Contacts of the strand formed by residues 198 - 209 (chain A) in PDB entry 2JIF
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 TYR 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LYS* 3.5 7.3 - - - +
195A GLU* 2.9 40.7 + - + +
196A GLY 3.2 1.2 - - - -
197A ASP* 1.3 96.1 - - + +
199A TYR* 1.3 71.2 + - - +
200A VAL* 5.6 1.3 - - + -
269A LYS* 5.2 11.4 - - + -
270A VAL 3.2 11.4 - - - +
271A PRO* 3.6 35.9 - - + -
272A GLU 4.1 0.9 - - - +
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Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ALA* 3.9 14.8 - - + -
193A ASP 3.4 5.6 - - - -
194A LYS* 3.7 47.4 - - + +
198A TYR* 1.3 77.2 - - - +
200A VAL* 1.3 61.9 + - - +
201A LEU* 3.8 7.3 + - + +
223A VAL* 3.9 21.8 - - + -
235A PHE* 3.9 19.3 - + + -
268A VAL 3.4 2.6 - - - +
269A LYS* 3.5 1.4 - - - -
270A VAL* 2.7 43.2 + - + +
272A GLU* 4.3 19.5 - - + -
275A ILE* 3.7 24.7 - - + -
279A ILE* 3.0 26.0 - - + +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ARG* 3.6 1.4 - - - +
192A ALA* 3.5 1.0 - - - -
193A ASP* 2.8 44.3 + - + +
195A GLU* 4.1 19.5 - - + -
198A TYR* 5.5 2.7 - - + -
199A TYR* 1.3 76.7 - - - +
201A LEU* 1.3 61.9 + - - +
202A ASN* 3.7 13.7 + - - +
267A ASN* 3.5 38.1 - - + +
268A VAL 3.4 2.7 - - - -
269A LYS* 4.4 16.8 - - + -
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A THR* 4.9 2.2 - - + -
191A ARG 3.1 9.9 - - - +
192A ALA* 3.8 19.5 - - + -
199A TYR* 3.9 9.9 - - + +
200A VAL* 1.3 77.0 - - - +
202A ASN* 1.3 59.7 + - - +
219A VAL* 4.1 29.2 - - + -
221A ALA* 4.2 6.1 - - + -
235A PHE* 4.2 23.6 - - + -
237A VAL* 4.4 4.9 - - + -
265A PHE* 3.8 19.5 - - + +
267A ASN 3.3 7.4 + - - -
268A VAL* 2.8 41.6 + - + +
270A VAL* 3.7 26.9 - - + -
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Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS 4.2 1.2 - - - +
190A THR* 3.4 4.8 - - - +
191A ARG* 2.8 45.4 + - + +
193A ASP* 5.0 7.3 + - - +
200A VAL* 3.7 15.5 + - - +
201A LEU* 1.3 76.9 + - - +
203A GLY* 1.3 58.0 + - - +
265A PHE* 3.3 8.5 - - - +
266A GLU* 3.5 3.1 - - - -
267A ASN* 2.9 41.9 + - - +
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Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS 5.2 1.3 - - - -
190A THR* 3.7 11.2 - - - -
202A ASN* 1.3 75.3 - - - +
204A SER* 1.3 61.9 + - - -
264A THR* 3.5 3.1 - - - -
265A PHE* 2.7 41.5 + - - +
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 3.2 22.8 + - - +
179A ALA* 5.6 2.6 + - - +
190A THR* 2.9 17.3 + - - -
203A GLY* 1.3 76.3 - - - -
205A LYS* 1.3 68.1 + - - +
263A LEU 3.2 13.9 - - - -
264A THR* 4.2 11.7 - - - +
265A PHE* 4.3 2.2 - - - -
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A CYS* 3.4 25.6 - - + +
176A LEU 3.1 19.7 + - - +
177A SER 3.3 15.7 - - - +
178A GLU* 2.8 24.4 + - + -
188A LEU* 3.9 6.5 - - - +
190A THR* 3.8 7.2 + - - -
204A SER* 1.3 80.3 - - - +
206A MET* 1.3 62.4 + - - +
208A ILE* 3.9 18.6 - - + -
219A VAL* 4.1 8.1 - - - -
220A MET 2.6 30.0 + - - -
262A PRO* 3.4 6.1 - - - +
263A LEU* 2.9 36.3 + - + +
265A PHE* 3.8 16.4 - - + -
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Residues in contact with MET 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 2.9 18.1 + - - +
178A GLU 3.9 1.3 - - - -
179A ALA* 3.8 37.9 - - + +
205A LYS* 1.3 76.4 - - - +
207A TRP* 1.3 106.8 + - + +
208A ILE* 3.4 10.6 - - - +
250A GLU* 3.8 22.0 - - - +
262A PRO* 4.0 23.6 - - + -
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Residues in contact with TRP 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 4.1 7.6 - - - -
178A GLU 4.8 5.4 + - - -
179A ALA* 5.4 1.6 - - - +
182A GLY* 6.0 0.2 - - - -
206A MET* 1.3 108.6 - - + +
208A ILE* 1.3 62.7 + - - +
250A GLU* 3.6 26.2 + - + -
252A LYS* 6.2 0.4 - - + -
260A THR* 3.7 19.6 - - + +
261A CYS 3.7 6.4 + - - +
1433A FAD 2.8 95.2 + + + +
391C GLY* 3.4 25.1 - - - -
392C VAL* 3.5 33.2 - - + -
395C THR* 3.7 20.9 - - + -
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A SER* 3.5 33.2 - - - +
174A PHE 3.7 8.5 - - - +
175A CYS* 3.6 33.7 - - - -
176A LEU 4.3 0.7 - - - +
177A SER 4.4 0.4 - - - +
205A LYS* 3.9 15.9 - - + -
206A MET 3.4 16.6 - - - +
207A TRP* 1.3 72.9 - - - +
209A SER* 1.3 62.9 + - - +
211A ALA* 3.5 16.5 - - + +
259A SER 3.6 0.2 - - - +
260A THR* 3.4 2.2 - - - -
261A CYS 3.0 39.0 + - - +
263A LEU* 3.8 21.1 - - + -
1433A FAD 3.7 11.4 - - - +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 5.7 1.1 - - - +
141A ILE* 3.4 26.5 - - - +
173A SER* 2.8 30.1 + - - -
174A PHE 4.8 0.5 + - - -
207A TRP 3.2 0.6 + - - -
208A ILE* 1.3 72.3 - - - +
210A SER* 1.3 59.1 + - - +
211A ALA 3.2 0.4 - - - -
255A LEU* 5.7 0.9 - - - +
258A SER* 4.1 10.4 + - - -
259A SER 3.1 8.9 + - - -
260A THR* 4.4 1.4 + - - +
413A TYR* 5.3 2.1 - - - -
1433A FAD 2.8 52.8 + - - +
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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