Contacts of the strand formed by residues 198 - 207 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164H LEU* 4.3 19.5 - - + -
192H ASN* 3.4 22.2 - - + +
194H ARG* 3.5 26.9 - - - +
197H GLU* 1.3 74.0 - - - +
199H ASN* 1.3 62.9 + - - +
200H VAL* 3.9 2.7 + - + +
222H TRP 3.5 2.4 - - - +
223H VAL* 3.6 1.6 - - - +
224H ILE* 2.9 36.3 + - + +
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Residues in contact with ASN 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H ARG* 4.8 2.2 - - - +
197H GLU* 3.9 22.3 + - - +
198H ALA* 1.3 73.5 - - - +
200H VAL* 1.3 65.5 + - - +
222H TRP 3.5 2.9 - - - +
223H VAL* 3.3 29.0 - - - +
255H ASP* 3.5 6.4 + - - +
256H ILE* 2.9 43.9 + - + +
257H VAL* 4.7 19.2 - - + +
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Residues in contact with VAL 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H LEU* 3.2 31.2 - - + -
190H LEU* 4.6 9.0 - - + -
198H ALA* 4.7 3.8 - - + +
199H ASN* 1.3 82.8 - - - +
201H GLU* 1.3 61.0 + - - +
202H PHE* 5.2 2.0 - - + -
220H GLU 3.9 0.2 - - - +
221H LYS* 3.5 1.7 - - - -
222H TRP* 2.8 57.3 + - + +
224H ILE* 4.1 16.8 - - + -
253H VAL* 3.9 17.3 - - + -
254H VAL 3.1 11.7 - - - +
255H ASP* 4.3 8.1 - - + -
256H ILE* 3.5 8.6 - - - +
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Residues in contact with GLU 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ALA* 5.2 2.8 - - - +
121G PRO* 3.9 4.6 - - - +
123G TYR* 2.6 48.7 + - + +
124G MET* 3.5 9.4 - - - +
200H VAL* 1.3 74.3 - - - +
202H PHE* 1.3 64.9 + - - +
203H TRP* 3.7 22.0 - - + -
219H ARG* 3.8 29.9 + - + +
220H GLU 3.2 13.7 - - - +
221H LYS* 4.0 14.6 + - + +
253H VAL* 3.4 4.5 - - - +
254H VAL* 2.8 34.5 + - + +
256H ILE* 3.8 3.7 - - + +
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Residues in contact with PHE 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ILE* 4.5 4.5 - - + -
188H VAL* 4.0 24.0 - - + -
190H LEU* 4.3 18.8 - - + -
200H VAL* 5.2 3.1 - - + -
201H GLU* 1.3 77.6 - - - +
203H TRP* 1.3 71.0 + - - +
204H MET* 3.8 38.1 - - + -
217H ASN* 3.7 28.3 - - - -
218H ALA 3.4 2.4 - - - +
219H ARG* 3.5 0.5 - - - -
220H GLU* 2.8 45.5 + - + +
222H TRP* 5.2 3.1 - + + -
230H TYR* 4.2 24.7 - + - -
232H LYS* 4.6 1.1 - - - -
251H ALA* 4.5 8.1 - - + -
252H GLN 3.4 11.7 - - - +
253H VAL* 3.8 14.1 - - + -
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Residues in contact with TRP 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G ILE* 5.1 1.8 - - + -
87G TYR 2.7 27.2 + - - -
88G PHE* 3.5 28.7 - + + -
89G PRO* 3.9 4.5 - - + -
124G MET* 3.5 22.0 - - + -
201H GLU* 3.7 24.9 - - + -
202H PHE* 1.3 87.0 - - - +
204H MET* 1.3 72.9 - - - +
205H THR* 4.7 0.4 - - + -
217H ASN 3.5 14.6 - - - +
218H ALA 4.0 1.1 - - - +
219H ARG* 3.6 27.4 - - + -
250H ASN* 5.5 0.4 - - - -
252H GLN* 2.8 69.5 + - + +
254H VAL* 3.3 32.1 - - + -
261H ARG* 4.5 2.5 - - - -
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Residues in contact with MET 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G PRO* 4.0 1.2 - - - +
168H ILE* 4.3 15.5 - - + -
186H PHE* 4.5 13.5 - - + -
188H VAL* 4.2 13.7 - - - -
202H PHE* 3.8 22.0 - - + -
203H TRP* 1.3 83.5 - - - +
205H THR* 1.3 68.5 + - - +
215H PRO 4.0 0.3 - - - -
216H VAL* 2.9 20.6 + - + -
217H ASN* 2.9 44.4 + - + +
234H ARG* 4.5 7.9 - - - +
249H ILE* 4.0 25.4 - - + -
250H ASN 3.2 5.8 - - - +
251H ALA* 3.7 23.1 - - + -
266H MET* 5.2 0.2 - - + -
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Residues in contact with THR 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G SER* 5.7 0.2 - - - +
87G TYR* 3.8 29.1 - - - +
88G PHE* 4.1 2.5 - - - -
89G PRO* 4.0 25.4 - - + -
203H TRP* 4.7 0.4 - - + -
204H MET* 1.3 80.8 - - - +
206H ALA* 1.3 58.8 + - - +
207H VAL* 3.9 9.7 - - - +
213H ILE* 3.9 21.8 - - + -
214H ILE 3.2 11.7 - - - +
215H PRO* 4.7 1.6 - - + -
216H VAL* 3.7 6.5 - - - +
248H THR 3.7 0.3 - - - +
249H ILE* 3.6 3.3 - - - +
250H ASN* 2.8 43.7 + - - +
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Residues in contact with ALA 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H THR* 1.3 72.1 - - - +
207H VAL* 1.3 64.5 + - - +
208H GLY 3.6 2.4 + - - -
212H LEU 3.7 0.5 - - - +
213H ILE* 3.7 0.6 - - - -
214H ILE* 2.7 45.0 + - + +
216H VAL* 3.7 11.4 - - + -
236H ILE* 4.0 11.4 - - + -
247H TYR* 4.5 11.8 - - + -
248H THR 3.5 4.7 - - - -
249H ILE* 3.5 26.7 - - + -
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Residues in contact with VAL 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G TYR* 3.8 34.3 - - + -
1272G O4B 4.0 21.5 - - - +
205H THR* 3.9 14.8 - - - +
206H ALA* 1.3 71.1 - - - +
208H GLY* 1.3 62.5 + - - +
212H LEU 3.5 9.0 - - - +
213H ILE* 4.5 6.1 - - + +
246H GLU 3.8 1.6 - - - +
247H TYR* 3.5 0.8 - - - -
248H THR* 2.7 43.5 + - - +
250H ASN* 4.9 3.8 - - + -
1272H O4B 3.8 31.9 - - - +
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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