Contacts of the strand formed by residues 141 - 147 (chain B) in PDB entry 1QR2
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 LEU 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ASP 3.1 16.4 + - - +
96B LEU* 3.3 13.3 - - + -
97B VAL 2.9 23.4 + - - -
139B GLY 5.0 4.3 - - - +
140B LYS* 1.3 75.7 - - - +
142B ALA* 1.3 62.3 + - - +
181B PHE* 3.7 7.5 - - - -
182B LYS* 3.2 32.8 - - + +
184B LEU* 4.1 34.1 - - + -
214B ILE 5.3 3.8 - - - +
215B TRP* 4.6 22.2 - - + -
217B GLU 5.7 2.2 - - - +
219B PRO* 5.0 4.5 - - + -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 4.6 2.2 - - - -
97B VAL 3.2 8.7 - - - +
99B PHE* 4.6 3.8 - - + -
141B LEU* 1.3 74.5 - - - +
143B LEU* 1.3 62.3 + - - +
176B LEU* 3.8 27.8 - - + -
181B PHE* 3.5 29.4 - - + -
182B LYS 2.9 7.9 + - - +
183B VAL* 3.7 6.5 - - - +
184B LEU* 3.0 25.6 + - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.5 9.9 - - + -
97B VAL 3.0 8.6 + - - +
98B ILE* 3.4 9.4 - - + -
99B PHE* 2.9 28.0 + - - -
142B ALA* 1.3 77.2 - - - +
144B LEU* 1.3 82.8 + - - +
145B SER* 3.9 3.4 - - - +
183B VAL* 5.5 0.9 - - - -
184B LEU* 3.9 12.8 - - + -
185B ALA 3.6 10.1 - - - +
187B GLN* 4.2 4.7 - - + -
207B TRP* 3.4 30.3 - - + -
210B ARG* 3.2 34.5 - - - +
214B ILE* 3.9 17.7 - - + -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.8 31.6 - - + -
101B PHE* 4.3 10.1 - - + -
108B VAL* 5.9 0.4 - - + -
143B LEU* 1.3 76.6 - - - +
145B SER* 1.3 59.0 + - - +
146B VAL* 3.7 13.3 + - + +
168B LEU* 3.8 19.7 - - + -
171B LEU* 3.9 28.5 - - + -
172B GLN* 3.7 31.2 - - + +
176B LEU* 3.9 17.7 - - + -
183B VAL* 5.9 1.1 - - + +
184B LEU 5.2 0.6 + - - -
186B PRO* 3.5 10.4 - - + +
187B GLN 2.8 26.9 + - - +
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.5 6.9 - - - +
98B ILE* 4.5 2.9 - - - -
99B PHE 2.8 15.7 + - - +
100B GLN* 2.8 31.2 + - - -
101B PHE* 3.1 26.0 + - - -
143B LEU* 3.8 2.4 + - - -
144B LEU* 1.3 72.1 - - - +
146B VAL* 1.3 59.7 + - - +
187B GLN* 3.2 21.9 + - - +
189B SER* 5.2 0.5 + - - -
207B TRP* 3.9 24.2 + - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 5.9 0.2 - - - -
101B PHE* 3.3 39.5 - - + +
103B LEU* 3.9 22.2 - - + -
144B LEU* 3.9 21.1 - - + +
145B SER* 1.3 76.9 - - - +
147B THR* 1.3 74.2 + - - +
148B THR* 4.4 5.6 - - + -
167B PHE* 4.8 5.6 - - + -
168B LEU* 4.9 8.3 - - + -
171B LEU* 6.2 0.2 - - + -
186B PRO* 5.6 0.2 - - + -
187B GLN 2.8 9.9 + - - +
188B ILE* 3.2 20.0 - - + +
189B SER* 2.8 25.5 + - - -
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.5 27.1 - - + -
18B ASN* 2.8 35.4 + - - +
21B LEU* 3.6 17.9 - - + -
100B GLN* 4.0 0.9 - - - +
101B PHE 3.1 3.8 + - - -
102B PRO* 3.0 6.1 - - - +
103B LEU* 2.8 26.3 + - - +
146B VAL* 1.3 76.2 - - - +
148B THR* 1.3 64.0 + - - +
189B SER* 3.4 8.3 - - - -
192B PRO* 4.3 3.8 - - - -
233B FAD 2.7 25.5 + - - -
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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