 (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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96D ILE* 3.6 28.9 - - + -
97D ALA* 1.3 72.4 - - - +
99D ARG* 1.3 66.5 + - - +
102D ARG* 3.2 28.0 - - + +
103D GLU 3.4 15.5 - - - +
104D GLY* 3.8 7.9 - - - +
109D ASP* 3.7 14.1 - - - +
110D HIS* 3.6 40.6 - - + +
111D ALA* 4.8 1.1 - - - -
157D VAL* 3.4 5.3 - - - -
158D ILE* 2.8 47.5 + - + +
160D LYS* 3.8 12.3 - - - +
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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