Contacts of the strand formed by residues 207 - 213 (chain D) in PDB entry 3ORH
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 ILE 207 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D PHE* 4.2 24.5 - - + -
194D VAL* 4.6 7.0 - - + -
197D LEU* 3.9 31.9 - - + -
198D LEU* 3.9 21.1 - - + -
202D PHE* 4.4 5.2 - - + -
203D ARG 3.6 16.8 - - - +
204D ARG* 2.8 47.1 + - - +
205D GLU 3.4 1.2 - - - +
206D ASN* 1.3 79.8 - - - +
208D ARG* 1.3 70.9 + - - +
232D LEU 3.6 2.0 - - - -
233D VAL* 4.1 22.7 - - + -
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D PHE* 5.4 0.3 - - - -
205D GLU 3.4 24.2 + - - +
206D ASN* 3.9 23.8 + - - +
207D ILE* 1.3 82.0 - - - +
209D THR* 1.3 63.7 + - - +
231D PRO* 3.6 2.6 - - - +
232D LEU* 2.8 47.6 + - + +
234D THR* 4.3 12.7 + - - -
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Residues in contact with THR 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D THR* 4.5 17.9 - - + +
189D PHE* 5.0 13.4 - - + -
204D ARG* 6.4 0.4 - - - +
208D ARG* 1.3 79.0 - - - +
210D GLU* 1.3 71.3 + - - +
211D VAL* 4.2 2.5 - - + -
229D ILE* 2.7 44.5 - - + +
230D THR 3.3 9.0 + - - -
231D PRO* 4.4 2.4 - - - +
232D LEU* 4.5 0.9 - - - -
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Residues in contact with GLU 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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52D ALA* 4.9 10.6 - - + +
56D ALA* 5.8 0.5 - - - +
209D THR* 1.3 79.3 + - - +
211D VAL* 1.3 65.0 + - - +
212D MET* 4.0 1.6 + - + +
228D MET 3.9 0.2 - - - +
229D ILE* 3.4 1.7 - - - -
230D THR* 2.7 51.1 + - - +
232D LEU* 3.7 32.0 - - + +
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Residues in contact with VAL 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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185D ILE* 3.8 14.4 - - + -
186D THR* 3.6 23.6 - - - +
209D THR* 4.2 3.5 + - + +
210D GLU* 1.3 76.5 - - - +
212D MET* 1.3 66.0 + - - +
227D GLN* 3.7 37.0 - - + +
228D MET 3.4 8.7 - - - +
229D ILE* 4.1 10.5 - - + -
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Residues in contact with MET 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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48D PRO* 3.7 31.6 - - + +
49D TYR* 3.8 28.9 - - + +
52D ALA* 4.3 12.8 - - + -
210D GLU* 5.4 0.9 - - + +
211D VAL* 1.3 78.1 - - - +
213D ALA* 1.3 77.2 + - - +
214D LEU* 4.1 10.1 - - + -
227D GLN* 3.3 5.8 - - - +
228D MET* 2.9 48.6 + - + +
230D THR* 5.2 3.8 - - - +
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Residues in contact with ALA 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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212D MET* 1.3 83.3 - - - +
214D LEU* 1.3 61.4 + - - +
215D VAL* 6.4 1.1 - - + -
226D PRO 3.8 8.3 - - - +
227D GLN* 4.6 6.5 - - + +
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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