Contacts of the helix formed by residues 189 - 201 (chain L) in PDB entry 3CX5
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 VAL 189 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137L PHE* 3.7 12.6 - - + -
141L LYS* 5.3 2.0 - - - +
187L ASN 4.2 7.6 - - - +
188L LEU* 1.3 78.0 - - - +
190L VAL* 1.3 67.8 + - - +
191L ALA* 3.9 18.8 - - + +
192L ASP* 2.8 34.2 + - - +
193L LEU* 3.3 11.3 - - - +
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Residues in contact with VAL 190 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132L LEU* 3.9 41.1 - - + +
133L SER 5.6 0.9 - - - -
134L SER* 5.8 2.2 - - - +
137L PHE* 3.6 37.5 - - + -
189L VAL* 1.3 73.5 - - - +
191L ALA* 1.3 63.3 + - - +
193L LEU* 3.0 8.0 + - - +
194L GLU* 3.0 38.3 + - - +
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Residues in contact with ALA 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L VAL* 3.1 13.5 + - + +
190L VAL* 1.3 77.4 - - - +
192L ASP* 1.3 56.8 + - - +
194L GLU* 3.7 14.1 + - - +
195L SER* 2.8 32.1 + - - -
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Residues in contact with ASP 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L ASN* 5.1 9.8 - - + +
69L VAL* 3.8 6.7 - - + +
187L ASN 3.9 3.5 - - - +
188L LEU* 3.4 29.5 - - + +
189L VAL* 2.8 40.9 + - - +
191L ALA* 1.3 76.4 - - - +
193L LEU* 1.3 58.6 + - + +
195L SER* 3.4 6.8 + - - -
196L PHE* 2.9 30.7 + - - +
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Residues in contact with LEU 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L VAL* 3.6 22.4 - - + +
72L LEU* 3.7 25.1 - - + -
73L TRP* 2.9 59.0 + - + +
76L ILE* 3.9 13.7 - - + -
132L LEU* 4.5 7.9 - - + -
137L PHE* 3.6 25.8 - - + -
188L LEU* 4.9 1.1 - - + -
189L VAL 3.3 17.7 - - - +
190L VAL* 3.0 8.4 + - - +
192L ASP* 1.3 78.1 - - + +
194L GLU* 1.3 57.0 + - - +
196L PHE 3.3 1.0 + - - -
197L ALA* 2.9 18.4 + - - +
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Residues in contact with GLU 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L TRP* 4.6 1.6 - - - -
128L LYS 4.8 3.3 - - - +
129L ALA* 4.7 11.6 - - - +
132L LEU* 3.7 22.1 - - + +
190L VAL* 3.0 22.6 + - - +
191L ALA* 3.7 19.0 + - - +
193L LEU* 1.3 72.1 - - - +
195L SER* 1.3 60.8 + - - +
197L ALA* 3.3 6.2 + - - +
198L ASN* 2.9 43.0 + - - +
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Residues in contact with SER 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L ALA 2.8 19.3 + - - -
192L ASP* 3.5 9.0 - - - -
194L GLU* 1.3 77.4 - - - +
196L PHE* 1.3 61.1 + - - +
198L ASN* 3.5 8.4 + - - +
199L ASN* 2.8 37.4 + - - +
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Residues in contact with PHE 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L SER* 4.7 3.1 - - - -
58L GLY 4.4 8.7 - - - -
61L ASN* 4.1 8.3 - - + -
62L GLU* 3.9 17.9 - - + -
66L ASN* 4.4 9.6 - - - +
69L VAL* 3.6 22.9 - - + -
70L SER* 3.5 23.1 - - - -
73L TRP* 4.2 15.3 - + - -
102L GLN* 3.7 16.6 - - - -
192L ASP 2.9 18.3 + - - +
193L LEU 3.7 3.8 - - - +
195L SER* 1.3 77.9 - - - +
197L ALA* 1.3 57.6 + - - +
199L ASN* 3.1 2.6 + - - -
200L HIS* 2.9 69.7 + + + +
201L PHE* 4.2 8.1 - + - -
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Residues in contact with ALA 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L TRP* 3.6 14.6 - - + +
128L LYS* 4.3 10.3 - - + -
193L LEU 2.9 18.1 + - - +
194L GLU* 3.6 7.0 - - - +
196L PHE* 1.3 77.1 - - - +
198L ASN* 1.3 61.0 + - - +
201L PHE* 2.8 63.7 + - + +
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Residues in contact with ASN 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L GLU* 2.9 30.5 + - - +
195L SER* 3.8 7.5 - - - +
197L ALA* 1.3 78.1 - - - +
199L ASN* 1.3 63.5 + - - +
202L LEU* 3.2 25.3 - - - +
234L THR* 4.9 4.3 - - - +
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Residues in contact with ASN 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L SER* 2.8 28.3 + - - +
196L PHE* 3.1 2.4 + - - -
198L ASN* 1.3 83.4 + - - +
200L HIS* 1.3 74.5 + - + +
202L LEU* 3.4 17.1 - - - +
234L THR* 6.1 1.3 - - - +
235L LYS 5.9 1.0 + - - -
236L PRO* 3.4 17.3 - - - +
237L VAL* 3.7 26.6 - - + +
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Residues in contact with HIS 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L PHE* 3.8 4.6 - - + -
57L SER* 2.9 32.9 + - - +
61L ASN* 3.8 27.8 + - + -
196L PHE* 2.9 56.5 + + + +
199L ASN* 1.3 96.2 + - + +
201L PHE* 1.3 60.8 + - + +
202L LEU* 2.8 14.1 + - - -
205L ASN* 3.0 24.8 + - - +
236L PRO* 4.4 5.2 - - + +
237L VAL* 4.6 23.7 - - + +
239L LYS* 6.0 1.5 - - - -
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Residues in contact with PHE 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L PHE* 3.6 41.2 - + + -
73L TRP* 3.8 38.4 - + - -
102L GLN* 3.5 34.1 - - - -
104L TYR* 3.7 12.1 - + - -
124L PHE* 4.0 12.1 - + + -
128L LYS* 3.9 20.0 - - - -
196L PHE* 4.2 10.3 - + - -
197L ALA* 2.8 39.0 + - + +
200L HIS* 1.3 74.3 - - + +
202L LEU* 1.3 64.2 + - - +
231L GLN* 5.1 8.1 + - - -
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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