Contacts of the strand formed by residues 195 - 204 (chain D) in PDB entry 6BAA
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 ARG 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191D PRO* 3.8 1.6 - - - -
192D ARG 2.8 34.5 + - - +
193D HIS* 4.2 8.5 - - + +
194D GLY* 1.3 83.7 - - - +
196D LEU* 1.3 64.3 + - - +
197D CYS* 3.3 4.0 + - - +
260D VAL* 3.8 26.8 - - + +
261D ILE 3.1 26.8 + - - -
262D ASP* 3.5 21.0 - - - +
349D LEU* 5.6 0.4 - - - -
350D ASP* 4.3 22.7 + - - -
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Residues in contact with LEU 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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189D ILE* 3.7 23.6 - - + -
190D THR* 4.0 15.3 - - - -
191D PRO* 3.9 13.5 - - + +
194D GLY 4.0 2.0 + - - -
195D ARG* 1.3 73.6 - - - +
197D CYS* 1.3 58.2 + - - +
260D VAL* 4.0 1.6 - - - +
261D ILE* 3.0 36.9 + - + +
270D LEU* 6.3 0.2 - - + -
311D TRP* 3.6 33.7 - - + -
341D THR* 4.5 7.6 - - - +
342D PRO* 5.3 3.8 - - + +
344D CYS 4.6 1.8 - - - +
346D ALA* 4.0 34.3 - - + +
349D LEU* 4.2 21.5 - - + +
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Residues in contact with CYS 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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189D ILE* 3.3 10.0 - - - +
190D THR 2.8 54.8 + - - +
192D ARG* 3.7 18.2 - - - -
195D ARG 4.1 2.5 - - - +
196D LEU* 1.3 75.8 - - - +
198D PHE* 1.3 58.7 + - - +
199D MET* 3.5 33.4 - - - -
258D TYR* 4.4 8.5 - - + -
259D HIS 3.3 14.1 - - - +
260D VAL* 4.0 15.5 - - + -
261D ILE* 4.4 4.3 - - - +
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Residues in contact with PHE 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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187D ALA* 3.3 27.4 - - + -
188D VAL 3.5 8.3 - - - -
189D ILE* 4.3 14.4 - - + +
197D CYS* 1.3 71.0 - - - +
199D MET* 1.3 63.1 + - - +
200D LEU* 4.5 6.7 - - + -
217D MET* 4.1 35.2 - - + -
257D ILE 5.4 0.2 - - - -
258D TYR* 2.8 8.1 - - - +
259D HIS* 2.8 48.7 + - + +
261D ILE* 4.8 1.8 - - + +
267D LEU* 4.5 22.2 - - + -
270D LEU* 6.1 0.2 - - + -
283D ILE* 4.0 27.4 - - + -
304D TYR* 5.0 1.8 - + + -
309D ILE* 3.5 31.4 - - + -
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Residues in contact with MET 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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229C GLU* 6.0 6.1 - - + -
187D ALA* 2.9 10.0 - - - +
188D VAL* 2.7 51.1 + - + -
190D THR* 3.7 21.3 - - + -
191D PRO 5.4 0.2 - - - +
192D ARG* 3.0 44.6 - - + +
197D CYS* 3.5 24.9 - - - -
198D PHE* 1.3 77.9 - - - +
200D LEU* 1.3 62.1 + - - +
256D ILE* 3.9 19.3 - - + -
257D ILE 3.5 2.2 - - - -
258D TYR* 3.8 11.9 - - + -
314D ARG* 5.3 5.6 - - - -
315D PHE* 4.2 10.4 - - + -
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Residues in contact with LEU 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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183D PHE* 4.2 7.9 - - + -
184D SER* 4.6 0.4 - - - -
187D ALA* 4.1 8.1 - - + -
198D PHE* 4.5 7.2 - - + -
199D MET* 1.3 77.4 - - - +
201D ARG* 1.3 75.8 + - - +
202D VAL* 4.0 11.9 - - + +
217D MET* 4.5 7.4 - - + -
256D ILE* 3.4 5.4 - - - +
257D ILE* 2.6 56.1 + - + +
285D VAL* 3.4 27.4 - - + -
304D TYR* 3.3 44.0 - - + +
315D PHE* 4.5 4.5 - - - -
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Residues in contact with ARG 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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183D PHE* 3.6 1.4 - - - -
184D SER* 3.0 34.0 + - - -
200D LEU* 1.3 81.6 - - - +
202D VAL* 1.3 63.8 + - - +
254D PRO* 4.1 17.7 + - + +
255D LEU 3.2 7.2 - - - +
256D ILE* 3.5 19.9 - - + +
315D PHE* 3.2 51.9 - - + +
316D VAL 2.9 27.9 + - - -
317D PRO* 4.9 0.8 - - - +
318D ILE* 3.2 22.9 - - - +
332D LYS 5.0 0.2 + - - -
333D PHE* 3.4 53.5 + - + -
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Residues in contact with VAL 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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182D ILE 3.1 13.7 - - - +
183D PHE* 4.0 18.8 - - + -
200D LEU* 4.1 8.7 - - + -
201D ARG* 1.3 76.8 - - - +
203D GLY* 1.3 63.9 + - - +
215D ILE* 4.5 6.3 - - + -
251D LEU* 3.7 25.9 - - + +
254D PRO* 3.3 2.4 - - - +
255D LEU* 2.9 33.6 + - + +
257D ILE* 3.5 32.5 - - + -
287D LEU* 4.0 16.4 - - + -
333D PHE* 4.3 4.9 - - - -
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Residues in contact with GLY 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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181D LEU* 3.6 9.4 - - - +
182D ILE* 2.8 34.8 + - - +
202D VAL* 1.3 79.8 - - - +
204D ASP* 1.3 59.8 + - - +
251D LEU* 3.8 11.8 - - - +
254D PRO* 4.4 6.5 - - - -
330D TYR* 5.3 0.4 - - - -
333D PHE* 4.0 17.3 - - - -
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Residues in contact with ASP 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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46C HIS* 4.6 5.7 - - - -
177D ARG* 3.3 23.6 + - - -
180D THR* 3.9 7.4 + - - -
181D LEU* 3.3 21.5 - - + +
203D GLY* 1.3 75.2 - - - +
205D LEU* 1.3 63.0 + - - +
206D ARG* 2.9 26.7 + - - +
208D SER 4.3 4.3 - - - +
209D MET* 5.3 1.0 - - - -
210D ILE* 3.4 13.2 + - - +
251D LEU* 3.5 24.9 - - + +
252D VAL 4.7 4.7 + - - +
253D ALA 6.0 0.4 - - - -
254D PRO* 5.8 0.2 - - - +
330D TYR* 3.4 20.1 + - - -
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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