Contacts of the helix formed by residues 254 - 263 (chain B) in PDB entry 2QW4
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 PRO 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B GLN* 6.0 1.3 - - - +
76B TYR* 3.7 31.6 - - + -
80B SER* 4.1 16.4 - - - +
252B PRO 4.4 0.7 - - - +
253B PRO* 1.3 87.5 - - + +
255B PRO* 1.4 76.2 - - + -
256B ILE* 2.9 19.4 + - + -
257B ILE* 3.2 15.0 + - + -
258B ASP* 2.9 21.7 + - - +
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Residues in contact with PRO 255 (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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253B PRO 4.0 4.3 - - - +
254B PRO* 1.4 83.0 - - + +
256B ILE* 1.3 66.6 + - + +
258B ASP* 4.0 5.4 - - + +
259B LYS* 3.2 22.3 + - - +
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Residues in contact with ILE 256 (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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80B SER* 3.6 26.0 - - - +
83B LEU* 3.7 31.6 - - + -
87B ARG* 4.4 9.6 - - - +
109B GLU* 5.5 9.6 - - + +
254B PRO* 2.9 16.4 + - + -
255B PRO* 1.3 74.2 - - + +
257B ILE* 1.3 73.8 + - + +
259B LYS* 2.9 18.4 + - + +
260B ILE* 3.0 21.8 + - + +
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Residues in contact with ILE 257 (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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76B TYR* 4.4 14.8 - - + +
79B LEU* 4.2 35.4 - - + +
80B SER* 4.6 6.5 - - - +
83B LEU* 4.9 12.3 - - + -
112B PHE* 4.0 34.1 - - + -
242B ILE* 4.2 18.6 - - + -
253B PRO* 4.7 1.6 - - + -
254B PRO* 3.2 26.5 + - + +
256B ILE* 1.3 78.5 - - + +
258B ASP* 1.3 64.7 + - - +
260B ILE* 3.0 12.8 + - + +
261B PHE* 3.0 20.3 + - - +
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Residues in contact with ASP 258 (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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242B ILE* 5.7 0.6 - - - +
246B LYS* 2.6 42.2 + - - +
253B PRO* 3.4 26.2 - - + +
254B PRO 2.9 15.2 + - - +
255B PRO* 4.0 5.4 - - + +
257B ILE* 1.3 76.4 - - - +
259B LYS* 1.3 57.8 + - - +
261B PHE* 3.9 4.9 - - - +
262B MET* 2.9 48.1 + - - +
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Residues in contact with LYS 259 (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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109B GLU* 3.3 38.4 + - - +
255B PRO 3.2 15.5 + - - +
256B ILE* 2.9 16.4 + - + +
258B ASP* 1.3 74.4 - - - +
260B ILE* 1.3 60.3 + - - +
262B MET* 3.5 4.2 + - - +
263B ASP* 3.2 47.5 + - - +
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Residues in contact with ILE 260 (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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83B LEU* 5.7 4.9 - - + -
109B GLU* 3.2 59.2 - - + +
112B PHE* 4.7 22.0 - - + -
113B LEU* 4.6 21.8 - - + +
239B LEU* 5.3 2.6 - - + +
242B ILE* 6.5 1.1 - - + -
256B ILE* 3.0 23.7 + - + +
257B ILE* 3.3 15.3 - - + +
259B LYS* 1.3 73.1 - - - +
261B PHE* 1.3 68.7 + - - +
263B ASP* 3.3 18.9 + - - +
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Residues in contact with PHE 261 (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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239B LEU* 3.3 32.2 - - + +
242B ILE* 3.4 31.2 - - + -
243B PHE* 3.2 51.8 - + - -
246B LYS* 3.8 31.4 - - + -
257B ILE 3.0 9.2 + - - +
258B ASP* 3.9 7.4 - - - +
260B ILE* 1.3 78.9 - - - +
262B MET* 1.3 75.6 + - + +
264B THR* 2.9 28.7 + - - -
243C PHE* 3.6 21.1 - + - -
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Residues in contact with MET 262 (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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246B LYS* 3.3 39.9 - - - +
258B ASP* 2.9 37.1 + - - +
259B LYS* 4.0 6.1 - - - +
260B ILE 3.4 0.2 - - - -
261B PHE* 1.3 78.4 - - - +
263B ASP* 1.3 55.6 + - - +
264B THR* 2.8 24.2 + - - -
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Residues in contact with ASP 263 (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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106B LEU* 6.1 1.2 - - - +
109B GLU* 4.0 5.9 - - - +
259B LYS* 3.2 41.0 + - - +
260B ILE* 3.6 13.9 - - - +
261B PHE 3.1 2.2 + - - -
262B MET* 1.3 74.8 - - - +
264B THR* 1.3 61.3 + - - +
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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