Contacts of the helix formed by residues 252 - 262 (chain E) in PDB entry 1QZW
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 LYS 252 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E MET* 6.0 0.4 - - - -
37E SER* 2.6 30.5 - - - +
38E ASP* 2.9 32.7 - - + +
220E ALA 3.8 8.1 - - - +
221E SER* 4.7 8.9 - - - +
250E THR* 3.1 47.8 + - + +
251E ALA* 1.3 87.9 - - - +
253E GLY* 1.3 65.3 + - - +
254E GLY 2.8 1.4 + - - -
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Residues in contact with GLY 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 6.0 1.1 - - - +
38E ASP* 4.1 1.2 - - - +
220E ALA* 3.4 24.3 - - - +
247E MET* 4.9 9.4 - - - -
250E THR* 4.6 0.6 - - - -
251E ALA 3.8 1.8 - - - +
252E LYS* 1.3 76.4 - - - +
254E GLY* 1.3 69.7 + - - +
255E GLY* 2.9 1.0 + - - -
256E ALA* 2.4 24.6 + - - +
257E LEU* 4.1 6.7 - - - -
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Residues in contact with GLY 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E SER* 4.2 0.8 + - - -
39E VAL* 3.9 12.3 - - - -
82E PHE* 4.9 4.9 - - - -
252E LYS 2.8 7.0 + - - -
253E GLY* 1.3 70.5 - - - -
255E GLY* 1.3 54.2 + - - -
256E ALA 2.4 16.5 + - - -
257E LEU* 2.6 38.3 + - - +
258E SER* 2.6 13.7 + - - -
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Residues in contact with GLY 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASP* 2.9 18.4 - - - -
39E VAL* 3.0 23.6 - - - +
40E ASN 3.8 0.2 - - - -
224E GLN* 3.0 19.7 - - - -
253E GLY 2.9 1.8 + - - -
254E GLY* 1.3 70.5 - - - -
256E ALA* 1.3 67.0 + - - +
258E SER* 2.7 12.7 + - - -
259E ALA 2.6 18.0 + - - -
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Residues in contact with ALA 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ILE* 6.1 1.8 - - + -
219E ASP 5.2 0.2 - - - +
220E ALA* 3.6 24.5 - - + -
222E ILE* 5.9 0.4 - - + -
223E GLY* 3.2 29.1 - - - +
224E GLN 3.0 3.6 - - - +
226E ALA* 5.4 3.0 - - + +
244E ILE* 4.5 10.3 - - + -
247E MET* 6.4 0.2 - - + -
253E GLY 2.4 18.3 + - - +
254E GLY 2.4 6.3 + - - -
255E GLY* 1.3 76.5 - - - +
257E LEU* 1.3 57.1 + - + +
259E ALA* 3.1 6.2 + - - +
260E VAL* 2.8 26.6 + - - +
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Residues in contact with LEU 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E PHE* 3.0 40.4 - - + -
244E ILE* 4.5 13.4 - - + +
247E MET* 4.5 19.7 - - + -
253E GLY 4.1 2.2 - - - -
254E GLY* 2.6 47.7 + - - +
256E ALA* 1.3 77.2 - - + +
258E SER* 1.3 75.1 + - - +
260E VAL* 2.9 18.8 - - - +
261E VAL* 2.8 20.3 - - + +
267E ILE* 5.4 2.0 - - + +
270E ILE* 5.9 2.5 - - + -
287E PHE* 4.9 15.0 - - + -
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Residues in contact with SER 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E VAL* 4.3 6.6 - - - +
40E ASN* 4.8 6.5 - - - -
43E LEU* 4.9 12.3 - - - -
81E LEU* 5.1 6.8 - - - +
82E PHE* 3.8 12.1 - - - -
224E GLN* 5.3 0.2 - - - -
254E GLY* 2.6 37.0 + - - -
255E GLY* 2.7 14.1 + - - -
256E ALA 2.9 0.4 + - - -
257E LEU* 1.3 82.3 - - - +
259E ALA* 1.3 72.2 + - - +
261E VAL* 3.0 20.2 + - - +
262E ALA* 3.3 5.4 + - - +
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ASN* 5.8 2.0 - - - +
224E GLN* 3.0 35.2 - - + +
227E TYR* 3.1 40.2 - - + +
255E GLY 2.6 17.7 + - - +
256E ALA 3.4 2.7 - - - +
258E SER* 1.3 74.2 - - - +
260E VAL* 1.3 71.5 + - - +
262E ALA* 2.9 12.1 + - - -
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Residues in contact with VAL 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ILE* 5.8 5.6 - - + -
226E ALA* 6.0 3.4 - - + -
227E TYR* 4.6 4.6 - - - +
242E VAL* 4.6 10.3 - - + -
244E ILE* 4.3 12.6 - - + -
256E ALA 2.8 22.2 - - - +
257E LEU* 2.9 20.2 - - - +
259E ALA* 1.3 79.9 - - + +
261E VAL* 1.3 62.0 + - - +
263E THR* 2.3 30.5 + - - -
265E ALA* 3.0 21.3 - - + -
267E ILE* 3.2 29.6 - - + -
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Residues in contact with VAL 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LYS 4.2 3.1 - - - +
81E LEU 3.9 8.7 - - - +
82E PHE* 2.9 36.6 - - + +
83E GLY* 3.4 26.5 - - - +
84E GLY 4.2 1.8 - - - +
257E LEU* 2.8 21.1 - - + +
258E SER* 3.0 6.9 + - - +
260E VAL* 1.3 79.5 - - + +
262E ALA* 1.3 53.7 - - - +
263E THR 2.2 21.1 + - - -
264E GLY* 2.5 17.0 + - - -
265E ALA* 3.0 12.1 + - - +
267E ILE* 5.1 4.7 - - + -
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 6.3 5.8 - - + -
81E LEU 6.1 0.4 - - - +
227E TYR* 2.8 23.1 + - + +
258E SER 4.0 5.4 - - - +
259E ALA* 2.9 12.5 + - - +
260E VAL 2.9 2.0 + - - -
261E VAL* 1.3 72.6 - - + +
263E THR* 1.3 70.1 + - - +
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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