Contacts of the strand formed by residues 207 - 214 (chain v) in PDB entry 6FF7
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 207 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185v LEU* 4.6 2.0 - - - -
186v GLU* 2.9 46.0 + - - +
187v MET* 5.9 0.4 - - - -
205v GLN 4.9 2.5 - - - -
206v GLN* 1.3 75.1 - - - +
208v LEU* 1.3 62.4 + - - +
209v THR* 3.5 3.2 + - - -
225v SER* 5.1 9.4 - - - -
226v GLU 3.4 15.7 - - - -
227v PRO* 4.6 3.1 - - - -
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Residues in contact with LEU 208 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183v ALA* 6.0 3.8 - - + -
184v CYS 3.6 9.2 - - - +
185v LEU* 4.6 2.7 - - + +
206v GLN 4.2 0.6 - - - -
207v THR* 1.3 71.0 - - - +
209v THR* 1.3 58.9 + - - +
210v PHE 4.3 0.2 + - - -
224v TYR* 4.0 1.0 - - - +
225v SER* 3.3 1.9 + - - -
226v GLU* 2.9 39.9 + - + +
227v PRO 5.1 0.4 - - - -
228v LEU* 5.4 3.4 - - + +
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Residues in contact with THR 209 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182v PHE 3.4 2.3 - - - +
183v ALA* 3.4 5.2 - - - -
184v CYS* 2.9 38.5 + - - +
186v GLU* 4.9 10.5 - - - -
207v THR* 3.5 5.3 + - - -
208v LEU* 1.3 74.2 - - - +
210v PHE* 1.3 61.0 + - - +
222v ARG* 6.3 2.5 - - - -
224v TYR 3.3 8.5 - - - -
225v SER* 4.3 8.7 - - - +
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Residues in contact with PHE 210 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181v MET* 5.2 10.3 - - + -
182v PHE 3.4 6.1 - - - +
183v ALA* 4.7 3.6 - - + +
208v LEU 4.3 0.2 + - - -
209v THR* 1.3 73.6 - - - +
211v TYR* 1.3 61.2 + - - +
212v GLU 4.0 0.2 - - - -
222v ARG* 4.0 3.5 - - - -
223v LYS* 3.1 30.1 + - + +
224v TYR* 2.9 30.2 + - + +
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Residues in contact with TYR 211 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160v ALA* 5.8 6.5 - - + -
180v PRO 3.6 2.1 - - - +
181v MET* 3.2 5.2 - - - -
182v PHE* 2.9 49.4 + - + +
209v THR 5.6 0.2 - - - +
210v PHE* 1.3 71.0 - - - +
212v GLU* 1.3 61.1 + - - +
213v LEU* 4.0 0.3 + - - +
220v VAL* 5.4 10.8 - - + -
221v VAL 3.7 9.9 - - - +
222v ARG* 5.2 0.9 - - - +
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Residues in contact with GLU 212 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179v ASN* 5.2 9.9 - - + +
180v PRO 3.6 5.8 - - - +
181v MET* 4.5 6.7 - - + +
210v PHE 4.0 1.6 + - - -
211v TYR* 1.3 71.7 - - - +
213v LEU* 1.3 61.9 + - - +
214v ASP* 3.5 3.6 + - - +
219v HIS 3.9 2.4 - - - +
220v VAL* 3.9 2.1 - - - -
221v VAL* 3.5 29.1 + - + +
223v LYS* 4.3 18.2 - - + -
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Residues in contact with LEU 213 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129v ALA* 5.3 11.0 - - + -
141v VAL* 5.9 7.2 - - + -
179v ASN* 3.3 22.5 - - - +
180v PRO* 3.0 23.4 + - + +
211v TYR 4.0 1.2 + - - +
212v GLU* 1.3 69.1 - - - +
214v ASP* 1.3 62.4 + - - +
215v LEU* 3.2 8.9 + - + +
219v HIS 3.8 8.3 - - - +
220v VAL* 5.0 4.7 - - + +
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Residues in contact with ASP 214 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179v ASN* 4.6 6.5 - - + -
212v GLU 3.5 4.1 + - - +
213v LEU* 1.3 69.8 - - - +
215v LEU* 1.3 56.9 + - - +
216v GLY* 3.2 1.6 - - - +
217v LEU* 3.9 23.3 - - + +
218v ASN* 2.6 35.5 + - - -
219v HIS 3.4 13.1 + - - +
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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