Contacts of the strand formed by residues 212 - 217 (chain C) in PDB entry 1SOT
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 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C VAL* 4.7 1.3 - - + -
85C MSE 3.6 37.5 - - + -
141C ILE* 4.0 13.7 - - + -
142C PRO 3.0 17.1 + - - +
143C ILE* 4.0 16.9 - - + +
144C ASN 5.6 0.7 + - - -
204C ALA* 3.9 20.6 - - + -
205C LEU 3.7 6.3 - - - +
206C VAL* 4.0 3.4 - - + -
210C GLY 3.7 1.0 + - - -
211C GLU* 1.3 72.3 - - - +
213C MSE 1.3 60.4 + - - +
214C GLY 3.1 31.6 - - - +
215C ILE* 4.3 12.3 - - + -
238C PHE* 3.1 35.6 - - + +
241C ALA* 5.8 0.9 - - + -
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Residues in contact with MSE 213 (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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44B PRO* 6.1 0.2 - - + -
147C ARG* 5.0 6.3 - - + -
149C PRO* 3.7 27.0 - - + +
153C ASP* 3.3 27.8 - - + +
155C VAL* 4.1 4.9 - - + -
173C ILE* 3.3 28.0 - - + -
190C LEU* 4.0 14.7 - - + +
205C LEU* 2.7 24.5 + - + +
206C VAL 4.0 2.0 - - - -
207C ASN* 3.7 48.7 - - + +
211C GLU* 3.9 0.9 - - - +
212C LEU* 1.3 78.1 - - - +
214C GLY* 1.3 58.3 + - - +
237C PRO* 3.6 5.2 - - - +
238C PHE* 2.8 29.9 + - - +
239C GLN* 4.6 0.7 + - - -
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Residues in contact with GLY 214 (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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190C LEU* 5.1 0.9 - - - -
204C ALA 3.9 0.2 - - - -
205C LEU* 3.0 34.1 + - - +
212C LEU* 3.1 13.2 - - - +
213C MSE 1.3 83.0 - - - +
215C ILE* 1.3 65.1 + - - -
235C ALA* 4.5 4.3 - - - -
236C ILE 3.0 14.8 - - - -
238C PHE* 3.7 6.3 - - - -
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Residues in contact with ILE 215 (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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83C VAL* 3.8 29.6 - - + -
85C MSE 4.8 0.2 - - - -
92C ILE* 3.9 30.3 - - + -
93C THR 4.9 0.7 - - - +
94C ASN* 4.5 1.6 - - - +
127C LEU* 3.9 22.7 - - + -
202C GLY* 3.8 15.7 - - - +
203C GLY 3.5 6.7 - - - +
212C LEU* 4.3 14.4 - - + -
214C GLY* 1.3 77.3 - - - +
216C ASN* 1.3 73.2 + - - +
217C THR 3.4 0.5 + - - -
235C ALA* 3.0 3.1 - - - -
236C ILE* 2.8 36.2 + - + +
241C ALA* 4.0 20.6 - - + -
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Residues in contact with ASN 216 (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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94C ASN* 3.3 7.4 + - - -
157C ALA* 4.2 5.2 - - - +
158C ILE 4.2 1.9 + - - +
196C ILE* 3.0 40.0 - - + +
200C ASN* 3.9 18.9 - - - +
201C SER* 4.4 0.7 - - - -
202C GLY* 2.7 28.5 + - - +
203C GLY* 2.9 17.8 + - - +
204C ALA 3.1 20.5 + - - +
205C LEU* 3.3 30.3 - - - +
215C ILE* 1.3 71.8 - - - +
217C THR* 1.3 56.0 + - - +
234C PHE 3.8 4.3 - - - -
235C ALA* 4.0 4.2 - - - +
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Residues in contact with THR 217 (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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94C ASN* 3.7 13.7 - - - +
126C ASP* 3.0 29.1 + - - +
189C PHE* 4.3 16.2 - - + -
196C ILE* 4.0 8.6 - - - +
201C SER* 4.4 0.7 - - - -
216C ASN* 1.3 75.3 - - - +
218C LEU* 1.3 64.3 + - - +
219C SER* 3.9 9.4 + - - +
220C PHE 5.5 0.2 + - - -
234C PHE* 3.0 36.6 + - + +
235C ALA* 4.1 3.1 - - - +
236C ILE* 4.0 22.0 - - + -
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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