Contacts of the strand formed by residues 217 - 221 (chain B) 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 HIS 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLY* 3.4 24.7 - - - -
141B TYR 3.1 26.1 - - - -
142B GLN* 3.8 5.6 - - + -
145B TRP* 3.6 18.6 - - + -
212B GLY* 4.8 1.6 - - - -
214B ASP* 3.0 20.2 + - - -
215B VAL* 3.3 26.0 - - + +
216B ILE* 1.3 81.3 - - - +
218B SER* 1.3 59.4 + - - +
229B ASP* 3.4 0.9 - - - -
230B ALA* 2.7 36.0 + - + -
252B CYS* 4.0 4.5 - - - -
254B GLU* 3.8 5.4 - - - -
256B CYS* 3.4 19.7 - - + +
263B MET* 3.5 2.9 - - + +
288B CU1 2.1 32.4 - - - -
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TRP* 3.4 12.9 - - - -
217B HIS* 1.3 80.2 - - - +
219B TRP* 1.3 59.5 + - - +
220B THR 4.0 1.4 + - - -
227B LYS* 3.8 15.8 - - - +
228B GLN 3.4 13.6 + - - -
229B ASP* 2.7 25.1 + - - +
230B ALA 4.1 0.4 - - - +
251B GLN 4.0 0.9 - - - +
252B CYS* 3.4 9.7 - - - -
253B SER* 3.1 46.1 + - - -
254B GLU* 3.6 1.7 - - - +
265B ILE* 4.5 0.2 - - - +
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Residues in contact with TRP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B VAL* 3.5 25.8 - - + +
145B TRP* 3.6 23.1 - + + -
147B TYR* 3.0 25.6 + + - -
198B MET* 3.8 31.9 - - + -
208B VAL* 4.4 11.0 - - + -
210B VAL* 4.0 12.7 - - + +
218B SER* 1.3 71.2 - - - +
220B THR* 1.3 65.3 + - - +
221B VAL* 3.7 15.7 - - + -
226B VAL* 4.0 21.3 - - + -
227B LYS* 3.3 1.7 - - - -
228B GLN* 3.0 35.9 + - - +
238B LEU* 3.8 26.0 - - + -
240B PHE* 4.5 5.2 - + - -
265B ILE* 3.6 31.9 - - + +
267B VAL* 4.0 7.6 - - + -
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TRP* 1.3 82.9 - - - +
221B VAL* 1.3 72.3 + - - +
222B PRO* 4.1 10.2 - - + +
226B VAL 2.5 22.6 + - - -
227B LYS* 3.6 25.5 + - + +
250B GLY* 3.2 17.7 - - - -
251B GLN 3.4 17.9 - - - +
253B SER* 3.3 26.0 - - - +
265B ILE* 3.7 8.5 - - - +
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TRP* 3.7 26.5 - - + -
220B THR* 1.3 83.7 + - - +
222B PRO* 1.3 66.9 - - - +
223B ALA* 4.0 6.7 - - + +
224B PHE* 2.8 42.6 + - + +
225B GLY 3.2 8.5 + - - -
226B VAL* 3.1 11.7 + - + +
248B PHE* 3.8 27.6 - - + +
249B PHE 4.2 9.9 - - - +
250B GLY 4.9 1.8 - - - +
265B ILE* 4.2 5.8 - - + -
267B VAL* 3.9 16.4 - - + -
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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