Contacts of the strand formed by residues 205 - 212 (chain D) in PDB entry 3OMA
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 THR 205 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PRO* 4.0 26.2 - - + +
131D GLU 3.5 24.4 + - - +
132D ALA* 3.8 0.5 - - - -
133D ASP* 2.9 41.9 + - - -
134D VAL 3.1 8.5 + - - +
204D LYS* 1.3 69.5 - - - +
206D VAL* 1.3 62.8 + - - +
207D VAL* 4.4 13.9 - - + -
239D TRP* 4.4 10.4 - - + -
240D PHE 3.8 3.6 - - - -
241D ARG* 4.4 17.7 + - - +
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D VAL* 3.4 19.5 - - + +
136D VAL* 4.4 10.5 - - + -
198D MET* 4.6 0.2 - - + -
200D VAL* 4.0 29.4 - - + -
201D PRO 5.0 3.6 - - - +
204D LYS 3.7 12.6 - - - +
205D THR* 1.3 73.8 - - - +
207D VAL* 1.3 65.6 + - - +
208D VAL* 4.1 11.8 + - + -
239D TRP* 3.2 6.9 - - - +
240D PHE* 2.8 78.3 + - + +
242D ALA* 5.7 0.7 - - + +
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ILE* 3.6 28.9 - - + -
130D PRO 3.9 7.4 - - - +
132D ALA* 3.5 30.1 - - + -
134D VAL 2.9 6.3 + - - -
135D THR* 3.4 8.1 - - - +
136D VAL 3.0 24.8 + - - +
205D THR* 4.4 3.4 - - + -
206D VAL* 1.3 77.5 - - - +
208D VAL* 1.3 66.7 + - - +
209D GLN* 4.7 5.4 - - + +
237D GLN* 3.5 27.4 - - + +
238D LEU 3.4 8.7 - - - +
239D TRP* 4.2 6.7 - - + -
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Residues in contact with VAL 208 (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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136D VAL* 3.3 6.3 - - + +
138D VAL* 3.4 31.0 - - + -
198D MET* 4.5 6.1 - - + -
206D VAL* 4.1 7.6 - - + -
207D VAL* 1.3 76.8 - - - +
209D GLN* 1.3 63.2 + - - +
210D VAL* 3.8 16.6 + - + +
219D TRP* 4.3 17.3 - - + -
236D ALA 3.7 0.7 - - - +
237D GLN* 3.3 5.2 - - - +
238D LEU* 2.9 55.6 + - + +
240D PHE* 3.8 22.2 - - + -
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Residues in contact with GLN 209 (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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135D THR* 4.0 25.3 - - + +
136D VAL 2.8 13.0 + - - +
137D LYS* 3.4 18.6 - - + +
138D VAL* 2.7 33.8 + - - +
150D PRO* 5.1 3.6 - - - +
207D VAL* 4.7 4.5 - - + +
208D VAL* 1.3 74.6 - - - +
210D VAL* 1.3 56.8 + - - +
235D LEU* 4.1 32.7 - - + +
236D ALA 3.3 4.3 - - - +
237D GLN* 3.1 33.1 + - + +
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Residues in contact with VAL 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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138D VAL* 3.5 8.1 - - + +
145D TRP* 4.7 2.5 - - + -
208D VAL* 3.8 20.9 - - + +
209D GLN* 1.3 77.4 - - - +
211D THR* 1.3 64.6 + - - +
219D TRP* 3.9 18.6 - - + -
228D GLN* 3.8 22.0 - - + +
229D ASP 4.3 7.8 - - - +
230D ALA* 3.6 27.1 - - + -
231D VAL 5.0 0.3 + - - -
234D ARG 3.6 1.9 - - - +
235D LEU* 3.7 1.1 - - - -
236D ALA* 2.7 37.6 + - - +
238D LEU* 4.0 20.2 - - + -
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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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137D LYS* 3.5 28.3 - - - +
138D VAL 3.0 8.3 + - - +
139D THR* 3.3 21.0 - - + +
140D GLY 2.8 23.2 + - - -
210D VAL* 1.3 71.7 - - - +
212D GLY* 1.3 70.8 + - - +
230D ALA* 3.3 13.0 - - - +
231D VAL 3.1 6.2 + - - -
233D GLY 4.1 2.8 + - - -
234D ARG 2.6 29.1 + - - -
235D LEU* 3.9 6.7 - - + -
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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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139D THR* 4.4 2.7 - - - -
140D GLY 3.7 7.2 - - - -
211D THR* 1.3 83.3 + - - +
213D ALA* 1.3 59.7 + - - -
214D ASP 3.6 1.3 - - - -
215D VAL 4.0 4.9 - - - -
230D ALA* 3.3 28.5 - - - -
231D VAL 3.5 1.8 + - - -
232D PRO* 3.2 23.1 - - - +
233D GLY 4.3 1.2 + - - -
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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