Contacts of the strand formed by residues 150 - 157 (chain D) in PDB entry 4QRR
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 SER 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D LEU 5.3 5.8 - - - -
146D ASP* 4.0 14.8 - - - +
149D LYS* 1.3 73.0 - - - +
151D VAL* 1.3 61.2 + - - +
152D CYS* 4.5 6.6 - - - -
194D TRP* 3.7 3.0 - - - +
195D SER* 3.0 42.3 + - - -
200D PHE* 3.8 24.1 - - - +
141E PHE* 4.8 1.1 - - - -
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Residues in contact with VAL 151 (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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143D GLN* 4.2 1.4 - - - +
144D LEU* 3.4 43.8 + - + +
149D LYS 4.3 0.6 - - - -
150D SER* 1.3 72.1 - - - +
152D CYS* 1.4 71.1 + - - +
153D LEU* 6.3 0.2 - - + -
192D VAL* 3.6 30.5 - - + -
193D ALA 3.8 2.7 - - - +
194D TRP* 3.9 11.4 - - + -
141E PHE* 3.5 36.4 - - + -
157E VAL* 4.4 7.2 - - + -
159E LEU* 3.8 21.3 - - + -
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Residues in contact with CYS 152 (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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141D VAL* 4.6 5.6 - - + -
142D TYR 3.8 5.8 - - - -
143D GLN* 3.3 37.7 - - - +
144D LEU* 4.6 1.3 - - - -
150D SER* 4.5 8.3 - - - -
151D VAL* 1.4 81.1 - - - +
153D LEU* 1.3 59.8 + - - +
191D ALA 4.0 0.5 - - - +
192D VAL* 3.7 2.4 - - - -
193D ALA* 2.9 44.0 + - + +
195D SER* 5.9 2.7 - - - -
201D ALA* 4.7 6.1 - - - -
202D CYS* 3.7 16.2 - - + -
205D ALA* 5.3 5.2 - - + -
206D PHE* 4.3 8.9 - - + -
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Residues in contact with LEU 153 (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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140D ALA 3.9 1.0 - - - +
141D VAL* 3.4 5.0 - - - -
142D TYR* 2.8 45.5 + - + +
144D LEU* 3.9 19.0 - - + +
151D VAL* 6.3 0.2 - - + -
152D CYS* 1.3 73.2 - - - +
154D PHE* 1.3 58.2 + - - +
155D THR* 3.8 23.2 + - + -
190D SER* 4.1 21.1 - - - -
191D ALA 3.5 14.4 - - - +
192D VAL* 3.9 17.9 - - + +
147E GLU* 4.5 7.2 - - - +
155E THR* 3.8 31.0 - - + +
157E VAL* 4.1 12.8 - - + -
206E ARG* 4.3 4.7 - - + -
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Residues in contact with PHE 154 (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 PRO* 4.1 11.7 - - + -
140D ALA 3.5 14.4 - - - -
141D VAL* 3.7 15.3 - - + -
152D CYS 4.3 0.4 + - - -
153D LEU* 1.3 72.7 - - - +
155D THR* 1.3 57.9 + - - +
157D PHE* 3.3 44.6 - + + -
161D THR* 4.5 5.8 - - + -
163D VAL* 4.0 26.2 - - + -
191D ALA* 2.8 38.5 + - + +
206D PHE* 3.7 29.6 - + + -
211D ILE* 4.1 20.0 - - + -
212D PRO* 4.1 9.6 - - + -
215D THR* 4.0 22.7 - - + -
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Residues in contact with THR 155 (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 ASP 3.7 0.2 - - - +
139D PRO* 3.7 1.2 - - - +
140D ALA* 3.3 25.3 + - - +
142D TYR* 4.2 18.1 - - + -
153D LEU* 3.8 23.8 - - + -
154D PHE* 1.3 74.2 - - - +
156D ASP* 1.4 87.1 + - - +
157D PHE* 3.3 8.3 + - - -
188D SER* 4.1 2.8 + - - -
189D ASN 2.8 16.3 + - - -
190D SER* 3.5 14.5 - - - -
147E GLU* 5.4 0.7 - - - +
155E THR* 5.0 1.6 - - - +
208E ARG* 3.4 21.5 + - - +
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Residues in contact with ASP 156 (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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134D ILE* 4.7 3.8 - - - +
136D ASN 5.0 1.0 - - - +
137D PRO* 3.6 4.0 - - - +
138D ASP* 2.8 58.4 + - + +
142D TYR* 5.3 1.3 - - + -
155D THR* 1.4 83.0 + - - +
157D PHE* 1.3 61.0 + - - +
186D PHE* 3.3 27.7 - - - -
188D SER* 4.2 10.8 - - - -
189D ASN 3.1 5.4 + - - -
151E THR* 4.2 14.3 - - - +
208E ARG* 2.8 39.6 + - - -
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Residues in contact with PHE 157 (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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134D ILE* 3.6 15.2 - - - +
137D PRO* 4.4 2.9 - - - -
139D PRO* 4.1 12.1 - - + -
154D PHE* 3.3 68.2 - + + -
155D THR 3.8 4.7 - - - -
156D ASP* 1.3 78.8 - - - +
158D ASP* 1.4 83.0 + - - +
161D THR* 3.6 30.3 - - + +
163D VAL* 5.0 4.0 - - + -
176D LYS* 3.7 28.5 - - + -
189D ASN* 3.5 39.7 + - + +
190D SER* 3.7 5.2 - - - -
191D ALA* 4.4 3.1 - - + -
212D PRO* 5.1 1.1 - - + -
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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