Contacts of the strand formed by residues 198 - 207 (chain C) in PDB entry 4BEI
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 ALA 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C LEU* 4.3 19.7 - - + -
192C ASN* 3.4 21.5 - - + +
194C ARG* 3.5 27.1 - - - +
197C GLU* 1.3 74.0 - - - +
199C ASN* 1.3 61.9 + - - +
200C VAL* 3.9 3.0 + - + +
222C TRP 3.5 2.6 - - - +
223C VAL* 3.6 1.8 - - - -
224C ILE* 2.9 37.1 + - + +
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Residues in contact with ASN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ARG* 4.8 2.0 - - - +
197C GLU* 3.9 22.9 + - - +
198C ALA* 1.3 74.2 - - - +
200C VAL* 1.3 66.1 + - - +
222C TRP 3.4 2.9 - - - +
223C VAL* 3.3 29.0 - - - +
255C ASP* 3.5 6.9 + - - +
256C ILE* 2.9 44.5 + - + +
257C VAL* 4.6 18.5 - - + +
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C LEU* 3.3 31.6 - - + -
190C LEU* 4.5 9.0 - - + -
198C ALA* 4.7 3.4 - - + +
199C ASN* 1.3 82.8 - - - +
201C GLU* 1.3 61.6 + - - +
202C PHE* 5.2 1.6 - - + -
220C GLU 3.9 0.2 - - - +
221C LYS* 3.5 2.3 - - - -
222C TRP* 2.8 57.9 + - + +
224C ILE* 4.1 17.0 - - + -
253C VAL* 3.8 17.5 - - + -
254C VAL 3.1 11.9 - - - +
255C ASP* 4.3 7.9 - - + +
256C ILE* 3.5 8.9 - - - +
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C VAL* 1.3 73.9 - - - +
202C PHE* 1.3 64.1 + - - +
203C TRP* 3.7 22.0 - - + -
219C ARG* 3.8 27.1 + - + +
220C GLU 3.2 14.4 - - - +
221C LYS* 4.0 16.0 + - + +
252C GLN 4.1 0.2 - - - +
253C VAL* 3.4 4.2 - - - +
254C VAL* 2.8 35.4 + - + +
256C ILE* 3.8 8.4 - - + +
92D ALA* 5.5 1.9 - - - +
121D PRO* 4.1 4.8 - - - +
123D TYR* 2.6 44.4 + - + +
124D MET* 3.8 7.1 - - - +
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Residues in contact with PHE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ILE* 4.5 4.0 - - + -
188C VAL* 4.0 23.3 - - + -
190C LEU* 4.4 15.5 - - + -
200C VAL* 5.2 3.1 - - + -
201C GLU* 1.3 77.5 - - - +
203C TRP* 1.3 70.3 - - - +
204C MET* 3.8 38.6 - - + -
217C ASN* 3.7 28.0 - - - -
218C ALA 3.4 2.4 - - - +
219C ARG* 3.5 0.3 - - - -
220C GLU* 2.8 46.2 + - + +
222C TRP* 5.2 3.1 - + + -
230C TYR* 4.3 23.6 - + - -
232C LYS* 4.6 1.6 - - - -
251C ALA* 4.5 8.3 - - + -
252C GLN 3.4 12.8 - - - +
253C VAL* 3.8 17.9 - - + -
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Residues in contact with TRP 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C GLU* 3.7 24.9 - - + -
202C PHE* 1.3 87.6 - - - +
204C MET* 1.3 75.0 + - - +
205C THR* 4.8 0.4 - - + -
217C ASN 3.5 14.6 - - - +
218C ALA 4.0 3.6 - - - +
219C ARG* 3.7 22.9 - - + -
250C ASN* 5.5 0.4 - - - -
252C GLN* 2.8 67.9 + - + +
254C VAL* 3.3 31.0 - - + -
261C ARG* 4.6 2.2 - - - -
86D ILE* 5.3 1.3 - - + -
87D TYR 2.9 27.4 + - - -
88D PHE* 3.5 25.3 - + + +
89D PRO* 4.1 4.3 - - + -
124D MET* 3.5 27.8 - - + -
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Residues in contact with MET 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ILE* 4.3 15.5 - - + -
186C PHE* 4.5 13.2 - - + -
188C VAL* 4.2 12.8 - - - -
202C PHE* 3.8 22.9 - - + -
203C TRP* 1.3 82.5 - - - +
205C THR* 1.3 68.5 + - - +
215C PRO* 4.0 1.0 - - - +
216C VAL* 2.9 21.4 + - + -
217C ASN* 2.9 45.9 + - + +
234C ARG* 4.5 8.3 - - - +
249C ILE* 4.0 26.2 - - + -
250C ASN 3.2 5.4 - - - +
251C ALA* 3.7 23.1 - - + -
89D PRO* 4.1 0.7 - - - +
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Residues in contact with THR 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C TRP* 4.8 0.6 - - + -
204C MET* 1.3 79.2 - - - +
206C ALA* 1.3 58.6 + - - +
207C VAL* 3.9 9.4 - - - +
213C ILE* 3.9 22.9 - - + -
214C ILE 3.2 11.9 - - - +
215C PRO* 4.7 1.8 - - + -
216C VAL* 3.7 7.1 - - - +
248C THR 3.7 0.2 - - - +
249C ILE* 3.6 3.1 - - - +
250C ASN* 2.7 43.9 + - - +
79D SER* 5.7 0.7 - - - +
87D TYR* 3.7 33.1 - - - +
88D PHE* 4.1 2.0 - - - -
89D PRO* 4.0 22.0 - - + -
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C THR* 1.3 71.6 - - - +
207C VAL* 1.3 64.5 + - - +
208C GLY* 3.6 2.8 + - - -
212C LEU 3.7 0.2 - - - +
213C ILE* 3.7 0.5 - - - -
214C ILE* 2.7 45.7 + - + +
216C VAL* 3.6 12.1 - - + +
236C ILE* 4.0 11.4 - - + -
247C TYR* 4.5 11.2 - - + -
248C THR 3.5 4.9 - - - -
249C ILE* 3.5 26.7 - - + -
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C THR* 3.9 11.9 - - - +
206C ALA* 1.3 72.8 - - - +
208C GLY* 1.3 59.7 + - - +
212C LEU 3.5 9.9 - - - +
213C ILE* 4.5 3.6 - - + +
246C GLU 3.8 1.2 - - - +
247C TYR* 3.5 1.0 - - - -
248C THR* 2.7 44.8 + - - +
250C ASN* 4.9 1.8 - - + -
1272C O4B 3.6 37.3 - - - +
87D TYR* 3.6 45.8 - - + -
1272D O4B 4.0 16.4 - - - -
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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