Contacts of the strand formed by residues 148 - 157 (chain D) in PDB entry 3F12
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 148 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PHE* 4.3 4.0 - - - -
147D THR* 1.3 79.0 + - - +
149D ALA* 1.3 59.8 + - - +
150D LEU* 5.8 1.3 - - + -
195D THR* 3.1 6.2 - - - -
196D VAL* 2.6 51.9 + - + +
198D SER* 4.3 10.8 - - - +
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Residues in contact with ALA 149 (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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117C PHE* 3.7 39.6 - - + -
119C PHE* 3.6 19.9 - - + -
136C LEU* 4.2 9.4 - - + -
137D ALA 3.5 19.6 - - - +
148D ALA* 1.3 76.6 - - - +
150D LEU* 1.3 63.4 + - - +
194D VAL 3.1 10.3 - - - +
195D THR* 4.6 4.7 - - - -
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Residues in contact with LEU 150 (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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119C PHE* 4.4 3.3 - - - -
136D LEU* 4.3 8.3 - - - +
137D ALA 4.5 16.2 - - - +
148D ALA* 5.8 1.1 - - + -
149D ALA* 1.3 78.4 - - - +
151D GLY* 1.3 60.8 + - - +
166D TRP* 4.5 6.7 - - + -
193D VAL* 3.3 22.3 - - - +
194D VAL* 2.8 24.2 + - + -
196D VAL* 3.2 49.1 - - + -
206D TYR* 3.3 27.1 - - + -
223D VAL* 3.9 24.7 - - + +
224D GLU* 4.9 7.9 - - - -
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Residues in contact with GLY 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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135D PRO* 3.7 2.9 - - - +
136D LEU* 2.9 35.2 + - - +
137D ALA 4.9 0.2 - - - +
150D LEU* 1.3 82.6 - - - +
152D CYS* 1.3 62.4 + - - +
166D TRP* 3.3 17.9 - - - -
192D SER 3.1 13.9 - - - -
193D VAL* 3.7 0.7 - - - -
223D VAL* 4.0 6.0 - - - +
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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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133D VAL* 3.5 24.9 - - + -
134D PHE 3.1 9.0 - - - +
135D PRO* 4.5 0.2 - - - -
136D LEU* 4.1 4.6 - - - +
151D GLY* 1.3 75.9 - - - -
153D LEU* 1.3 59.9 + - - +
154D VAL* 3.7 8.1 + - + +
164D VAL* 5.7 0.4 - - + -
166D TRP* 3.8 2.8 - - + -
191D SER* 3.4 5.4 - - - -
192D SER* 2.9 31.2 + - - +
208D CYS* 2.0 50.7 - - + -
221D LYS* 4.1 10.1 - - - -
223D VAL* 4.2 6.5 - - - -
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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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125C GLN* 5.3 0.2 - - - +
132C SER* 3.6 28.3 - - - +
134C VAL* 3.2 33.7 - - + -
179C THR* 4.2 15.7 - - + +
132D SER 3.3 2.6 - - - +
133D VAL* 4.6 0.7 - - - -
134D PHE* 2.9 43.4 + - + +
136D LEU* 4.8 10.4 - - + +
152D CYS* 1.3 70.6 - - - +
154D VAL* 1.3 61.9 + - - +
155D LYS* 3.2 38.2 + - + -
189D SER* 4.7 6.1 - - - +
190D LEU 3.6 8.3 - - - +
191D SER* 4.1 13.9 - - - -
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Residues in contact with VAL 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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131D PRO* 3.4 24.0 - - + -
132D SER 4.0 2.5 - - - -
133D VAL* 4.4 6.1 - - + +
152D CYS* 3.7 8.5 - - + +
153D LEU* 1.3 70.1 - - - +
155D LYS* 1.3 56.4 + - - +
157D TYR* 4.0 4.7 - - + -
162D VAL* 4.3 11.4 - - + -
164D VAL* 4.1 7.4 - - + -
189D SER* 3.2 3.1 - - - -
190D LEU* 2.7 63.6 + - + +
192D SER 5.4 0.2 - - - +
210D VAL* 3.4 47.6 - - + -
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Residues in contact with LYS 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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125C GLN* 4.0 10.1 - - - +
130C THR* 5.3 7.5 - - - +
132C SER* 3.5 25.4 - - - +
179C THR* 5.7 2.5 - - - -
181C THR* 4.3 14.6 - - - +
131D PRO* 3.4 3.0 - - - +
132D SER* 2.9 43.5 + - - +
134D PHE* 4.5 11.9 - - + -
153D LEU* 3.2 18.8 + - + +
154D VAL* 1.3 74.9 - - - +
156D ASP* 1.3 102.7 + - - +
157D TYR* 3.9 0.7 - - - -
183D GLN* 3.4 21.8 + - - +
188D TYR 4.0 0.2 - - - -
189D SER* 3.9 12.3 - - - -
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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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129D LYS* 3.0 29.8 + - - +
130D GLY 3.2 10.6 - - - +
132D SER* 4.4 5.1 + - - +
155D LYS* 1.3 110.3 + - - +
157D TYR* 1.3 56.9 + - - +
183D GLN* 3.1 13.3 + - - -
185D SER* 5.9 0.7 - - - -
187D LEU* 3.9 16.8 - - + +
188D TYR 3.0 15.1 + - - -
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Residues in contact with TYR 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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129D LYS 3.1 14.1 - - - +
131D PRO* 3.6 31.0 - - + -
154D VAL* 4.0 13.5 - - + -
156D ASP* 1.3 75.4 - - - +
158D PHE* 1.3 64.5 + - - +
159D PRO 3.2 24.9 - - - -
160D GLU* 2.9 28.6 + - - -
162D VAL* 3.7 30.7 - - + +
180D ALA* 3.1 19.1 - - - +
187D LEU* 3.6 6.1 - - - +
188D TYR* 2.9 43.3 + - + -
189D SER* 3.6 22.0 - - - -
190D LEU* 3.9 3.3 - - - +
212D HIS* 3.6 9.6 - + + -
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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