Contacts of the strand formed by residues 144 - 147 (chain C) in PDB entry 2OTD
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 LEU 144 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C TRP* 3.7 26.5 - - + -
6C TYR* 3.7 14.3 + - + -
37C MSE 4.2 15.9 - - + -
111C ALA 2.9 13.8 + - - +
112C ASN* 2.8 20.9 + - + +
113C ILE 2.8 30.3 + - - -
142C PRO 3.7 2.2 + - - -
143C PRO* 1.3 68.9 - - - +
145C LEU* 1.3 57.4 + - - +
164C PRO* 4.0 15.0 - - + +
166C GLY 4.3 4.9 - - - +
186C VAL* 3.9 19.3 - - + -
187C SER* 3.7 17.5 - - - +
189C HIS* 3.6 25.8 - - + -
211C LEU* 4.8 4.5 - - + -
231C CYS* 5.7 0.7 - - - -
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ILE* 3.5 30.5 - - + +
115C ILE* 4.2 17.3 - - + -
129C VAL* 5.1 1.8 - - + -
130C ALA* 4.1 30.1 - - + -
133C ALA* 4.3 6.7 - - + -
143C PRO* 4.0 16.8 - - + +
144C LEU* 1.3 73.5 - - - +
146C SER* 1.3 60.0 + - - +
153C LEU* 4.2 2.5 - - + +
156C ALA* 4.1 15.7 - - + +
160C ALA 5.6 0.4 - - - +
163C LEU* 4.1 20.9 - - + -
164C PRO 3.0 13.4 + - - +
165C ARG* 3.1 13.4 - - + +
166C GLY 2.8 24.7 + - - +
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ASN* 3.0 24.4 + - - -
113C ILE 3.0 5.9 + - - -
114C GLU* 3.3 8.8 - - - +
115C ILE* 2.8 29.1 + - - +
144C LEU 3.7 1.2 + - - -
145C LEU* 1.3 74.7 - - - +
147C SER* 1.3 64.3 + - - +
153C LEU* 4.4 3.4 - - - -
166C GLY 3.2 13.5 - - - -
168C LEU* 3.2 23.1 - - - +
189C HIS* 4.0 16.1 + - - -
301D PO4 4.9 0.7 + - - -
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLU* 4.5 1.6 - - - -
115C ILE* 3.0 28.5 + - - -
146C SER* 1.3 80.3 - - - +
148C PHE* 1.3 61.8 + - - +
149C GLU* 2.8 33.6 + - - +
152C ALA* 4.0 4.9 - - - +
153C LEU* 3.6 22.6 - - - +
166C GLY 3.4 4.4 + - - -
167C LEU* 4.3 1.6 - - - +
168C LEU* 3.1 25.8 + - - +
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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