Contacts of the helix formed by residues 196 - 204 (chain D) in PDB entry 6NIL
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 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D MET* 1.3 74.6 - - - +
197D PRO* 1.3 79.4 - - - +
198D HIS* 3.1 29.4 + - + +
199D ILE* 3.2 25.7 + - + +
200D PHE* 3.4 3.5 + - - +
345D TYR* 3.6 13.3 - - - +
20L THR* 4.2 10.2 + - - -
23L ARG* 3.3 37.0 + - - +
24L LEU* 3.9 16.8 - - - +
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Residues in contact with PRO 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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195D MET 3.9 0.4 - - - -
196D ASP* 1.3 98.2 - - - +
198D HIS* 1.3 57.9 + - + +
199D ILE 3.2 0.7 - - - -
200D PHE* 3.5 11.8 - - + +
201D TYR* 3.2 36.6 + - + -
340D TRP* 3.7 29.4 - - + -
344D VAL* 3.8 7.2 - - + -
345D TYR 3.5 19.3 - - - +
346D ASN* 5.5 0.7 - - - -
347D ASP* 5.8 3.8 - - - +
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Residues in contact with HIS 198 (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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196D ASP* 3.1 30.8 + - + +
197D PRO* 1.3 81.1 - - + +
199D ILE* 1.3 75.8 + - + +
201D TYR* 4.3 4.9 - - - -
202D PHE* 3.4 8.8 + - - +
23L ARG* 6.0 0.7 - - + -
24L LEU* 4.8 3.5 - - + +
27L HIS* 3.2 35.7 + + + -
159L ILE 4.3 8.3 - - - +
160L LYS* 3.3 29.5 - - + +
161L PRO* 3.5 43.4 - - + +
162L PRO* 4.7 5.8 - - + +
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Residues in contact with ILE 199 (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 MET* 6.2 0.9 - - - -
195D MET* 3.7 25.4 - - + +
196D ASP* 3.2 18.3 + - + +
198D HIS* 1.3 101.6 - - + +
200D PHE* 1.3 64.2 + - - +
201D TYR 3.3 1.1 - - - -
202D PHE* 3.6 9.2 - - + -
203D HIS* 3.1 39.3 + - + +
217D TRP* 3.6 35.0 - - + -
27L HIS* 5.6 0.2 - - - +
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Residues in contact with PHE 200 (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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195D MET* 3.7 14.6 - - + -
196D ASP 3.4 1.2 + - - +
197D PRO* 3.3 18.6 + - + +
199D ILE* 1.3 83.2 - - - +
201D TYR* 1.3 81.9 + + - +
204D PHE* 2.8 72.4 + + + +
336D PHE* 4.1 28.0 - + - -
339D CYS* 3.6 18.6 - - + -
340D TRP* 3.5 25.8 - + - -
344D VAL* 3.7 20.6 - - + -
351D PHE* 4.5 7.4 - + - -
354D TRP* 4.8 6.5 - + - -
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Residues in contact with TYR 201 (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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197D PRO* 3.2 18.8 + - + +
198D HIS* 4.9 4.9 - - - +
200D PHE* 1.3 104.3 - + - +
202D PHE* 1.3 63.2 + - - +
203D HIS 3.2 0.6 + - - -
205D LYS* 3.3 46.8 - - + +
340D TRP* 3.5 23.5 - + - -
352D LYS* 3.2 56.2 + - + +
354D TRP* 4.3 8.7 - + - -
158L GLN* 6.1 4.7 - - - -
160L LYS* 5.5 7.9 - - + -
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Residues in contact with PHE 202 (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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198D HIS 3.4 19.5 + - - +
199D ILE* 3.4 12.0 + - + -
200D PHE 3.3 0.8 - - - -
201D TYR* 1.3 78.5 - - - +
203D HIS* 1.3 84.7 + + - +
205D LYS* 5.9 0.2 - - - -
210D ALA* 5.6 5.5 - - - +
213D ARG* 3.5 49.6 - - + -
160L LYS* 4.3 28.5 - - + +
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Residues in contact with HIS 203 (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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195D MET* 5.6 0.9 - - + -
199D ILE* 3.1 33.2 + - + +
201D TYR 3.2 0.2 - - - -
202D PHE* 1.3 111.1 + + - +
204D PHE* 1.3 71.3 + - + +
205D LYS 3.3 8.1 + - - +
210D ALA* 5.6 1.0 - - - +
213D ARG* 4.7 13.2 + - + -
215D GLU* 4.8 18.6 + - + -
217D TRP* 3.1 49.2 + + + -
276D SER* 3.9 9.0 - - - -
305D ARG* 3.7 26.2 + - - +
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Residues in contact with PHE 204 (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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195D MET* 4.4 10.8 - - + -
200D PHE* 2.8 55.7 + + + +
203D HIS* 1.3 81.6 - - + +
205D LYS* 1.3 58.8 + - - +
206D ASN 4.1 0.2 + - - -
217D TRP* 3.7 25.8 - - + -
219D CYS* 3.7 26.5 - - - -
274D TYR* 4.0 16.6 - - + -
275D THR 4.4 0.9 - - - -
276D SER* 3.5 33.7 - - - +
304D ALA* 5.3 10.5 - - + -
305D ARG* 5.6 0.7 - - - +
331D MET* 5.9 4.5 - - + -
336D PHE* 3.6 18.0 - + + -
339D CYS* 4.0 8.3 - - - -
354D TRP* 3.2 18.8 - - - -
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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