Contacts of the helix formed by residues 190 - 197 (chain D) in PDB entry 3FZ7
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 ASP 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D GLN* 4.0 11.3 - - + +
188D PHE 3.1 3.2 + - - +
189D MET* 1.3 73.5 - - - +
191D PRO* 1.3 75.8 - - + +
192D LYS* 3.1 12.6 + - - +
193D ARG* 2.8 59.8 + - - +
194D MET* 3.0 20.8 + - - +
223D LEU* 4.0 2.5 - - - -
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Residues in contact with PRO 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ASP* 1.3 87.2 - - + +
192D LYS* 1.3 57.2 + - - +
194D MET* 3.5 6.0 - - + +
195D ILE* 2.9 35.5 + - - +
222D PRO* 4.1 21.5 - - + +
223D LEU* 3.6 23.3 - - + -
226D ALA* 3.9 20.4 - - + -
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Residues in contact with LYS 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ASP* 3.2 9.9 + - - +
191D PRO* 1.3 76.4 - - - +
193D ARG* 1.3 65.0 + - + +
195D ILE* 3.3 5.6 + - - +
196D GLU* 2.8 55.7 + - + +
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Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D ILE* 3.2 32.2 - - + +
181D PRO* 2.4 42.0 + - - +
183D ARG* 3.7 19.8 - - - +
186D GLN* 3.3 44.2 + - - +
188D PHE 3.1 26.1 + - - -
190D ASP* 2.8 27.6 + - - +
192D LYS* 1.3 82.2 - - + +
194D MET* 1.3 64.6 + - - +
196D GLU* 3.4 20.3 + - - +
197D ALA* 3.3 19.6 + - - +
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Residues in contact with MET 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D VAL* 3.8 15.8 - - + +
180D ILE* 4.4 2.1 - - - +
189D MET* 3.6 26.9 - - + +
190D ASP 3.0 19.2 + - - +
191D PRO* 3.5 5.8 - - + +
193D ARG* 1.3 76.4 - - - +
195D ILE* 1.3 69.3 + - + +
197D ALA* 3.0 14.9 + - - +
198D CYS* 3.3 16.8 + - - -
205D VAL* 3.6 30.1 - - + -
223D LEU* 3.5 44.4 - - - +
226D ALA* 3.8 19.1 - - + -
227D LEU* 3.9 15.9 - - + -
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Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D PRO 2.9 23.0 + - - +
192D LYS* 3.8 5.2 - - - +
194D MET* 1.3 86.8 - - + +
196D GLU* 1.3 66.3 + - + +
197D ALA 2.9 1.2 + - - -
198D CYS* 2.9 21.3 + - - +
226D ALA* 3.7 23.6 - - + +
227D LEU* 4.1 8.7 - - + -
230D PHE* 3.7 49.8 - - + -
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Residues in contact with GLU 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D LYS* 2.8 47.2 + - + +
193D ARG* 3.8 25.2 - - - +
194D MET 3.3 0.4 - - - -
195D ILE* 1.3 74.0 - - + +
197D ALA* 1.3 57.7 + - - +
198D CYS 3.7 3.3 + - - +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D VAL* 3.4 15.9 - - + +
178D ARG* 2.8 48.2 + - + +
180D ILE* 4.3 14.4 - - + -
193D ARG 3.3 10.3 + - - +
194D MET 3.0 9.7 + - - +
195D ILE 3.0 1.0 - - - -
196D GLU* 1.3 79.1 - - + +
198D CYS* 1.3 55.4 + - - +
202D THR* 4.0 0.3 + - - -
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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