Contacts of the strand formed by residues 208 - 218 (chain D) in PDB entry 4JF7
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 PRO 208 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D TYR* 3.6 16.4 - - + +
148D MET* 3.6 19.7 - - - +
200D ILE* 3.5 22.7 - - + -
201D GLU 3.7 0.2 - - - +
203D THR* 4.5 0.2 - - - +
207D PHE* 1.3 103.0 - - + +
209D PHE* 1.3 59.2 + - - +
210D PHE* 4.3 2.9 - - + -
529D PHE* 3.5 31.4 - - + -
538D TYR* 3.8 20.4 - - + -
559D ILE* 3.8 17.9 - - + -
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Residues in contact with PHE 209 (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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148D MET* 4.6 3.4 - - + -
149D PRO* 4.0 45.5 - - + -
200D ILE* 3.4 3.8 - - - -
201D GLU* 2.8 59.7 + - + +
203D THR* 3.6 19.5 - - + -
207D PHE 3.7 0.2 + - - -
208D PRO* 1.3 73.0 - - - +
210D PHE* 1.3 78.2 + - - +
211D ARG* 3.3 40.4 + - + -
212D THR 4.8 1.6 - - - -
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Residues in contact with PHE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D MET* 3.6 33.1 - - + -
149D PRO 4.8 1.6 - - - +
151D PHE* 3.5 44.3 - + + +
167D PHE* 3.6 24.9 - + - -
169D LEU* 5.2 1.6 - - + -
174D TRP* 3.6 23.8 - + + +
199D ILE 3.6 3.1 - - - -
200D ILE* 4.1 16.4 - - + -
208D PRO* 4.3 4.7 - - + -
209D PHE* 1.3 88.1 - - - +
211D ARG* 1.3 62.7 + - - +
212D THR* 3.4 4.0 + - - -
529D PHE* 3.8 36.1 - + - -
540D ILE* 4.5 13.5 - - + -
559D ILE* 4.2 8.7 - - + -
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Residues in contact with ARG 211 (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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174D TRP* 3.9 1.3 - - - -
198D GLY* 3.1 3.6 - - - -
199D ILE* 2.7 58.5 + - + +
201D GLU* 3.5 34.7 + - - -
209D PHE* 3.3 28.8 + - + +
210D PHE* 1.3 70.1 - - - +
212D THR* 1.3 63.9 + - - +
213D LEU* 3.6 28.9 + - + +
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Residues in contact with THR 212 (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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151D PHE* 3.8 19.8 + - - +
174D TRP* 3.7 15.2 - - - -
196D SER* 4.2 6.4 + - - -
197D MET 3.8 6.3 - - - +
209D PHE* 4.8 2.0 - - - -
210D PHE 3.4 2.7 + - - -
211D ARG* 1.3 74.4 + - - +
213D LEU* 1.3 68.1 + - - +
214D LYS 3.7 22.0 - - - +
215D THR* 3.8 20.4 - - + -
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Residues in contact with LEU 213 (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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116D ALA* 4.7 4.0 - - + -
117D LEU* 3.6 42.8 - - + +
197D MET 2.9 10.0 + - - +
198D GLY* 4.0 2.7 - - - -
199D ILE* 3.9 18.2 - - + -
211D ARG* 3.8 41.3 - - + +
212D THR* 1.3 81.9 - - - +
214D LYS* 1.3 64.3 + - - +
266D TYR* 3.8 30.3 + - + +
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Residues in contact with LYS 214 (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 SER* 3.2 7.0 - - - -
197D MET* 3.0 46.4 + - + +
212D THR* 3.6 2.4 - - - +
213D LEU* 1.3 82.6 + - - +
215D THR* 1.3 72.5 + - - +
216D LEU* 3.9 20.9 - - + -
264D MET* 6.4 0.2 - - + -
265D TYR 3.6 12.6 - - - +
266D TYR* 2.9 43.1 + - + +
268D ASP* 3.0 35.9 + - - +
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Residues in contact with THR 215 (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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194D PHE* 3.7 30.1 - - + -
195D VAL 3.3 6.5 - - - -
196D SER* 3.9 1.1 - - - -
212D THR* 3.8 18.4 - - + -
214D LYS* 1.3 83.1 - - - +
216D LEU* 1.3 70.5 + - - +
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Residues in contact with LEU 216 (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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193D GLN 4.7 0.2 - - - -
194D PHE* 3.6 7.5 - - - -
195D VAL* 2.7 58.2 + - + +
196D SER* 5.0 0.2 - - - -
197D MET* 4.3 12.3 - - + -
214D LYS* 3.9 24.5 - - + +
215D THR* 1.3 84.2 - - - +
217D TYR* 1.3 62.7 + - - +
218D LEU* 4.1 10.5 - - + -
264D MET* 3.9 22.7 - - + -
268D ASP* 5.1 3.8 - - - +
270D ILE* 3.6 32.1 - - + -
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Residues in contact with TYR 217 (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 VAL* 3.6 32.6 - - + +
182D LEU* 4.3 5.0 - - - +
192D ASN* 3.1 43.7 + - + +
193D GLN 3.7 11.0 - - - -
194D PHE* 4.1 16.8 - + + -
216D LEU* 1.3 75.8 - - - +
218D LEU* 1.3 63.7 + - - +
219D SER* 3.3 22.0 + - - -
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Residues in contact with LEU 218 (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 SER 4.9 0.3 - - - +
192D ASN* 3.4 7.8 - - - +
193D GLN* 2.9 40.2 + - + +
195D VAL* 4.5 6.7 - - + -
216D LEU* 4.9 17.3 - - + -
217D TYR* 1.3 72.3 - - - +
219D SER* 1.3 58.9 + - - +
220D ASP 3.9 2.0 + - - -
222D VAL 5.7 0.5 - - - +
224D ARG* 3.8 38.5 + - - +
238D MET* 3.6 31.6 - - + -
262D ILE* 4.8 14.8 - - + -
264D MET* 5.0 4.0 - - - -
270D ILE* 5.4 8.7 - - + -
272D GLU* 5.9 0.2 - - - +
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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