Contacts of the strand formed by residues 122 - 125 (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 122 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D PHE* 3.6 27.1 - - + -
116D ILE* 3.7 22.1 - - - +
117D ILE 4.6 0.5 + - - -
118D ASP* 2.9 33.5 + - + +
119D GLU* 3.8 14.4 - - - +
121D GLU* 1.3 79.7 - - - +
123D GLN* 1.3 64.8 + - - +
132D VAL* 4.4 9.4 - - + +
133D THR 3.3 7.6 - - - -
135D SER* 3.3 5.2 + - - -
140D ARG* 4.7 0.9 - - - +
143D ILE* 4.5 15.9 - - + -
144D GLN 5.0 8.2 + - - +
145D VAL* 4.9 3.1 - - + +
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Residues in contact with GLN 123 (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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116D ILE* 4.4 11.8 - - - +
122D THR* 1.3 78.3 - - - +
124D PHE* 1.3 78.2 + - - +
125D MET* 4.8 3.4 - - - +
126D SER* 5.0 4.9 - - - +
132D VAL* 3.5 3.9 - - - +
133D THR* 2.8 51.9 + - - +
134D GLU 4.1 8.9 + - - -
135D SER* 3.4 22.4 + - - +
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Residues in contact with PHE 124 (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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114D PHE* 3.3 45.5 - - + -
115D GLN* 4.7 0.9 - - - -
116D ILE* 4.2 28.0 - - + +
123D GLN* 1.3 89.1 + - - +
125D MET* 1.3 63.9 + - - +
126D SER* 3.4 4.3 + - - -
129D PRO* 2.9 32.8 - - + +
130D VAL* 4.6 6.1 - - - -
131D ALA 3.2 13.0 - - - -
132D VAL* 3.9 8.5 - - + -
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Residues in contact with MET 125 (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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46D ARG* 5.3 8.1 - - - -
47D ILE* 4.1 6.7 - - + -
94D THR* 3.2 34.5 - - + -
123D GLN* 3.6 4.6 + - - +
124D PHE* 1.3 69.4 - - - +
126D SER* 1.3 62.1 + - - +
127D ASN* 3.3 6.5 - - + +
128D CYS* 2.9 51.9 - - - +
129D PRO* 3.2 7.3 - - - +
131D ALA* 3.0 24.9 + - + +
133D THR* 3.4 26.2 + - + +
169D ILE* 4.0 19.1 - - + -
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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