Contacts of the strand formed by residues 207 - 214 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H LEU* 3.6 33.7 - - + +
202H LYS* 3.8 32.7 + - + +
203H VAL* 3.2 21.8 - - + +
204H GLY 3.0 22.2 + - - +
205H GLN 3.6 0.2 - - - -
206H HIS* 1.3 81.9 - - + +
208H GLN* 1.3 64.3 + - - +
224H LEU* 4.2 18.6 - - + -
225H HIS 3.3 15.7 - - - +
226H ILE* 3.3 27.8 - - + -
233H PHE* 5.4 12.1 - - + -
237H TYR* 5.9 3.1 - - + +
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Residues in contact with GLN 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H VAL* 4.5 10.0 - - - +
204H GLY 2.8 28.9 + - - +
205H GLN* 4.5 8.0 + - - +
206H HIS 5.6 0.4 - - - -
207H LEU* 1.3 75.8 + - - +
209H LEU* 1.3 70.3 + - - +
224H LEU* 3.9 2.1 - - - +
225H HIS* 2.9 52.4 + - + +
227H THR* 5.7 6.7 - - + +
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Residues in contact with LEU 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H VAL 6.1 1.1 - - - +
191H TRP* 3.5 36.3 - - + +
199H LEU* 5.4 2.0 - - + +
200H SER* 3.8 35.7 - - - +
203H VAL* 3.9 17.7 - - + +
207H LEU* 6.4 0.4 - - + -
208H GLN* 1.3 78.1 + - - +
210H HIS* 1.3 61.7 + - - +
211H ASP* 4.3 4.7 + - - +
223H GLU 3.8 3.1 - - - +
224H LEU* 3.6 22.2 - - + -
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Residues in contact with HIS 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208H GLN 4.2 0.2 - - - -
209H LEU* 1.3 76.7 + - - +
211H ASP* 1.3 75.8 + - - +
212H SER* 4.2 19.6 - - - -
221H LEU 4.1 1.1 - - - +
222H PHE 3.7 0.2 - - - -
223H GLU* 2.8 62.8 + - + +
225H HIS* 3.8 22.4 - - + +
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Residues in contact with ASP 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H VAL* 4.0 12.6 - - - +
191H TRP* 5.6 0.7 + - - -
209H LEU* 4.3 4.1 - - - +
210H HIS* 1.3 94.9 + - - +
212H SER* 1.3 61.1 + - - +
221H LEU 3.9 2.2 - - - -
222H PHE* 3.2 35.8 - - + +
223H GLU 4.4 0.9 + - - +
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Residues in contact with SER 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H HIS* 4.2 18.7 + - - -
211H ASP* 1.3 76.3 - - - +
213H TYR* 1.3 61.6 + - - +
214H ASP 4.3 0.4 + - - -
220H TYR* 3.8 6.1 - - - +
221H LEU* 3.1 56.0 + - - +
222H PHE* 4.9 1.7 - - - -
223H GLU* 5.7 0.2 - - - -
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Residues in contact with TYR 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H SER* 1.3 78.3 - - - +
214H ASP* 1.3 77.9 + - - +
215H ARG* 3.9 38.9 + - + -
218H LYS* 4.5 18.6 - - - +
219H VAL 4.3 3.4 - - - -
220H TYR* 3.3 49.8 - + + -
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Residues in contact with ASP 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H SER 4.3 0.2 - - - -
213H TYR* 1.3 81.5 - - - +
215H ARG* 1.3 66.7 + - - +
216H ALA* 3.1 19.8 + - - +
217H SER* 4.6 10.8 - - - +
218H LYS 3.3 17.0 + - - -
219H VAL* 3.6 19.0 + - + +
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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