Contacts of the strand formed by residues 146 - 156 (chain D) in PDB entry 3Q3G
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 MET 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D GLN* 5.2 0.5 - - - +
144D ASN* 3.2 32.7 + - - +
145D SER* 1.4 88.1 + - - +
147D VAL* 1.3 61.4 + - - +
193D THR* 3.6 37.5 - - + +
194D VAL 3.5 3.6 - - - -
195D PRO* 4.0 26.7 - - + -
196D SER* 3.6 7.4 + - - -
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Residues in contact with VAL 147 (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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137D PRO* 4.3 19.5 - - + -
142D GLN* 5.6 2.7 - - - +
146D MET* 1.3 75.7 - - - +
148D THR* 1.3 72.7 + - - +
149D LEU* 4.0 8.1 + - + +
192D VAL 3.7 1.0 - - - +
193D THR* 3.4 2.5 - - - -
194D VAL* 2.7 60.6 + - + +
195D PRO 3.7 8.7 - - - +
196D SER* 4.1 13.5 - - - +
199D ARG* 4.2 22.2 - - + +
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Residues in contact with THR 148 (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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120C THR* 4.9 10.9 - - - +
122C SER* 3.7 23.9 + - - +
124C PHE* 3.4 18.9 - - + -
141C PHE* 4.0 16.8 - - + -
143C ASN* 3.9 12.1 + - - +
137D PRO* 4.2 3.5 - - - +
147D VAL* 1.3 77.3 - - - +
149D LEU* 1.3 69.1 + - - +
191D SER* 3.8 22.2 - - - +
192D VAL 3.3 4.9 - - - +
193D THR* 2.8 20.5 + - - +
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Residues in contact with LEU 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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124C PHE* 4.2 5.2 - - - -
135D LEU 3.5 6.3 - - - +
137D PRO* 3.6 23.8 - - + -
147D VAL* 4.5 6.7 - - + +
148D THR* 1.3 79.0 - - - +
150D GLY* 1.3 59.3 + - - +
191D SER* 3.5 3.3 - - - -
192D VAL* 2.8 43.7 + - + -
194D VAL* 4.5 7.9 - - + -
199D ARG* 3.6 54.7 - - + +
204D VAL* 3.8 28.3 - - + -
221D ILE* 3.8 16.6 - - + -
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Residues in contact with GLY 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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124C PHE* 4.4 0.2 - - - -
141C PHE* 3.9 5.4 - - - -
135D LEU* 2.8 49.6 + - - +
149D LEU* 1.3 75.9 - - - +
151D CYS* 1.3 58.5 + - - -
165D TRP* 3.5 5.4 - - - -
190D SER 3.1 12.6 - - - -
221D ILE* 3.4 14.7 - - - +
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Residues in contact with CYS 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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132D VAL* 3.6 21.3 - - - -
133D TYR 3.6 5.6 - - - -
135D LEU* 3.6 3.4 - - - +
150D GLY* 1.3 74.4 - - - -
152D LEU* 1.3 61.4 + - - +
153D VAL* 4.0 5.3 + - + +
163D VAL* 4.7 1.6 - - + -
165D TRP* 3.4 14.6 - - + -
189D SER* 3.2 6.1 - - - -
190D SER* 3.0 33.3 + - - +
206D CYS* 2.0 47.8 - - + -
208D VAL* 3.8 11.2 - - - -
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Residues in contact with LEU 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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130C GLN* 4.4 3.6 - - - +
137C SER* 4.1 26.2 - - - +
139C VAL* 4.3 17.7 - - + -
184C THR* 4.7 3.8 - - + -
131D SER 3.2 5.7 - - - +
132D VAL* 3.5 1.5 - - - -
133D TYR* 2.8 65.7 + - + +
135D LEU* 4.0 15.9 - - + +
151D CYS* 1.3 71.7 - - - +
153D VAL* 1.3 58.0 + - - +
154D LYS* 3.7 11.8 + - + -
187D THR* 3.8 21.1 - - + -
188D LEU 3.5 15.0 - - - +
189D SER* 4.3 10.3 - - - -
605D EDO 4.5 5.2 - - - -
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Residues in contact with VAL 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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130D PRO* 3.5 26.2 - - + -
131D SER 3.6 3.8 - - - -
132D VAL* 4.6 2.5 - - + -
151D CYS* 4.5 9.0 - - + +
152D LEU* 1.3 71.5 - - - +
154D LYS* 1.3 56.4 + - - +
156D TYR* 3.8 17.4 - - + -
161D VAL* 4.1 7.9 - - + -
163D VAL* 4.1 3.8 - - + -
187D THR* 3.3 4.4 - - - -
188D LEU* 2.8 61.3 + - + +
208D VAL* 3.7 41.1 - - + -
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Residues in contact with LYS 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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130C GLN* 3.6 29.7 - - - +
137C SER* 3.7 11.9 - - - +
184C THR* 6.3 0.2 - - - -
186C THR* 4.1 8.9 - - - +
130D PRO* 3.5 1.9 - - - +
131D SER* 2.8 44.5 + - - +
133D TYR* 4.1 17.7 - - + -
152D LEU* 4.4 10.3 - - + -
153D VAL* 1.3 73.0 - - - +
155D GLY* 1.3 66.5 + - - +
156D TYR* 3.6 2.0 - - - -
182D GLN* 3.3 26.0 + - - +
186D TYR 3.8 0.2 - - - -
187D THR* 3.4 20.0 - - + +
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Residues in contact with GLY 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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128D THR* 3.3 24.1 - - - +
129D PRO 3.4 6.3 - - - +
131D SER* 5.7 0.2 + - - -
154D LYS* 1.3 81.9 - - - +
156D TYR* 1.3 56.5 + - - -
182D GLN 5.8 0.2 - - - -
185D LEU* 3.8 24.3 - - - +
186D TYR 2.9 13.8 + - - -
187D THR* 3.6 1.9 + - - -
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Residues in contact with TYR 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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128D THR 3.3 13.7 - - - +
129D PRO 4.2 0.2 - - - -
130D PRO* 3.6 22.9 - - + -
153D VAL* 3.8 38.1 - - + -
155D GLY* 1.3 76.5 - - - +
157D PHE* 1.3 61.4 + - - +
158D PRO 3.4 22.9 - - - -
159D GLU* 2.6 31.0 + - - -
161D VAL* 3.9 15.6 - - + +
179D ALA* 3.3 14.0 - - - +
185D LEU* 3.8 2.2 - - - -
186D TYR* 2.9 56.7 + + + -
187D THR 4.2 0.9 - - - -
188D LEU* 3.7 14.2 - - + +
210D HIS* 3.8 8.5 - + - +
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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