Contacts of the strand formed by residues 207 - 214 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L LEU* 3.6 48.0 - - + +
202L LYS* 3.9 14.5 + - + +
203L VAL* 3.5 27.3 - - + +
204L GLY 3.1 16.2 + - - +
205L GLN 3.6 0.4 - - - -
206L HIS* 1.3 80.8 - - + +
208L GLN* 1.3 83.1 + - - +
209L LEU* 4.2 14.4 - - + -
224L LEU* 3.9 14.4 - - + -
225L HIS 3.4 8.3 - - - +
226L ILE* 4.8 11.2 - - + -
233L PHE* 6.3 0.7 - - + -
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Residues in contact with GLN 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203L VAL* 3.6 17.2 - - - +
204L GLY* 2.9 27.5 + - - +
205L GLN 5.2 4.3 - - - +
207L LEU* 1.3 82.9 + - - +
209L LEU* 1.3 71.2 + - - +
224L LEU* 4.3 0.5 - - - +
225L HIS* 2.8 57.0 + - + +
227L THR* 5.8 4.3 - - + +
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Residues in contact with LEU 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L VAL 5.8 2.5 - - - +
191L TRP* 3.9 25.1 - - + +
199L LEU* 5.6 0.4 - - + -
200L SER* 4.3 29.8 - - - +
203L VAL* 4.5 9.8 - - + +
207L LEU* 4.2 9.9 - - + -
208L GLN* 1.3 81.2 - - - +
210L HIS* 1.3 62.6 + - - +
211L ASP* 5.6 5.6 - - - +
223L GLU 3.7 6.7 - - - +
224L LEU* 3.4 33.0 - - + -
225L HIS* 4.7 1.1 - - - -
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Residues in contact with HIS 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L LEU* 1.3 76.4 + - - +
211L ASP* 1.3 77.5 + - - +
212L SER* 4.1 19.4 + - - -
221L LEU* 3.9 2.3 - - + +
222L PHE* 3.9 1.0 - - - -
223L GLU* 3.0 51.9 + - + +
225L HIS* 3.9 21.5 - - + +
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Residues in contact with ASP 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L VAL* 3.9 15.1 - - - +
191L TRP* 5.6 0.5 + - - -
209L LEU* 4.4 4.6 - - - +
210L HIS* 1.3 93.2 + - - +
212L SER* 1.3 62.4 + - - +
221L LEU 3.9 2.9 - - - -
222L PHE* 3.1 35.5 - - + +
223L GLU 4.3 0.9 + - - +
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Residues in contact with SER 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L HIS* 4.1 19.4 + - - -
211L ASP* 1.3 75.7 - - - +
213L TYR* 1.3 62.3 + - - +
214L ASP 4.5 0.2 + - - -
220L TYR* 3.8 7.9 - - - +
221L LEU* 3.3 44.2 + - - +
222L PHE* 5.0 2.3 - - - -
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Residues in contact with TYR 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L GLY* 6.2 0.4 - - - -
212L SER* 1.3 77.9 - - - +
214L ASP* 1.3 80.7 + - - +
215L ARG* 3.7 40.8 + - + -
218L LYS* 4.4 20.6 - - - +
219L VAL 4.4 3.6 - - - -
220L TYR* 3.3 47.6 - + + -
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Residues in contact with ASP 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L TYR* 1.3 87.4 - - - +
215L ARG* 1.3 63.9 + - - +
216L ALA* 3.1 26.9 + - - +
217L SER 4.0 3.0 + - - +
218L LYS 3.6 14.2 + - - -
219L VAL 3.8 14.5 + - - +
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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