Contacts of the strand formed by residues 218 - 223 (chain A) in PDB entry 3OV6
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 TRP 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 1.3 73.7 - - - +
219A VAL* 1.3 64.1 + - - +
220A MET* 3.4 30.3 - - + +
222A MET* 3.0 26.2 - - + -
227A GLU* 3.6 23.7 + - - -
233A LEU* 6.5 0.9 - - + -
263A ARG* 3.6 32.3 - - + -
264A VAL* 3.2 3.8 - - - -
265A LYS* 2.5 90.2 + - + -
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Residues in contact with VAL 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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207A CYS* 4.2 1.6 - - - -
209A VAL* 3.3 31.9 - - + -
217A VAL* 4.0 15.8 + - + -
218A TRP* 1.3 82.3 - - - +
220A MET* 1.3 73.6 + - - +
233A LEU* 3.6 25.6 - - + +
246A LEU* 4.2 20.0 - - + +
248A ALA* 3.7 25.1 - - + +
262A CYS* 3.8 23.3 - - - -
263A ARG 3.2 3.1 - - - +
264A VAL* 4.3 4.3 - - + -
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Residues in contact with MET 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A TRP* 3.4 27.6 - - + +
219A VAL* 1.3 86.7 - - - +
221A TRP* 1.3 71.8 + - - +
222A MET* 3.1 31.3 - - + +
227A GLU* 4.0 21.1 - - + +
228A GLN 4.1 7.0 - - - +
229A GLN* 5.9 0.7 - - - -
231A THR* 3.9 27.1 - - - -
233A LEU* 4.9 11.0 - - + -
262A CYS* 3.5 3.7 - - - -
263A ARG 2.9 32.0 + - - -
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Residues in contact with TRP 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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192A LEU* 4.0 24.7 - - + -
205A LEU* 3.4 47.7 + - + -
206A VAL 3.9 3.6 - - - -
207A CYS* 3.8 21.7 - - + +
220A MET* 1.3 84.8 - - - +
222A MET* 1.3 60.6 + - - +
227A GLU* 3.6 0.2 - - - -
228A GLN* 2.8 25.3 + - + -
231A THR* 3.2 30.2 + - + +
248A ALA* 3.1 24.2 + - + -
249A THR 3.8 3.4 - - - -
250A LEU* 3.6 32.3 - - + -
260A LEU* 4.0 15.3 - - + -
261A SER* 3.3 45.1 - - - -
262A CYS* 3.7 2.7 - - + -
278A TRP* 4.4 5.6 - + + -
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Residues in contact with MET 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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218A TRP* 3.0 37.9 - - + -
220A MET* 3.1 31.4 - - + +
221A TRP* 1.3 77.4 - - - +
223A ARG* 1.3 59.8 + - - +
224A GLY 3.6 14.4 - - - +
225A GLU 3.9 11.4 - - - +
226A GLN 3.1 16.2 - - - +
227A GLU* 3.7 15.3 - - + -
228A GLN* 3.6 5.8 - - - -
260A LEU* 3.0 16.6 - - - +
261A SER* 2.7 39.3 + - - +
263A ARG* 3.7 29.6 - - + -
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Residues in contact with ARG 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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222A MET* 1.3 73.7 - - - +
224A GLY* 1.3 63.5 + - - +
225A GLU 3.1 4.2 + - - -
226A GLN* 2.8 36.7 + - - +
228A GLN* 3.2 20.0 + - - +
252A VAL* 5.2 0.8 - - - +
256A GLU* 2.7 34.6 + - - +
258A ALA 2.9 27.5 + - - -
259A GLY* 4.1 14.1 - - - +
260A LEU* 3.5 22.1 - - + +
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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