Contacts of the strand formed by residues 210 - 219 (chain D) in PDB entry 5FJV
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 ALA 210 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D GLN* 5.7 1.4 - - - +
196D LEU* 4.7 20.3 - - + +
197D LYS* 5.7 3.1 - - + -
207D ILE* 4.3 11.2 - - + -
208D VAL 4.2 1.6 + - - -
209D ASN* 1.3 75.6 + - - +
211D THR* 1.3 63.1 + - - +
231D TYR* 6.3 0.7 - - + -
232D ALA 2.9 14.4 - - - +
233D PHE* 3.4 34.5 - - + -
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Residues in contact with THR 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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192D GLN* 4.3 17.9 - - + +
196D LEU* 5.9 0.4 - - - -
209D ASN* 5.0 7.8 + - - +
210D ALA* 1.3 79.0 + - - +
212D GLY* 1.3 71.8 + - - +
213D THR* 4.0 13.0 + - + +
230D THR 3.9 1.0 - - - +
231D TYR* 3.6 2.4 - - - -
232D ALA* 2.8 39.5 + - - +
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Residues in contact with GLY 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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189D GLN* 3.4 17.7 + - - +
192D GLN* 3.8 21.7 + - - +
196D LEU* 5.5 1.0 - - - +
211D THR* 1.3 72.5 - - - +
213D THR* 1.3 69.7 + - - +
230D THR 3.2 9.6 - - - -
231D TYR* 3.6 28.0 - - - -
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Residues in contact with THR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D GLN* 3.3 6.8 - - - +
211D THR* 4.3 17.0 - - + +
212D GLY* 1.3 80.9 - - - +
214D TYR* 1.3 63.8 + - - +
215D ASN* 3.7 13.4 + - - +
229D VAL* 4.5 0.9 - - - +
230D THR* 2.8 37.6 + - - +
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Residues in contact with TYR 214 (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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182D LYS* 2.8 25.1 + - - -
186D ASP* 2.7 25.6 + - - -
187D LEU* 2.8 31.6 - - + -
188D GLU* 5.2 1.6 - - - -
189D GLN* 3.0 18.5 - - + +
213D THR* 1.3 73.3 + - - +
215D ASN* 1.3 75.4 + - - +
216D SER* 2.9 21.4 + - - -
227D PRO* 3.2 12.8 - - + +
228D ASP 3.6 5.8 - - - -
229D VAL* 4.3 10.5 - - + -
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Residues in contact with ASN 215 (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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213D THR* 3.7 13.0 + - - +
214D TYR* 1.3 96.1 + - - +
216D SER* 1.3 64.7 + - - +
217D LYS* 3.9 23.0 + - + +
227D PRO* 3.0 1.2 - - - +
228D ASP* 2.8 58.6 + - - +
230D THR* 3.5 12.5 + - - -
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Residues in contact with SER 216 (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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182D LYS* 4.0 10.3 + - - +
214D TYR* 2.9 31.6 + - - -
215D ASN* 1.3 71.8 + - - +
217D LYS* 1.3 69.9 + - - +
225D ILE* 4.3 15.3 - - - -
226D TYR 3.9 6.7 - - - -
227D PRO* 4.0 3.2 - - - +
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Residues in contact with LYS 217 (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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174D LYS* 3.2 23.8 - - - +
215D ASN* 3.9 28.1 + - + +
216D SER* 1.3 86.5 - - - +
218D LYS* 1.3 59.6 + - - +
219D TYR* 3.7 20.2 - - + +
225D ILE* 2.9 13.3 - - - +
226D TYR 2.9 31.3 + - - +
228D ASP* 4.2 2.2 + - - +
230D THR* 5.4 0.8 + - - -
199E TYR* 3.2 38.8 - - + +
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Residues in contact with LYS 218 (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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217D LYS* 1.3 74.3 - - - +
219D TYR* 1.3 76.5 + - - +
220D ASP* 3.7 25.6 + - - +
222D CYS 3.5 17.5 + - - +
223D ALA* 4.1 20.2 - - - +
224D GLU 4.0 4.7 - - - +
225D ILE* 3.1 20.9 - - + +
198E ASP* 4.8 0.7 - - - +
199E TYR* 3.4 17.7 + - - -
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Residues in contact with TYR 219 (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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122D TYR* 3.6 7.0 - + - -
174D LYS* 3.4 29.0 + - - -
217D LYS* 3.7 23.9 - - + +
218D LYS* 1.3 84.6 + - - +
220D ASP* 1.3 60.5 + - - +
221D CYS* 3.0 24.3 + - - -
222D CYS* 2.8 26.2 + - + +
224D GLU 4.5 1.4 + - - -
226D TYR* 4.3 14.5 + + + -
228D ASP* 3.9 6.6 + - - -
300D EPJ 3.7 30.1 - - + -
84E TRP* 3.8 28.5 - + + -
199E TYR* 3.3 47.1 - + + -
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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