Contacts of the strand formed by residues 206 - 211 (chain E) in PDB entry 6F0X
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 TYR 206 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 5.0 8.3 - - + -
127E LEU* 3.5 16.1 - - + +
204E TYR* 3.1 10.9 - - - +
205E ARG* 1.3 91.0 - - + +
207E GLY* 1.3 84.2 + - - +
208E GLN* 3.5 20.0 - - + -
242E ASP* 2.4 28.8 + - - +
244E ASP 3.5 6.0 + - - -
245E ALA* 2.9 29.4 - - + -
246E LEU 3.0 4.5 + - - -
122P ARG* 4.3 26.9 + - - +
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Residues in contact with GLY 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 3.8 0.2 - - - +
127E LEU* 3.0 32.6 + - - +
206E TYR* 1.3 81.5 - - - +
208E GLN* 1.3 84.1 + - - -
245E ALA* 4.1 1.3 - - - -
246E LEU 3.0 18.8 - - - -
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Residues in contact with GLN 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E HIS* 2.8 26.7 + - - +
125E TRP 2.8 25.0 - - - +
126E VAL* 3.3 19.6 - - - +
127E LEU* 4.0 8.1 - - - +
206E TYR* 3.5 21.0 - - + -
207E GLY* 1.3 91.6 + - - +
209E LEU* 1.3 61.8 + - - +
210E ILE* 5.0 7.6 - - + -
239E LEU* 5.4 17.9 - - + +
245E ALA* 5.7 1.3 - - + -
246E LEU 2.9 10.2 + - - +
247E VAL* 5.4 7.6 - - + -
248E PHE* 3.3 29.8 + - - +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E HIS* 3.7 1.4 - - - -
125E TRP* 2.9 70.7 + - + +
126E VAL 4.9 2.7 - - - +
127E LEU* 5.8 2.5 - - + -
132E PHE* 4.3 7.2 - - + -
189E CYS 6.4 0.4 - - - -
190E LYS* 3.7 33.0 - - + -
193E ALA* 5.1 9.4 - - + -
208E GLN* 1.3 75.8 - - - +
210E ILE* 1.3 80.2 + - - +
248E PHE* 3.3 31.9 - - + +
250E LEU* 4.0 15.0 - - + -
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Residues in contact with ILE 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E ALA* 5.4 6.1 - - + -
123E ASN 3.9 4.9 - - - +
124E HIS* 3.9 21.3 - - + +
125E TRP* 5.3 0.2 - - - -
208E GLN* 5.0 6.5 - - + -
209E LEU* 1.3 88.4 - - - +
211E GLU* 1.3 66.2 + - - +
212E ILE* 4.5 7.2 - - + +
232E MET* 4.7 21.8 - - + -
236E ILE* 4.9 13.2 - - + -
239E LEU* 4.7 15.5 - - + -
247E VAL* 5.6 4.3 - - + -
248E PHE 3.2 12.4 + - - +
249E VAL* 4.6 18.2 - - + -
250E LEU* 3.2 30.4 + - - +
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Residues in contact with GLU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E ALA 4.5 0.2 - - - -
123E ASN* 2.8 47.9 + - + +
125E TRP* 3.1 20.9 - - + -
186E THR* 4.0 19.3 + - - +
190E LYS* 2.9 31.2 + - - -
209E LEU* 5.4 0.2 - - + -
210E ILE* 1.3 78.6 - - - +
212E ILE* 1.3 60.3 + - - +
213E ASN* 3.3 31.5 - - - +
250E LEU* 3.6 12.3 - - + +
252E ASP* 5.1 2.3 - - - +
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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