Contacts of the strand formed by residues 229 - 233 (chain M) in PDB entry 6VEN
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 LEU 229 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175M THR* 6.1 0.4 - - + -
185M ILE* 3.7 30.7 - - + -
193M LEU* 4.9 3.4 - - + -
195M PHE* 5.4 3.4 - - + -
220M LEU* 3.7 13.9 - - + -
221M ILE 3.5 14.6 - - - +
222M VAL* 4.6 8.1 - - + -
228M ARG* 1.3 75.9 - - - +
230M ALA* 1.3 83.9 + - - +
231M ILE* 3.7 23.1 - - + -
239M ARG 4.7 0.2 - - - -
240M GLN* 3.4 6.2 - - - +
241M TYR* 2.9 46.8 + - + +
243M ILE* 4.4 24.7 - - + -
254M LEU* 5.7 2.5 - - + -
274M PHE* 3.9 4.9 - - - -
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Residues in contact with ALA 230 (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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219M HIS 3.8 2.1 - - - +
220M LEU* 3.9 0.3 - - - -
221M ILE* 3.1 43.2 + - + -
229M LEU* 1.3 78.0 - - - +
231M ILE* 1.3 72.0 + - - +
238M ILE* 4.8 6.3 - - + -
239M ARG 3.4 7.6 - - - +
240M GLN* 4.8 4.5 - - + -
272M ILE* 4.3 7.6 - - + -
274M PHE* 3.5 20.4 - - + -
282M LEU* 4.3 9.0 - - + -
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Residues in contact with ILE 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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193M LEU* 3.5 41.7 - - + -
212M ILE* 3.6 15.5 - - + -
217M ILE* 3.6 35.0 - - + -
219M HIS 3.6 4.7 - - - +
220M LEU* 3.7 10.1 - - + -
229M LEU* 3.7 13.7 - - + -
230M ALA* 1.3 82.9 - - - +
232M ASN* 1.3 62.3 + - - +
233M CYS* 3.9 12.3 + - - -
238M ILE* 3.4 6.6 - - - +
239M ARG* 2.9 38.6 + - + +
241M TYR* 3.9 7.4 - - + -
272M ILE* 4.1 4.0 - - - -
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Residues in contact with ASN 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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217M ILE* 3.8 0.7 - - - -
218M LYS* 2.9 34.0 + - - +
219M HIS* 3.5 32.7 + - + +
231M ILE* 1.3 74.3 - - - +
233M CYS* 1.3 71.3 + - - +
237M THR 3.7 3.4 - - - +
238M ILE* 4.7 3.1 - - + -
268M GLN* 5.7 0.7 - - - +
269M TRP* 3.2 60.4 + - - +
270M ASN 4.3 1.4 - - - +
271M CYS 4.6 1.0 - - - +
272M ILE* 3.8 20.5 - - + +
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Residues in contact with CYS 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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213M THR* 4.1 7.0 - - + +
215M SER* 3.7 10.3 - - - +
216M ASN 3.6 5.6 - - - +
217M ILE* 4.0 18.6 - - - -
218M LYS* 4.0 5.2 - - - +
231M ILE* 4.1 3.6 - - - -
232M ASN* 1.3 86.4 + - - +
234M SER* 1.3 59.9 + - - +
235M ASP* 2.7 31.3 - - + +
237M THR* 3.4 9.2 + - - +
239M ARG* 3.0 48.2 - - - -
268M GLN* 5.0 3.6 - - - +
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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