Contacts of the strand formed by residues 209 - 215 (chain D) in PDB entry 5BOU
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 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D VAL 3.5 11.9 - - - +
44D LYS* 4.5 6.3 - - - -
193D LEU* 5.4 5.2 - - + -
196D LEU* 4.7 6.1 - - + -
200D MET* 4.5 4.3 - - - -
204D LEU* 3.9 29.2 - - + -
205D ASP 3.4 12.8 + - - +
206D GLU* 3.3 22.2 - - - +
207D ASN 3.6 0.9 - - - -
208D ASN* 1.3 80.2 + - - +
210D GLN* 1.3 62.4 + - - +
225D ASN* 5.0 1.4 + - - -
228D THR* 4.9 6.9 - - + +
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Residues in contact with GLN 210 (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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41D GLY* 3.3 4.7 - - - -
42D VAL* 3.0 42.9 + - + +
44D LYS* 4.0 29.0 + - - +
56D ILE 4.6 8.5 + - - +
57D GLU* 5.3 1.2 - - - +
58D LYS 4.7 0.8 - - - +
59D ILE* 3.6 37.4 + - + +
193D LEU* 5.9 0.4 - - - -
196D LEU* 4.9 1.4 - - - +
209D ALA* 1.3 77.3 - - - +
211D LEU* 1.3 74.4 + - - +
222D ILE* 3.6 23.7 - - + +
223D TYR 4.8 5.4 - - - +
225D ASN* 5.4 7.4 + - - +
228D THR* 5.4 2.2 - - - -
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Residues in contact with LEU 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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39D VAL* 4.1 16.2 - - + -
40D LEU 3.5 1.3 - - - -
41D GLY* 4.2 5.8 - - - -
59D ILE* 4.3 1.3 - - - -
189D GLU* 4.3 9.4 - - + +
192D VAL* 3.7 31.6 - - + -
193D LEU* 3.5 41.5 - - + -
196D LEU* 5.2 0.9 - - + -
210D GLN* 1.3 82.6 - - - +
212D SER* 1.3 62.2 + - - +
222D ILE* 3.9 0.9 - - - -
223D TYR* 3.0 43.9 + - + +
228D THR* 4.2 15.8 + - + +
231D LEU* 3.9 22.0 - - + -
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Residues in contact with SER 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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39D VAL* 3.4 7.3 - - - +
40D LEU* 2.8 52.3 + - - +
59D ILE* 3.4 26.1 - - - +
211D LEU* 1.3 77.8 - - - +
213D CYS* 1.3 63.5 + - - +
220D PHE* 3.9 8.3 - - - -
221D LYS 3.3 15.5 - - - -
222D ILE* 4.0 5.6 - - - -
223D TYR* 3.8 8.0 - - - -
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Residues in contact with CYS 213 (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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38D VAL 3.2 13.7 - - - +
39D VAL* 4.3 4.7 - - + +
40D LEU* 4.6 1.1 - - - +
185D LEU* 4.5 14.6 - - + -
212D SER* 1.3 76.6 - - - +
214D ILE* 1.3 62.7 + - - +
215D THR* 4.3 20.0 - - - -
219D GLY 3.7 2.0 - - - +
220D PHE* 3.4 8.2 - - - -
221D LYS* 3.0 40.8 + - - +
223D TYR* 3.4 30.5 - - - +
227D LYS* 5.9 0.7 - - - -
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Residues in contact with ILE 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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37D GLY* 3.4 5.7 - - - -
38D VAL* 2.9 51.1 + - + +
40D LEU* 6.2 0.7 - - + -
65D HIS* 3.7 34.5 - - + +
67D GLY 5.2 0.7 - - - +
137D ALA* 4.1 10.8 - - + +
138D GLY* 3.9 24.5 - - - +
139D HIS* 4.1 7.2 - - + +
145D TYR* 3.6 2.8 - - + -
213D CYS* 1.3 75.4 - - - +
215D THR* 1.3 82.1 + - - +
219D GLY* 3.5 19.5 - - - -
220D PHE* 3.7 14.6 - - + +
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Residues in contact with THR 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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36D GLU 3.7 18.8 - - - +
37D GLY* 4.6 0.7 - - - -
145D TYR* 3.7 9.4 - - - -
185D LEU* 4.1 21.3 - - + -
213D CYS* 4.3 10.9 - - - -
214D ILE* 1.3 84.5 - - - +
216D LYS* 1.3 60.7 + - - +
217D GLN* 4.2 4.7 - - - -
218D ASP* 3.3 30.8 + - - +
219D GLY* 2.9 30.2 + - - -
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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