Contacts of the strand formed by residues 198 - 205 (chain D) in PDB entry 3B4M
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 VAL 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C ASP 4.8 0.9 - - - +
208C PHE* 4.0 23.5 - - + -
189D GLU* 4.0 30.6 + - + +
192D PHE* 4.5 9.2 - - + +
196D GLY 3.4 14.3 + - - +
197D SER* 1.3 76.2 + - - +
199D ASN* 1.3 67.8 + - - +
200D ARG 3.9 14.6 - - - +
201D VAL* 4.1 8.7 - - + -
218D ILE* 3.8 23.1 - - + -
219D GLU 3.9 4.3 - - - +
220D PHE* 3.9 19.7 - - + +
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Residues in contact with ASN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ARG* 3.8 38.4 + - - +
199B ASN* 5.1 0.2 + - - -
221B SER 4.6 1.5 + - - +
223B LYS* 6.3 0.4 - - - +
206C ASP* 3.0 32.3 - - - +
208C PHE* 4.1 2.0 - - - -
172D ARG* 3.6 9.9 + - - -
197D SER* 4.9 0.8 + - - -
198D VAL* 1.3 75.8 + - - +
200D ARG* 1.3 58.2 + - + +
219D GLU* 2.8 30.2 + - - +
220D PHE 3.5 4.5 - - - +
221D SER* 2.8 39.0 + - - -
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Residues in contact with ARG 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ALA* 5.9 6.8 - - - +
204C LEU* 3.8 23.7 - - - +
205C CYS 3.5 6.3 - - - +
206C ASP* 2.6 43.7 + - - +
208C PHE* 4.2 1.1 - - - -
215C PHE* 3.9 19.2 - - - -
198D VAL* 3.8 2.3 - - - +
199D ASN* 1.3 78.2 - - + +
201D VAL* 1.3 70.1 + - - +
202D THR* 3.6 22.7 - - - +
217D TYR 3.8 0.9 - - - +
218D ILE* 3.7 2.6 - - - -
219D GLU* 3.0 50.7 + - + +
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Residues in contact with VAL 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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203C ILE 3.6 1.2 - - - +
204C LEU* 3.4 3.1 - - - -
205C CYS* 3.0 33.3 + - - +
208C PHE* 3.7 28.0 - - + -
185D ALA* 4.3 12.8 - - + +
188D LEU* 3.8 31.4 - - + -
189D GLU* 4.2 13.2 - - - +
198D VAL* 4.1 9.2 - - + -
200D ARG* 1.3 75.4 - - - +
202D THR* 1.3 65.1 + - - +
203D ILE* 4.1 10.3 - - + -
217D TYR 3.5 2.9 - - - +
218D ILE* 3.9 21.1 - - + -
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Residues in contact with THR 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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202C THR* 3.8 26.0 - - + -
203C ILE 3.3 5.4 - - - +
204C LEU* 4.0 14.3 - - + +
200D ARG* 3.6 21.5 - - - +
201D VAL* 1.3 74.6 + - - +
203D ILE* 1.3 63.8 + - - +
204D LEU* 4.1 12.7 - - + +
216D ALA* 2.8 7.0 - - - +
217D TYR* 2.6 55.3 + - + +
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Residues in contact with ILE 203 (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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185C ALA* 5.2 0.9 - - + -
201C VAL 3.7 1.0 - - - +
202C THR* 3.1 7.2 - - - +
203C ILE* 2.8 54.0 + - + +
179D VAL* 4.3 9.4 - - + -
183D ALA* 3.6 21.5 - - + +
184D THR* 3.6 4.0 - - - -
185D ALA* 3.5 33.7 - - + +
188D LEU* 3.5 29.2 - - + -
201D VAL* 4.1 3.1 - - + -
202D THR* 1.3 74.5 - - - +
204D LEU* 1.3 62.9 + - - +
205D CYS* 3.8 24.7 - - - -
215D PHE 3.7 7.6 - - - +
216D ALA* 4.2 0.7 - - + -
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Residues in contact with LEU 204 (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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200C ARG* 4.4 23.3 - - - +
201C VAL 3.4 4.0 - - - -
202C THR* 4.0 23.8 - - + +
202D THR* 4.1 12.3 - - + +
203D ILE* 1.3 78.4 - - - +
205D CYS* 1.3 66.2 + - - +
206D ASP* 5.7 0.2 - - - -
214D GLY* 3.3 2.4 - - - -
215D PHE* 2.9 79.9 + - + +
216D ALA* 4.6 0.2 - - - -
217D TYR* 4.0 22.4 - - + -
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Residues in contact with CYS 205 (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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185C ALA* 3.7 31.2 - - + -
200C ARG* 3.3 3.7 - - - +
201C VAL 2.9 30.2 + - - +
179D VAL 4.5 5.4 - - - -
180D ASP 3.7 25.6 - - - -
181D TYR* 4.0 5.6 - - - -
183D ALA 6.0 0.2 - - - -
203D ILE* 3.8 12.3 - - - -
204D LEU* 1.3 81.7 - - - +
206D ASP* 1.3 64.4 + - - +
207D LYS 4.0 8.1 - - - +
208D PHE* 3.2 13.2 - - + -
213D LYS 3.6 5.8 - - - +
214D GLY* 4.3 0.4 - - - -
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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