Contacts of the strand formed by residues 208 - 212 (chain D) 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 GLN 208 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D HIS* 2.8 33.5 + - - -
125D TRP 4.0 6.5 - - - +
126D VAL* 4.5 5.3 - - - +
127D LEU* 3.1 12.6 - - - +
206D TYR* 3.3 25.1 - - + -
207D GLY* 1.3 84.6 + - - -
209D LEU* 1.3 59.0 + - - +
210D ILE* 4.1 1.8 - - + -
239D LEU* 4.0 36.2 - - + +
245D ALA* 4.7 7.4 - - + -
246D LEU 2.5 13.5 + - - +
247D VAL* 4.8 6.3 - - + -
248D PHE* 2.9 25.9 + - - +
157P ASN* 3.2 21.8 + - - +
159P LEU* 4.3 1.6 - - - +
160P SER* 6.1 0.2 - - - -
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASN 3.6 0.7 - - - +
124D HIS* 3.5 5.0 - - - -
125D TRP* 2.9 77.6 + - + +
127D LEU* 3.5 15.0 - - + -
132D PHE* 4.8 7.2 - - + -
190D LYS* 5.0 6.1 - - + -
193D ALA* 5.2 6.1 - - + -
208D GLN* 1.3 74.6 - - - +
210D ILE* 1.3 64.4 + - - +
211D GLU* 4.8 3.3 - - + +
248D PHE* 3.1 30.3 - - + +
250D LEU* 3.5 42.0 - - + -
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Residues in contact with ILE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D GLU* 4.9 6.5 - - + +
122D ALA* 5.4 5.2 - - + -
123D ASN 3.5 9.2 - - - +
124D HIS* 3.2 35.9 - - + -
208D GLN* 4.1 2.2 - - + -
209D LEU* 1.3 78.1 - - - +
211D GLU* 1.3 62.9 + - - +
212D ILE* 3.7 11.8 + - + -
232D MET* 5.2 4.7 - - + -
236D ILE* 3.8 38.1 - - + -
239D LEU* 3.6 20.9 - - + -
247D VAL* 5.8 4.7 - - + -
248D PHE 2.9 12.0 + - - +
249D VAL* 3.4 7.3 - - + +
250D LEU 2.9 25.6 + - - -
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Residues in contact with GLU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA 4.2 0.7 - - - +
122D ALA* 3.6 4.2 - - - -
123D ASN* 2.9 68.0 + - + +
125D TRP* 3.6 26.3 - - + -
186D THR* 5.4 3.7 - - - +
190D LYS* 4.4 12.1 + - - -
209D LEU* 4.0 3.8 - - + +
210D ILE* 1.3 72.9 - - - +
212D ILE* 1.3 73.2 + - - +
213D ASN* 4.7 2.1 - - + +
250D LEU* 4.1 32.9 - - + +
252D ASP* 5.6 5.2 - - + +
286E GLN* 4.6 5.7 + - - +
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Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA 4.4 3.8 - - - +
122D ALA* 5.0 0.2 - - - +
210D ILE* 3.7 11.9 + - + -
211D GLU* 1.3 83.8 - - - +
213D ASN* 1.3 66.4 + - - +
214D SER* 4.1 6.1 - - - +
216D SER* 4.2 12.1 - - - +
217D LEU* 5.2 11.0 - - + -
232D MET* 3.5 32.3 - - + -
233D PHE* 3.4 33.7 - - + -
236D ILE* 4.0 5.4 - - + -
249D VAL* 4.4 4.0 - - + -
250D LEU 4.3 9.9 + - - +
251D ILE* 3.5 31.6 - - + -
252D ASP* 4.6 12.1 + - - +
257D LEU* 6.1 2.2 - - + -
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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