Contacts of the strand formed by residues 216 - 223 (chain A) in PDB entry 1OMW
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A HIS* 5.3 5.2 - - + -
208A CYS 3.7 7.6 - - - +
209A ARG* 3.1 44.6 - - - +
214A GLY 3.0 1.5 + - - +
215A LYS* 1.3 86.3 - - + +
217A TYR* 1.3 66.4 + - - +
273A LEU* 4.1 27.2 + - + +
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Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 4.3 10.3 - + - -
207A GLY* 3.7 1.9 - - - -
208A CYS* 2.8 49.5 + - - +
209A ARG 5.1 0.2 - - - +
210A LYS* 4.2 11.4 - - + -
215A LYS* 3.4 46.7 + - + +
216A MET* 1.3 75.9 - - - +
218A ALA* 1.3 59.8 + - - +
258A SER* 3.7 26.2 + - - -
259A TYR* 4.1 8.2 - + - -
270A ILE* 3.7 19.7 - - + -
271A LEU 3.8 17.9 - - - -
272A ASP* 4.9 10.1 - - - -
273A LEU* 3.9 12.4 - - - +
516A ARG 4.7 2.6 + - - -
520A GLU* 2.5 39.0 + - - +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE* 5.2 1.6 - - + -
205A VAL* 4.9 10.5 - - + -
206A TYR 3.7 9.9 - - - +
208A CYS* 4.2 2.2 - - - -
217A TYR* 1.3 75.1 - - - +
219A MET* 1.3 60.5 + - - +
270A ILE* 3.2 7.3 - - - +
271A LEU* 2.7 51.1 + - + +
272A ASP 3.8 4.7 - - - +
273A LEU* 3.7 25.3 - - + +
274A MET 5.0 0.4 - - - +
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Residues in contact with MET 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A MET* 4.0 17.9 - - - +
191A PHE* 3.6 32.8 - - + -
193A VAL* 4.6 18.6 - - + -
204A GLU 3.9 1.0 - - - +
205A VAL* 3.3 5.5 - - - -
206A TYR* 3.0 43.6 + - + +
208A CYS* 4.2 9.4 - - + -
218A ALA* 1.3 74.7 - - - +
220A LYS* 1.3 60.2 + - - +
221A CYS* 3.6 25.5 + - - -
261A PHE* 4.0 14.1 - - + -
268A SER* 4.4 4.5 - - - -
269A PHE 3.3 4.7 - - - +
270A ILE* 3.6 26.0 - - + -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLY* 6.1 4.3 - - - -
203A GLY 5.7 1.6 - - - +
204A GLU 3.8 4.7 - - - +
205A VAL* 4.2 24.9 - - + +
218A ALA 4.2 0.6 - - - -
219A MET* 1.3 71.4 - - - +
221A CYS* 1.3 60.0 + - - +
222A LEU* 4.1 20.0 - - + -
239A GLU* 3.4 20.1 + - - +
243A LEU* 6.3 0.4 - - + -
267A LEU 3.3 3.8 - - - +
269A PHE* 2.8 61.5 + - + +
271A LEU* 3.9 28.4 - - + +
334A SER* 5.4 3.6 + - - -
335A ASP* 3.4 23.3 + - - +
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Residues in contact with CYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A MET* 4.5 7.2 - - - -
203A GLY* 3.4 6.1 - - - -
204A GLU* 3.1 36.6 + - + +
206A TYR* 4.3 20.2 - - + -
219A MET* 3.6 32.8 - - - -
220A LYS* 1.3 73.9 - - - +
222A LEU* 1.3 63.2 + - - +
223A ASP 4.2 0.7 - - - -
266A LYS* 4.4 23.6 - - + -
267A LEU 3.1 7.0 - - - +
268A SER* 4.3 7.2 - - - -
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLY* 6.4 0.4 - - - -
202A PHE* 4.2 25.1 - - + +
203A GLY* 4.3 7.9 - - - +
220A LYS* 4.1 24.2 - - + -
221A CYS* 1.3 85.1 - - - +
223A ASP* 1.3 64.5 + - - +
224A LYS* 3.4 2.8 + - - -
227A ILE* 3.9 22.6 - - + +
236A ALA* 4.7 11.9 - - + -
239A GLU* 4.4 8.3 - - - +
266A LYS* 3.8 3.2 - - - -
267A LEU* 2.9 44.8 + - + +
269A PHE* 3.6 31.6 - - + -
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE 3.3 10.1 + - - +
203A GLY* 4.8 0.6 - - - -
204A GLU* 5.3 1.5 + - - +
221A CYS 4.2 1.0 + - - -
222A LEU* 1.3 68.2 - - - +
224A LYS* 1.3 65.7 + - - +
225A LYS* 2.9 46.9 + - - +
226A ARG* 3.5 32.4 + - + +
227A ILE* 3.3 25.5 + - - +
265A ASP* 4.1 9.4 - - - +
266A LYS* 3.7 29.6 + - - +
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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