Contacts of the strand formed by residues 207 - 213 (chain I) in PDB entry 6G2T
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 207 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I LEU* 3.8 46.9 - - + +
202I LYS* 4.2 13.6 + - + +
203I VAL* 3.6 17.7 - - + +
204I GLY 3.1 27.3 + - - +
206I HIS* 1.3 82.0 - - + +
208I GLN* 1.3 69.7 + - - +
209I LEU* 4.1 16.8 - - + -
224I LEU* 3.7 22.0 - - + -
225I HIS 3.4 9.0 - - - +
226I ILE* 4.6 12.8 - - + -
233I PHE* 6.1 1.1 - - + -
237I TYR* 6.2 0.7 - - + -
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Residues in contact with GLN 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I VAL* 4.5 10.9 - - - +
204I GLY* 2.7 33.1 + - - +
205I GLN* 4.8 4.5 + - - +
207I LEU* 1.3 76.1 + - - +
209I LEU* 1.3 71.2 + - - +
224I LEU* 4.2 1.4 - - - +
225I HIS* 2.8 50.3 + - + +
227I THR* 5.8 6.3 - - + +
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Residues in contact with LEU 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I VAL 6.2 0.4 - - - +
191I TRP* 3.5 29.8 - - + +
199I LEU* 5.5 0.2 - - + -
200I SER* 4.0 34.1 - - - +
203I VAL* 4.2 13.3 - - + +
207I LEU* 4.1 7.4 - - + -
208I GLN* 1.3 79.3 + - - +
210I HIS* 1.3 63.0 + - - +
211I ASP* 5.7 3.4 - - - +
223I GLU 3.7 5.6 - - - +
224I LEU* 3.5 31.6 - - + -
225I HIS* 4.9 0.7 - - - -
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Residues in contact with HIS 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I LEU* 1.3 74.8 + - - +
211I ASP* 1.3 79.6 + - - +
212I SER* 3.8 25.3 - - - -
221I LEU 4.2 0.3 - - - +
222I PHE* 3.8 0.2 - - - -
223I GLU* 2.8 56.6 + - + +
225I HIS* 4.1 21.0 - - + +
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Residues in contact with ASP 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I VAL* 4.0 13.6 - - - +
191I TRP* 5.5 0.9 + - - -
209I LEU* 5.7 2.4 - - - +
210I HIS* 1.3 95.6 + - - +
212I SER* 1.3 61.6 + - - +
221I LEU 3.9 2.7 - - - -
222I PHE* 3.2 33.2 - - + +
223I GLU 4.5 0.5 + - - +
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Residues in contact with SER 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210I HIS* 3.8 20.0 + - - -
211I ASP* 1.3 76.5 - - - +
213I TYR* 1.3 62.8 + - - +
220I TYR* 3.9 6.0 - - - +
221I LEU* 3.0 59.0 + - - +
222I PHE* 4.9 1.9 - - - -
223I GLU* 5.6 0.2 - - - -
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Residues in contact with TYR 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I SER* 1.3 78.1 - - - +
214I ASP* 1.3 72.1 + - - +
215I ARG* 3.0 44.7 + - + -
218I LYS* 5.2 10.6 - - - +
219I VAL 4.6 2.9 - - - -
220I TYR* 3.2 51.0 + + + -
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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