Contacts of the strand formed by residues 163 - 169 (chain M) in PDB entry 3V3K
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 GLY 163 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162M CYS* 1.3 83.1 - - - +
164M HIS* 1.3 64.7 + - - -
198M PHE* 3.3 11.1 - - - -
199M MET* 2.9 30.2 + - - +
227M LEU* 3.7 18.6 - - - -
229M CYS 3.6 12.3 - - - -
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Residues in contact with HIS 164 (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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163M GLY* 1.3 76.2 - - - -
165M CYS* 1.3 60.1 + - - +
166M LEU 4.2 0.4 - - - -
198M PHE* 3.7 3.5 - - - -
199M MET* 3.4 41.1 + - + +
201M GLU* 5.9 1.0 + - - -
218M LEU* 3.4 28.5 - - + +
221M GLN* 4.4 21.9 + - + +
222M ASP 5.5 1.2 + - - -
224M HIS* 3.8 16.0 - + + -
227M LEU* 3.3 28.3 - - + +
229M CYS 4.4 2.4 + - - -
230M CYS* 3.9 4.1 - - - -
231M VAL 3.4 20.6 + - - -
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Residues in contact with CYS 165 (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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164M HIS* 1.3 77.4 - - - +
166M LEU* 1.3 59.7 + - - +
167M ILE* 3.7 12.4 + - - -
193M PHE* 3.6 39.9 - - - -
198M PHE* 3.8 21.8 - - + -
199M MET 3.2 7.5 + - - -
200M VAL* 3.4 12.5 - - + +
201M GLU* 3.0 23.9 + - - +
231M VAL* 3.4 20.9 - - + -
233M VAL* 4.9 0.4 - - - -
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Residues in contact with LEU 166 (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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164M HIS 4.2 0.2 - - - -
165M CYS* 1.3 72.9 - - - +
167M ILE* 1.3 61.6 + - - +
168M ILE* 4.0 19.5 - - + -
201M GLU* 3.6 24.7 - - + +
203M LYS* 4.2 28.9 - - + -
214M ALA* 4.0 25.4 - - + +
215M LEU* 3.8 27.6 - - + +
218M LEU* 3.6 26.0 - - + +
231M VAL 3.3 6.8 + - - +
232M VAL* 3.5 6.9 - - + +
233M VAL* 2.9 26.9 + - - +
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Residues in contact with ILE 167 (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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165M CYS* 4.0 17.0 - - - +
166M LEU* 1.3 77.5 - - - +
168M ILE* 1.3 67.4 + - - +
169M ASN* 3.7 1.8 + - + -
186M CYS* 3.7 28.3 - - + +
189M LEU* 4.1 14.8 - - + +
190M ARG* 4.0 23.1 - - + +
193M PHE* 4.7 1.8 - - + -
200M VAL* 3.8 22.9 - - + -
201M GLU 3.1 11.2 + - - +
202M VAL* 3.5 9.1 - - + +
203M LYS 2.9 25.0 + - - -
233M VAL* 3.5 25.4 - - + -
235M LEU* 4.9 3.6 - - + -
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Residues in contact with ILE 168 (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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166M LEU* 4.2 23.1 - - + -
167M ILE* 1.3 73.1 - - - +
169M ASN* 1.3 62.8 + - - +
170M ASN* 3.5 22.9 - - - +
203M LYS* 3.5 5.4 - - + +
206M LEU* 3.6 31.9 - - + -
211M MET* 3.7 48.5 - - + +
214M ALA* 5.0 0.2 - - + -
215M LEU* 4.4 9.0 - - + -
232M VAL* 5.9 0.2 - - + -
233M VAL 3.1 11.5 + - - +
234M ILE* 3.5 13.7 - - + -
235M LEU* 2.9 29.1 + - - +
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Residues in contact with ASN 169 (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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167M ILE* 3.7 2.0 + - + +
168M ILE* 1.3 73.6 - - - +
170M ASN* 1.3 61.7 + - - +
171M VAL* 3.4 12.2 + - - +
179M ARG* 4.0 0.2 + - - -
182M SER* 2.7 32.6 + - - -
183M ASN* 3.5 24.2 - - - +
186M CYS* 3.4 41.1 - - - +
202M VAL* 4.8 1.9 - - + +
203M LYS 3.3 8.3 + - - -
204M GLY* 3.4 10.2 - - - -
205M ASP* 3.0 18.6 + - - +
235M LEU* 3.6 9.1 - - + +
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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