Contacts of the strand formed by residues 211 - 216 (chain D) in PDB entry 4OA5
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 MET 211 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.8 24.9 - - + -
44D GLU* 4.6 15.0 - - + +
47D MET* 5.2 7.2 - - + -
48D LEU* 4.5 10.1 - - + -
134D PHE* 3.9 15.0 - - + -
160D VAL* 3.9 10.1 - - + -
161D ALA 3.6 22.0 - - - +
162D ASP* 3.7 24.7 - - + +
204D ILE* 3.9 1.1 - - - -
205D ILE* 2.8 53.0 + - + +
207D THR* 3.5 11.3 + - + +
210D GLY* 1.3 69.2 - - - +
212D MET* 1.3 69.4 + - - +
213D VAL* 3.5 7.8 + - + +
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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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159D ILE 4.5 5.6 - - - +
160D VAL* 3.2 12.8 - - - +
161D ALA* 2.8 40.2 + - + +
164D THR* 3.5 20.1 + - + +
190D PHE* 4.1 5.2 - - + -
191D ASN* 3.5 29.2 - - + +
194D LEU* 3.7 40.4 - - + -
202D SER* 4.0 19.7 - - - -
203D THR 3.6 11.9 - - - +
204D ILE* 3.6 20.9 - - + +
211D MET* 1.3 70.9 - - - +
213D VAL* 1.3 68.5 + - - +
214D SER* 4.5 0.2 - - - -
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Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.7 37.7 - - + -
158D LEU* 5.0 11.7 - - + -
159D ILE 3.6 3.1 - - - -
160D VAL* 4.4 10.1 - - + -
201D LEU 4.0 1.0 - - - +
202D SER* 3.4 1.7 - - - -
203D THR* 2.9 39.8 + - - +
205D ILE* 3.7 31.2 - - + -
211D MET* 3.9 4.5 - - + +
212D MET* 1.3 79.5 - - - +
214D SER* 1.3 63.5 + - - +
215D ILE* 6.3 1.1 - - + -
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Residues in contact with SER 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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157D GLY 3.7 0.2 - - - +
158D LEU* 3.3 8.9 - - - +
159D ILE* 2.8 48.5 + - - +
194D LEU* 3.7 18.2 - - - +
200D TYR* 3.3 17.5 - - - +
201D LEU 3.4 4.3 - - - -
202D SER* 2.7 26.2 + - - -
212D MET* 4.5 5.4 - - - -
213D VAL* 1.3 77.4 - - - +
215D ILE* 1.3 63.4 + - - +
216D LYS 3.9 0.5 + - - -
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Residues in contact with ILE 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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156D GLY* 3.8 21.1 - - - +
157D GLY 3.5 2.7 - - - -
158D LEU* 3.8 17.5 - - + -
200D TYR* 3.2 7.3 - - - +
201D LEU* 2.9 54.2 + - + +
213D VAL* 6.3 1.1 - - + -
214D SER* 1.3 74.1 - - - +
216D LYS* 1.3 73.3 + - - +
217D LEU* 3.4 5.0 + - + +
314D IOD 4.0 14.6 - - + -
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Residues in contact with LYS 216 (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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149D ALA 3.4 13.2 - - - +
150D LYS* 3.3 33.1 + - - +
151D MET 5.5 0.2 + - - -
153D ILE* 2.8 36.7 + - + +
154D ARG 3.7 11.3 - - - +
155D LYS 3.9 0.6 - - - +
156D GLY* 2.7 34.0 + - - -
157D GLY 2.9 16.6 + - - +
159D ILE* 4.3 20.0 - - + -
199D LYS 4.0 4.0 - - - +
200D TYR* 4.0 12.1 - - + -
214D SER 3.9 0.8 + - - -
215D ILE* 1.3 71.7 - - - +
217D LEU* 1.3 56.6 + - - +
218D THR* 2.8 35.5 + - - +
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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