Contacts of the strand formed by residues 148 - 153 (chain B) in PDB entry 2QA5
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 CYS 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B PHE* 4.8 7.4 - - + -
39B THR 3.6 2.4 + - - -
40B LEU* 3.3 13.0 - - + +
41B MSE 2.7 31.9 + - - -
146B VAL* 3.2 8.6 - - - +
147B HIS* 1.3 83.3 - - - +
149B CYS* 1.3 63.5 + - - +
150B PHE* 3.4 34.3 - - - -
175B VAL* 4.5 2.0 - - - -
176B ASN* 3.6 10.3 - - - +
178B VAL* 4.3 8.1 - - - -
280B LEU* 5.0 4.5 - - + -
286B ASP* 3.5 20.9 - - + +
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Residues in contact with CYS 149 (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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41B MSE 3.2 29.4 - - + -
43B VAL* 4.6 12.6 - - - -
148B CYS* 1.3 74.2 - - - +
150B PHE* 1.3 76.4 + - - +
151B TYR* 3.9 4.7 - - - -
167B PHE* 4.9 2.5 - - - -
171B ILE* 4.1 12.1 - - + -
175B VAL* 3.6 22.4 - - + +
176B ASN 2.7 14.0 + - - +
177B ILE* 4.4 12.1 - - + -
178B VAL 2.8 27.5 + - - -
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Residues in contact with PHE 150 (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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40B LEU* 3.6 18.6 - - + -
41B MSE 2.7 13.7 + - - +
42B VAL* 4.6 3.4 - - + -
43B VAL 2.7 29.3 + - - +
53B LEU* 5.5 2.5 - - + -
54B ILE* 4.2 11.0 - - + -
57B LEU* 4.1 13.9 - - + -
148B CYS* 3.4 22.2 - - - -
149B CYS* 1.3 86.5 - - - +
151B TYR* 1.3 54.0 + - - +
152B PHE* 3.3 27.6 - + + -
178B VAL* 3.5 25.6 - - + -
180B VAL* 4.3 6.3 - - + -
276B LEU* 3.6 35.7 - - + -
279B MSE 6.2 2.0 - - - -
280B LEU* 3.9 23.3 - - + -
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Residues in contact with TYR 151 (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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43B VAL* 3.0 40.1 - - + +
44B GLY 4.6 2.3 + - - -
45B GLU* 4.3 5.8 + - - -
149B CYS* 3.9 4.0 + - - -
150B PHE* 1.3 72.0 - - - +
152B PHE* 1.3 70.9 + - - +
153B ILE* 3.6 17.6 + - + +
163B LEU* 4.1 14.9 - - - +
164B ASP* 2.8 53.0 + - + -
167B PHE* 3.3 31.6 - + + +
168B MSE 3.4 26.0 - - + -
177B ILE* 4.1 8.7 - - + -
178B VAL 3.0 9.6 + - - +
179B PRO* 3.5 2.9 - - - +
180B VAL* 2.9 26.2 + - - +
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Residues in contact with PHE 152 (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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42B VAL* 3.8 16.6 - - + -
43B VAL 3.0 11.8 + - - +
44B GLY* 3.8 5.0 - - - -
45B GLU* 3.2 23.9 + - - +
48B LEU* 4.4 5.2 - - + +
49B GLY 4.7 1.8 - - - -
50B LYS* 3.6 42.0 - - + -
53B LEU* 3.7 33.4 - - + -
54B ILE* 5.4 2.2 - - + -
150B PHE* 3.3 29.4 - + + -
151B TYR* 1.3 76.8 - - - +
153B ILE* 1.3 63.2 + - - +
154B SER 4.1 0.2 + - - -
180B VAL* 3.3 29.8 - - + -
182B ALA* 3.9 25.8 - - + -
239B VAL* 4.8 2.7 - - + -
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Residues in contact with ILE 153 (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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45B GLU* 5.1 0.4 - - - -
48B LEU* 4.4 1.8 - - - -
151B TYR* 3.6 32.3 - - + +
152B PHE* 1.3 73.9 - - - +
154B SER* 1.3 70.8 + - - +
155B PRO 3.8 0.3 - - - -
159B GLY 5.0 1.8 - - - +
160B LEU* 4.3 29.4 - - + -
164B ASP* 3.7 21.8 - - - +
168B MSE 4.1 14.1 - - + -
179B PRO* 4.5 6.7 - - + -
180B VAL 3.0 18.0 + - - +
181B ILE* 3.7 7.4 - - + +
182B ALA* 3.0 24.0 + - - +
195B LEU* 5.7 1.1 - - + -
199B ILE* 4.1 24.5 - - + -
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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