Contacts of the strand formed by residues 208 - 213 (chain B) in PDB entry 4XDO
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 LYS 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B TYR* 3.6 9.5 + - - -
179B TYR* 5.3 0.8 - - - +
187B PHE* 3.6 24.8 - - + -
200B ASN* 4.0 11.0 - - - +
202B LEU* 4.0 6.3 - - + +
207B PRO* 1.3 74.0 - - - +
209B SER* 1.3 62.3 + - - +
210B TRP* 3.3 37.4 - - + +
263B THR* 4.4 1.6 - - - -
264B GLN* 2.8 46.0 + - - +
281B PHE 3.6 4.5 - - - +
282B ASN* 2.7 31.4 + - - +
286B ASN* 4.2 5.4 + - - +
288B ALA* 4.1 15.7 - - - +
403B OGA 2.9 24.0 + - - +
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TYR* 5.5 1.9 + - - +
120B GLU* 5.9 0.5 - - - +
187B PHE* 3.7 3.8 - - - -
208B LYS* 1.3 74.2 - - - +
210B TRP* 1.3 61.1 + - - +
211B TYR* 5.7 0.9 - - - -
262B ILE 3.6 4.5 - - - -
263B THR* 2.9 18.3 + - - +
280B GLY* 3.1 4.8 - - - -
281B PHE* 2.8 63.6 + - - +
283B HIS* 2.7 24.6 + - - -
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Residues in contact with TRP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.6 33.9 - - + -
187B PHE* 3.7 15.0 - + - -
200B ASN* 3.9 13.2 - - + -
208B LYS* 3.3 35.7 - - + +
209B SER* 1.3 76.3 - - - +
211B TYR* 1.3 64.1 + - - +
261B LYS* 3.1 8.0 - - - +
262B ILE* 2.8 38.8 + - + +
264B GLN* 2.8 36.1 + - + -
270B MET* 3.6 23.4 - - + +
272B THR* 3.8 15.7 - - + -
278B HIS* 3.7 27.8 - + + -
279B ALA 3.4 4.9 - - - -
403B OGA 3.8 27.6 - - - -
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Residues in contact with TYR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 4.3 2.1 - - - +
120B GLU* 2.5 36.2 + - - +
123B TYR* 5.5 0.2 - + - -
124B TRP* 3.0 37.9 + + - -
189B TRP* 3.6 26.2 - + + -
209B SER* 5.3 1.3 - - - -
210B TRP* 1.3 75.0 - - - +
212B ALA* 1.3 60.7 + - - +
247B ILE 5.9 0.7 - - - -
249B PRO* 3.7 18.8 - - + -
259B PHE* 4.2 15.0 - + + -
260B ASP 3.4 4.9 - - - +
261B LYS* 3.9 21.5 - - + -
278B HIS* 3.1 28.2 - - - +
279B ALA* 2.8 27.5 + - + +
280B GLY* 4.2 2.7 - - - -
281B PHE* 3.8 22.9 - + - -
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 4.4 7.4 - - + -
44B ALA 3.7 12.7 - - - +
45B GLY 4.7 2.0 - - - -
46B LEU* 3.6 35.9 - - + +
189B TRP* 4.5 0.4 - - - -
211B TYR* 1.3 76.8 - - - +
213B ILE* 1.3 64.1 + - - +
214B PRO* 4.3 1.4 - - - +
259B PHE* 3.2 4.6 - - - +
260B ASP* 2.9 33.3 + - - +
277B TYR 3.3 10.5 - - - +
278B HIS* 4.5 2.2 - - + -
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA 3.9 4.1 - - - +
45B GLY* 4.5 0.2 - - - -
189B TRP* 3.5 28.3 - - + -
212B ALA* 1.3 76.1 - - - +
214B PRO* 1.3 84.3 - - + +
215B PRO* 3.4 4.2 - - - +
217B HIS* 4.0 22.7 - - + +
218B GLY* 4.3 5.2 - - - +
221B LEU* 3.7 34.1 - - + -
252B LEU* 4.2 4.3 - - + -
257B ILE* 4.0 11.9 - - + -
258B PRO 3.6 15.0 - - - +
259B PHE* 3.9 7.2 - - + -
276B GLY* 3.9 1.7 - - - -
277B TYR* 3.0 27.1 + - + +
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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