Contacts of the strand formed by residues 210 - 219 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLN* 3.6 17.4 - - - +
196C LEU* 3.9 29.6 - - + -
207C ILE* 5.5 4.9 - - + -
208C VAL 3.6 4.9 + - - +
209C ASN* 1.3 75.6 - - - +
211C THR* 1.3 65.5 + - - +
232C ALA 4.3 1.3 - - - -
233C PHE* 5.4 7.6 - - + -
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Residues in contact with THR 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLN* 4.1 4.3 - - - -
196C LEU* 5.2 0.6 - - - +
209C ASN* 4.6 15.9 - - + +
210C ALA* 1.3 86.9 - - - +
212C GLY* 1.3 64.6 + - - +
213C THR* 4.1 4.5 + - - +
230C THR 4.2 0.2 - - - +
231C TYR* 3.8 3.7 - - - -
232C ALA* 3.2 38.9 + - - +
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Residues in contact with GLY 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLN* 3.1 30.3 + - - +
192C GLN* 3.7 12.8 + - - +
211C THR* 1.3 75.5 - - - +
213C THR* 1.3 62.7 + - - -
230C THR 3.5 7.2 - - - -
231C TYR* 3.6 19.3 - - - -
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Residues in contact with THR 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLN* 3.6 3.3 + - - -
211C THR* 5.1 6.1 - - - +
212C GLY* 1.3 75.7 - - - -
214C TYR* 1.3 73.6 + - - +
215C ASN* 3.6 13.1 + - - +
229C VAL* 4.2 3.4 - - - +
230C THR* 2.7 49.3 + - - +
232C ALA* 6.0 3.4 - - + +
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Residues in contact with TYR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LYS* 2.2 42.6 + - - +
186C ASP* 3.0 10.3 + - - -
187C LEU* 3.0 29.6 - - + -
188C GLU* 5.1 0.2 - - - -
189C GLN* 3.7 16.2 + - + +
213C THR* 1.3 79.7 + - - +
215C ASN* 1.3 83.7 + - - +
216C SER* 4.2 7.6 - - - -
227C PRO* 3.5 13.8 - - + +
228C ASP 3.5 12.3 - - - -
229C VAL* 4.2 12.3 - - + -
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Residues in contact with ASN 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C THR* 3.6 17.0 + - - +
214C TYR* 1.3 88.4 + - - +
216C SER* 1.3 67.2 + - - +
217C LYS* 5.3 5.4 - - + -
227C PRO* 3.5 2.1 - - - +
228C ASP* 2.8 52.1 + - - +
230C THR* 4.8 5.7 + - - -
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Residues in contact with SER 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LYS* 4.4 8.5 - - - +
214C TYR* 4.2 15.3 - - - -
215C ASN* 1.3 79.8 + - - +
217C LYS* 1.3 67.6 + - - +
225C ILE* 2.9 33.4 - - - +
226C TYR 4.0 7.8 + - - -
227C PRO* 4.3 5.6 - - - -
228C ASP* 4.6 0.2 - - - -
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Residues in contact with LYS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LYS* 4.6 5.9 - - - +
215C ASN* 5.3 4.0 - - + -
216C SER* 1.3 86.0 + - - +
218C LYS* 1.3 66.5 + - - +
219C TYR* 3.7 47.3 - - + +
225C ILE* 3.3 11.0 - - - -
226C TYR 3.2 28.3 + - - -
228C ASP* 4.6 8.1 - - - +
198D ASP* 4.6 11.9 + - - -
199D TYR* 5.8 4.2 - - - +
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Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C LYS* 1.3 86.3 - - - +
219C TYR* 1.3 76.3 + - - +
220C ASP* 4.3 13.0 + - - +
222C CYS 3.3 21.0 + - - +
223C ALA* 3.3 25.0 - - - +
224C GLU 3.4 12.3 - - - +
225C ILE* 4.3 12.1 - - + +
198D ASP* 5.2 2.9 - - - +
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Residues in contact with TYR 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR* 3.8 7.7 - + - -
174C LYS* 2.2 40.0 + - - -
217C LYS* 3.7 47.6 - - + +
218C LYS* 1.3 86.5 + - - +
220C ASP* 1.3 60.8 + - - +
221C CYS* 2.9 29.3 + - - -
222C CYS* 3.0 22.2 + - + +
224C GLU 4.3 0.4 + - - -
226C TYR* 3.9 33.7 + + + -
228C ASP* 3.9 5.0 + - - +
300C EPJ 4.0 16.4 - - + -
84D TRP* 4.1 22.2 - + - -
198D ASP* 4.9 2.7 - - - -
199D TYR* 4.4 12.1 - + + -
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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