Contacts of the strand formed by residues 208 - 213 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.6 11.1 + - - -
179A TYR* 5.2 1.4 + - - +
187A PHE* 3.1 40.4 - - + -
200A ASN* 4.3 9.6 - - - +
202A LEU* 4.1 4.6 - - + +
207A PRO* 1.3 73.2 - - - +
209A SER* 1.3 59.9 + - - +
210A TRP* 3.4 16.8 - - + +
263A THR* 3.6 1.5 - - - -
264A GLN* 2.7 55.4 + - - +
281A PHE 3.5 6.5 - - - +
282A ASN* 2.8 29.8 + - - +
286A ASN* 4.2 10.6 + - - +
288A ALA* 4.1 16.6 - - - +
403A OGA 3.2 22.4 + - - +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 5.6 1.0 + - - +
187A PHE* 3.8 4.0 - - - -
208A LYS* 1.3 73.6 - - - +
210A TRP* 1.3 62.6 + - - +
211A TYR* 5.6 1.8 - - - -
261A LYS* 6.5 0.7 - - - -
262A ILE 3.7 4.3 - - - -
263A THR* 2.9 17.3 + - - +
280A GLY* 3.1 4.6 - - - -
281A PHE* 2.9 64.0 + - - +
283A HIS* 2.8 23.3 + - - -
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Residues in contact with TRP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.7 34.0 - - + +
187A PHE* 3.8 19.3 - + - -
198A SER* 5.6 0.2 - - - -
200A ASN* 3.9 18.4 - - + -
208A LYS* 3.4 27.8 + - + +
209A SER* 1.3 78.8 - - - +
211A TYR* 1.3 62.5 + - - +
261A LYS* 3.3 7.6 - - - +
262A ILE* 2.9 35.8 + - + +
264A GLN* 3.0 37.0 + - + +
270A MET* 3.6 23.8 - - + +
272A THR* 3.9 13.2 - - + -
278A HIS* 3.6 29.6 - + + -
279A ALA 3.3 3.8 - - - -
403A OGA 3.7 26.0 - - - -
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Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.5 2.4 - - - +
120A GLU* 2.5 36.4 + - - +
124A TRP* 2.9 38.9 + + - -
189A TRP* 3.5 26.2 - + + -
209A SER* 5.6 1.6 - - - -
210A TRP* 1.3 76.2 - - - +
212A ALA* 1.3 62.6 + - - +
249A PRO* 3.9 16.6 - - + -
252A LEU* 6.2 0.2 - - + -
259A PHE* 4.4 14.4 - + + -
260A ASP 3.5 6.1 - - - +
261A LYS* 3.9 23.1 - - + -
278A HIS* 3.1 28.8 - - - +
279A ALA* 2.7 30.5 + - + +
280A GLY* 4.2 2.9 - - - -
281A PHE* 3.7 23.1 - + - -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.2 9.0 - - + -
44A ALA 3.7 12.9 - - - +
45A GLY 4.7 1.8 - - - -
46A LEU* 3.6 36.1 - - + +
189A TRP* 4.6 0.2 - - - -
211A TYR* 1.3 76.2 - - - +
213A ILE* 1.3 64.9 + - - +
214A PRO* 4.3 1.2 - - - +
259A PHE* 3.1 5.1 - - - +
260A ASP* 2.9 32.1 + - - +
277A TYR 3.3 8.7 - - - +
278A HIS* 4.4 2.0 - - + +
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 3.9 4.5 - - - +
45A GLY* 4.4 0.2 - - - -
189A TRP* 3.7 27.1 - - + -
212A ALA* 1.3 78.0 - - - +
214A PRO* 1.3 84.2 - - + +
215A PRO* 3.3 4.9 - - - +
217A HIS* 3.8 23.8 - - + +
218A GLY* 4.5 2.5 - - - +
221A LEU* 3.6 28.7 - - + -
252A LEU* 4.1 5.4 - - + -
257A ILE* 3.6 21.8 - - + -
258A PRO 3.6 17.7 - - - +
259A PHE* 3.9 4.3 - - + -
276A GLY* 3.9 1.7 - - - -
277A TYR* 3.0 26.7 + - + +
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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