Contacts of the strand formed by residues 229 - 233 (chain M) in PDB entry 6DZT
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 PHE 229 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M THR* 3.4 9.2 - - - +
181M CYS* 3.1 32.2 + - + +
183M ALA* 4.6 1.6 - - + -
187M ILE* 3.7 36.1 - - + -
189M SER* 4.0 8.3 - - - -
191M LEU* 3.6 32.1 - - + -
193M TRP* 4.7 2.5 - - + +
209M ALA* 3.8 21.1 - - + -
223M SER 3.5 6.5 - - - +
224M GLY* 3.5 18.4 - - - -
225M SER* 3.6 17.9 - - - -
226M GLY 3.5 24.9 - - - -
227M GLN* 3.4 20.6 + - - -
228M ASP* 1.3 73.8 - - - +
230M SER* 1.3 66.1 + - - +
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Residues in contact with SER 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178M THR* 5.4 5.4 - - - -
179M ILE 3.2 10.5 - - - -
180M THR* 4.5 9.9 - - - -
193M TRP* 4.2 6.8 + - - -
221M SER 4.0 0.2 - - - +
222M GLY* 3.4 3.3 - - - -
223M SER* 2.8 53.9 + - - +
224M GLY* 4.6 0.7 + - - -
229M PHE* 1.3 78.3 - - - +
231M LEU* 1.3 62.6 + - - +
232M THR* 4.6 6.0 + - - -
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Residues in contact with LEU 231 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M VAL 3.7 0.5 - - - +
178M THR* 3.3 5.9 - - - -
179M ILE* 2.8 49.3 + - + +
193M TRP* 3.7 45.7 - - + +
205M LEU* 4.4 7.9 - - + -
206M ILE* 3.7 27.8 - - + -
220M PHE* 4.6 9.4 - - + -
221M SER 3.6 3.1 - - - +
222M GLY* 4.6 0.4 - - - -
230M SER* 1.3 72.1 - - - +
232M THR* 1.3 80.0 + - - +
233M ILE* 4.6 5.2 - - + -
244M TYR* 3.9 28.0 - - + -
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Residues in contact with THR 232 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M ARG* 4.0 23.8 - - + +
177M VAL 3.2 14.1 - - - +
178M THR* 4.4 11.0 - - + +
219M ARG 3.4 1.7 - - - +
220M PHE* 3.3 4.0 - - - -
221M SER* 2.7 52.8 + - - -
222M GLY* 5.5 0.2 - - - -
223M SER* 5.4 3.5 + - - -
230M SER* 4.6 9.0 + - - -
231M LEU* 1.3 78.8 + - - +
233M ILE* 1.3 62.8 + - - +
234M ASN* 4.1 11.7 - - - +
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Residues in contact with ILE 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M GLU 3.8 2.6 - - - +
176M ARG* 3.3 1.4 - - - -
177M VAL* 3.1 44.0 + - + -
179M ILE* 5.0 2.2 - - + -
219M ARG* 3.7 14.8 - - + +
220M PHE* 3.8 22.7 - - + -
231M LEU* 4.6 9.9 - - + -
232M THR* 1.3 75.6 - - - +
234M ASN* 1.3 65.5 + - - +
235M ASN 4.3 3.1 - - - +
236M LEU* 3.8 11.7 - - + -
240M ASP* 3.6 21.5 - - - +
244M TYR* 3.9 35.0 - - + +
262M LEU* 4.3 15.5 - - + -
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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