Contacts of the helix formed by residues 217 - 222 (chain C) in PDB entry 3TQS
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 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C ARG 3.8 1.7 + - - +
216C LYS* 1.3 76.3 - - - +
218C VAL* 1.3 59.4 + - - +
219C GLY* 4.2 0.3 - - - -
220C ASN* 3.1 34.3 + - - +
221C ALA* 2.8 25.6 + - - +
238C PRO 3.3 14.9 + - - -
239C GLN* 3.4 36.3 + - - +
240C LEU 3.5 6.3 - - - -
241C ARG* 4.3 3.8 - - + +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ALA* 4.9 4.3 - - + -
216C LYS 3.7 1.2 + - - -
217C THR* 1.3 72.8 - - - +
219C GLY* 1.3 60.9 + - - +
221C ALA* 4.1 6.1 - - - -
222C LEU* 2.9 54.6 + - + +
231C TRP* 3.8 15.2 - - + -
236C ILE* 4.7 0.2 - - + -
237C ASN 4.0 5.4 - - - +
238C PRO* 3.6 18.6 - - + +
240C LEU 2.7 23.0 + - - +
242C PRO* 4.2 19.6 - - + +
245C LEU* 3.9 28.5 - - + -
250C PHE* 5.0 0.2 - - + -
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Residues in contact with GLY 219 (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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217C THR* 4.2 0.7 - - - -
218C VAL* 1.3 78.9 - - - +
220C ASN* 1.3 57.7 + - - +
222C LEU 3.7 1.0 - - - -
223C LYS* 3.1 27.7 + - - +
226C ILE 4.8 0.5 - - - +
231C TRP* 3.8 25.4 + - - -
238C PRO* 3.1 23.6 + - - -
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Residues in contact with ASN 220 (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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216C LYS* 4.4 17.9 + - + +
217C THR* 3.1 32.8 + - - +
219C GLY* 1.3 75.9 - - - +
221C ALA* 1.3 66.3 + - - +
222C LEU 3.2 0.5 + - - -
223C LYS* 3.3 37.5 + - + +
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Residues in contact with ALA 221 (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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209C GLU* 4.3 14.6 - - - +
210C ALA* 3.9 31.6 - - - +
213C TYR 5.1 1.1 - - - +
216C LYS* 3.9 24.7 + - + +
217C THR 2.8 21.1 + - - +
218C VAL* 3.7 9.2 - - - +
220C ASN* 1.3 73.2 - - - +
222C LEU* 1.3 66.3 + - + +
223C LYS* 3.7 1.2 + - - +
224C LYS* 5.0 1.4 + - - +
225C LEU* 5.8 0.2 - - - +
242C PRO* 5.4 0.4 - - + -
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Residues in contact with LEU 222 (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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206C VAL* 3.9 15.5 - - + +
209C GLU* 3.9 9.4 - - + -
210C ALA* 3.7 31.6 - - + +
218C VAL* 2.9 37.7 + - + +
219C GLY 3.7 2.7 - - - -
221C ALA* 1.3 83.9 - - + +
223C LYS* 1.3 54.4 + - - +
224C LYS* 3.1 4.0 - - - -
225C LEU* 2.7 45.1 + - + +
226C ILE* 2.8 16.8 + - + +
231C TRP* 4.0 17.5 - - + -
250C PHE* 5.2 1.6 - - + -
253C ILE* 4.1 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