Contacts of the strand formed by residues 192 - 202 (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 ASN 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D ASN* 3.3 8.1 + - - -
180D VAL* 2.7 37.9 + - + +
182D LEU* 4.4 19.8 - - - +
191D SER* 1.3 82.3 - - - +
193D GLN* 1.3 59.7 + - - +
194D PHE 4.2 0.2 - - - -
217D TYR* 3.1 35.8 + - + +
218D LEU 3.4 7.9 - - - +
219D SER* 3.1 37.3 + - - -
220D ASP 4.5 0.5 + - - -
221D GLY 4.9 3.3 + - - -
222D VAL 5.6 0.4 - - - -
224D ARG* 5.6 0.7 - - - -
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Residues in contact with GLN 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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164D ILE 4.8 2.8 + - - -
177D THR* 2.8 28.4 + - - +
178D HIS* 3.4 20.1 - - - +
179D ASN* 2.9 31.5 + - - +
192D ASN* 1.3 76.0 - - - +
194D PHE* 1.3 58.9 + - - +
195D VAL 3.9 0.2 + - - -
217D TYR* 3.7 3.7 - - - -
218D LEU* 2.9 47.4 + - + +
224D ARG* 3.8 12.3 - - + +
225D LYS* 5.4 0.2 - - - -
227D CYS* 3.6 34.3 + - - +
238D MET* 4.1 18.2 - - + -
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Residues in contact with PHE 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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151D PHE 4.9 2.0 - - - -
153D PRO* 3.5 43.7 - - + -
176D TYR* 4.2 13.7 - + - -
177D THR* 2.6 27.0 + - - -
178D HIS* 2.8 37.4 + - + +
180D VAL* 4.3 5.3 - - + +
192D ASN 4.2 0.8 - - - -
193D GLN* 1.3 72.5 - - - +
195D VAL* 1.3 57.5 + - - +
196D SER* 3.5 25.8 - - - -
215D THR* 3.7 38.1 - - + -
216D LEU 3.6 10.8 - - - -
217D TYR* 4.1 16.9 - + + -
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D TYR 3.3 10.3 - - - +
177D THR* 3.5 11.7 - - - +
193D GLN* 4.4 7.0 - - + +
194D PHE* 1.3 82.5 - - - +
196D SER* 1.3 69.0 + - - +
197D MET* 5.3 0.7 - - + -
215D THR* 3.3 4.0 - - - -
216D LEU* 2.7 55.3 + - + +
218D LEU* 4.5 5.4 - - + -
229D ILE* 3.9 16.6 - - + -
236D CYS* 5.1 4.7 - - - -
238D MET* 3.7 24.5 - - + -
264D MET* 3.9 22.2 - - + -
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Residues in contact with SER 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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151D PHE* 4.5 6.1 + - - -
174D TRP* 3.6 16.4 - - - -
175D CYS* 3.5 1.9 - - - +
176D TYR* 2.8 42.7 + - - +
194D PHE* 3.5 24.0 - - - -
195D VAL* 1.3 82.5 - - - +
197D MET* 1.3 63.5 + - - +
212D THR* 4.2 8.0 - - - +
214D LYS 3.2 14.6 - - - -
215D THR* 3.9 6.3 - - - -
216D LEU* 5.0 0.9 - - - -
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Residues in contact with MET 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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117D LEU* 4.5 10.8 - - + -
173D HIS* 5.0 3.4 - - + -
174D TRP* 3.2 22.7 - - - +
175D CYS* 4.5 0.2 - - - -
195D VAL* 5.3 1.1 - - + -
196D SER* 1.3 77.0 - - - +
198D GLY* 1.3 58.5 + - - +
212D THR* 3.8 2.8 - - - -
213D LEU 2.9 20.1 + - - -
214D LYS* 3.0 35.1 + - + +
216D LEU* 4.3 17.3 - - + -
235D GLY* 4.4 7.2 - - - -
236D CYS* 3.7 22.9 - - - -
264D MET* 3.6 34.8 - - + +
265D TYR 4.5 0.9 - - - +
266D TYR* 4.2 29.4 - - - -
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Residues in contact with GLY 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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117D LEU* 4.3 4.4 - - - +
173D HIS* 3.1 9.6 - - - +
174D TRP* 2.9 39.1 + - - -
197D MET* 1.3 76.8 - - - +
199D ILE* 1.3 63.3 + - - -
211D ARG 3.1 13.0 - - - -
213D LEU* 3.8 12.8 - - - -
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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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116D ALA 4.1 8.5 - - - +
117D LEU* 3.6 12.8 - - + -
118D ILE 3.5 43.3 - - - +
119D ASN* 3.3 11.7 - - - +
120D ASP 5.6 0.4 - - - +
172D THR 3.9 4.3 - - - +
173D HIS* 4.3 1.6 - - + -
174D TRP* 3.0 11.5 + - - +
198D GLY* 1.3 78.4 - - - +
200D ILE* 1.3 60.8 + - - +
201D GLU* 4.4 9.2 - - + +
210D PHE 3.6 0.3 - - - -
211D ARG* 2.7 66.8 + - + +
213D LEU* 3.9 13.2 - - + -
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Residues in contact with ILE 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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119D ASN* 2.9 17.9 + - - +
120D ASP* 3.1 27.0 + - - +
123D TYR* 3.5 23.7 - - + -
127D ILE* 4.9 0.4 - - + -
169D LEU* 3.7 32.8 - - + -
174D TRP* 4.0 12.6 - - + -
199D ILE* 1.3 78.7 - - - +
201D GLU* 1.3 63.8 - - - +
208D PRO* 3.5 31.6 - - + -
209D PHE 3.4 8.7 - - - +
210D PHE* 4.1 14.4 - - + -
529D PHE* 4.1 17.0 - - + -
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Residues in contact with GLU 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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120D ASP* 4.1 4.9 - - + +
123D TYR* 3.7 4.9 - - - -
199D ILE* 4.4 8.7 - - + +
200D ILE* 1.3 76.8 - - - +
202D PRO* 1.3 76.5 - - + +
208D PRO 3.7 0.2 - - - -
209D PHE* 2.8 55.3 + - + +
211D ARG* 3.5 42.4 + - + -
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Residues in contact with PRO 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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120D ASP* 3.5 32.1 - - + +
122D ARG* 3.5 38.1 - - + +
123D TYR* 3.3 18.6 - - + +
201D GLU* 1.3 95.9 - - + +
203D THR* 1.3 62.7 + - - +
206D GLY 4.8 1.8 - - - +
207D PHE 3.9 2.7 - - - +
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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