Contacts of the strand formed by residues 229 - 236 (chain D) in PDB entry 1SBB
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 LYS 229 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D THR 4.7 4.0 - - - +
135D ARG* 6.0 4.7 - - - +
188D LYS 3.6 1.7 - - - +
189D PHE* 3.9 0.5 - - - -
190D ILE* 2.8 82.7 + - + +
191D GLU 4.7 6.1 - - - +
192D ASN 5.6 2.0 - - - +
227D ASP 5.8 0.2 - - - -
228D VAL* 1.3 71.7 - - - +
230D ILE* 1.3 61.8 + - - +
231D GLU* 4.1 17.1 + - + -
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Residues in contact with ILE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ILE* 4.2 20.6 - - + -
133D THR 3.3 10.7 + - - +
134D VAL* 3.9 24.5 - - + -
135D ARG* 3.0 23.7 + - - +
148D VAL* 5.2 2.5 - - + -
160D LEU* 3.9 39.0 - - + -
164D THR* 4.0 9.4 - - - +
187D ILE* 3.6 33.7 - - + -
188D LYS 3.4 4.5 - - - +
189D PHE* 3.9 15.7 - - + -
228D VAL* 5.0 2.5 - - + -
229D LYS* 1.3 75.0 - - - +
231D GLU* 1.3 68.8 + - - +
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Residues in contact with GLU 231 (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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135D ARG* 3.2 43.4 + - + +
137D PHE* 3.8 4.2 - - + -
186D TYR 4.0 0.9 - - - +
187D ILE* 3.6 0.6 - - - -
188D LYS* 2.8 46.0 + - + +
190D ILE* 3.5 27.2 - - + +
229D LYS* 4.1 14.8 + - - -
230D ILE* 1.3 84.4 - - - +
232D VAL* 1.3 61.9 + - - +
233D TYR* 3.1 33.8 + - + -
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D VAL* 3.8 11.0 - - + -
135D ARG 2.9 8.7 + - - +
136D VAL* 3.0 11.4 - - + +
137D PHE 2.7 32.9 + - - +
164D THR* 3.7 30.5 - - + -
168D LEU* 3.9 14.6 - - + -
186D TYR 3.7 2.9 - - - +
187D ILE* 3.9 13.9 - - + -
200D MET* 3.8 26.2 - - + -
230D ILE* 4.8 0.4 - - + -
231D GLU* 1.3 75.2 - - - +
233D TYR* 1.3 59.3 + - - +
234D LEU* 3.8 19.5 - - + -
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Residues in contact with TYR 233 (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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5D ASP* 6.0 0.2 - - - -
137D PHE* 3.4 46.6 - + + +
140D GLY* 5.6 4.5 - - - -
184D THR* 4.0 0.7 + - - +
185D GLY* 3.1 22.7 - - - -
186D TYR* 3.1 60.1 + + + +
188D LYS* 4.4 12.3 + - + +
231D GLU* 3.1 43.1 + - + -
232D VAL* 1.3 72.6 - - - +
234D LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 234 (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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136D VAL* 4.1 21.3 - - + -
137D PHE 2.8 12.3 + - - +
138D GLU* 3.3 7.9 - - + -
139D ASP* 2.8 31.4 + - - -
168D LEU* 4.7 8.7 - - + -
172D LYS* 5.9 0.4 - - + -
174D LEU* 4.3 16.8 - - + -
182D TYR* 3.6 44.2 - - + +
184D THR 3.4 4.3 - - - +
185D GLY* 3.6 23.3 - - - -
200D MET* 4.2 8.3 - - - -
201D MET* 5.1 1.1 - - + -
232D VAL* 3.8 20.9 - - + -
233D TYR* 1.3 75.2 - - - +
235D THR* 1.3 60.3 + - - +
236D THR 4.2 0.2 - - - -
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Residues in contact with THR 235 (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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139D ASP* 3.3 15.1 + - - +
182D TYR* 3.2 6.8 - - - +
183D GLU* 2.7 33.0 + - + -
184D THR* 2.8 33.6 + - - +
234D LEU* 1.3 75.1 - - - +
236D THR* 1.3 71.7 + - - +
238D LYS* 5.5 10.3 - - - +
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Residues in contact with THR 236 (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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138D GLU* 4.6 12.8 - - + +
139D ASP* 2.8 28.0 + - - +
181D PRO 3.8 6.7 - - - +
182D TYR* 4.0 23.1 - - + +
183D GLU* 3.9 6.9 - - - +
235D THR* 1.3 85.6 - - - +
237D LYS* 1.3 68.3 + - - +
238D LYS* 3.6 9.3 + - - +
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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