Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 6DO5
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 ARG 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ALA 3.6 0.2 - - - +
225A THR* 3.4 4.3 - - - +
226A VAL 2.9 37.3 + - - +
227A GLY 3.3 1.4 + - - -
228A ASN* 1.3 94.0 + - - +
230A GLY* 1.3 59.8 + - - +
231A PHE* 3.5 26.5 + - + -
247A TYR* 3.4 54.2 + - + -
248A LEU 3.6 3.4 - - - -
249A ASN* 5.2 3.0 - - - +
250A LEU* 4.3 2.9 - - - -
258A LEU* 5.5 4.0 - - - +
302A ILE* 4.6 17.3 - - - +
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Residues in contact with GLY 230 (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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151A TRP* 3.1 45.7 - - - -
225A THR* 4.6 0.2 - - - -
229A ARG* 1.3 69.6 - - - +
231A PHE* 1.3 60.4 + - - -
232A VAL 3.7 0.3 + - - -
247A TYR* 3.2 2.5 - - - -
248A LEU 2.8 39.6 + - - -
250A LEU* 4.0 6.0 - - - +
255A TRP* 4.6 0.2 - - - -
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Residues in contact with PHE 231 (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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151A TRP* 3.1 6.5 + - - -
222A ALA 4.4 0.4 - - - -
223A CYS* 3.1 1.0 - - - -
224A ALA 2.6 47.1 + - - +
226A VAL* 4.1 10.1 - - + -
229A ARG* 3.8 34.5 - - + -
230A GLY* 1.3 71.6 - - - +
232A VAL* 1.3 59.6 + - - +
245A LEU* 4.6 8.3 - - + -
246A HIS 3.4 6.1 - - - +
247A TYR* 3.5 16.2 - + + -
258A LEU* 3.6 28.5 - - + -
273A LEU* 4.4 7.2 - - + -
281A LEU* 3.4 26.5 - - + -
300A TYR* 4.2 10.3 - + - -
302A ILE* 3.7 42.2 - - + -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TRP* 4.2 2.7 - - + -
160A PHE* 3.7 9.0 - - + -
215A PRO* 4.0 16.4 - - + -
218A ARG* 4.2 6.5 - - - +
221A HIS* 3.5 40.4 - - + -
222A ALA 3.2 7.0 - - - +
223A CYS* 4.0 9.2 - - - -
230A GLY 3.7 0.2 + - - -
231A PHE* 1.3 75.4 - - - +
233A PHE* 1.3 65.2 + - - +
244A ASP 4.2 0.5 - - - +
245A LEU* 3.6 3.0 - - - +
246A HIS* 3.0 34.9 + - + +
255A TRP* 4.0 31.0 - - + -
273A LEU* 4.8 0.2 - - - -
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Residues in contact with PHE 233 (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 ARG* 5.0 0.4 - - - +
222A ALA 2.9 17.5 + - - -
232A VAL* 1.3 75.4 - - - +
234A GLY* 1.3 64.2 + - - +
242A MET 4.5 0.7 - - - -
243A ASN* 3.1 36.8 - - + -
244A ASP 3.3 20.6 - - - -
245A LEU* 3.6 20.9 - - + -
264A CYS* 6.2 0.2 - - + -
265A PRO* 4.1 23.8 - - + -
266A VAL 4.5 4.3 - - - -
268A ARG* 4.0 17.3 - - + -
271A HIS* 2.8 34.6 + - - +
273A LEU* 4.2 13.5 - - + -
283A LEU* 3.5 31.0 - - + -
307A TRP* 4.0 19.5 - + + -
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Residues in contact with GLY 234 (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 ARG* 3.3 20.3 + - - +
221A HIS* 3.2 10.7 - - - +
233A PHE* 1.3 82.6 - - - +
235A GLY* 1.3 61.3 + - - -
242A MET* 3.2 27.4 - - - -
244A ASP* 3.1 15.9 + - - -
268A ARG 3.7 4.0 - - - -
271A HIS* 3.9 2.9 - - - -
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Residues in contact with GLY 235 (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 ARG* 4.6 1.1 - - - -
219A ALA 3.6 11.2 - - - -
220A ALA 3.7 3.4 - - - -
221A HIS* 3.6 13.2 - - - -
234A GLY* 1.3 74.3 - - - -
236A ARG* 1.3 60.6 + - - -
241A ARG* 3.4 0.3 - - - -
242A MET* 2.8 36.3 + - - +
268A ARG 2.8 18.0 + - - -
269A SER* 4.0 2.5 - - - -
271A HIS* 3.7 1.8 - - - -
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Residues in contact with ARG 236 (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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178A ASP* 4.6 8.7 + - - -
180A THR* 5.1 2.8 + - - -
191A TRP* 3.7 21.9 + - - +
218A ARG* 3.3 5.7 - - - -
219A ALA 3.0 28.8 + - - +
235A GLY* 1.3 73.0 - - - -
237A TYR* 1.3 59.8 + - - +
238A ARG 2.8 28.0 + - - -
239A ASP* 4.6 7.7 + - - +
240A ALA 3.2 15.7 + - - -
241A ARG* 4.0 19.3 - - + +
269A SER* 3.9 4.4 - - - -
670C GLY* 3.4 33.3 - - - +
671C GLY* 2.7 51.2 + - - +
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Residues in contact with TYR 237 (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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176A GLU* 3.1 28.4 + - + +
191A TRP* 3.8 13.0 - + - -
216A SER* 3.6 23.8 - - - -
217A PRO* 3.0 48.2 - - + +
235A GLY 4.0 0.6 + - - -
236A ARG* 1.3 75.5 - - - +
238A ARG* 1.3 116.6 + - + +
239A ASP 3.0 4.2 + - - -
240A ALA* 2.9 19.6 + - - +
242A MET* 3.8 18.8 - - + +
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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