Contacts of the helix formed by residues 271 - 276 (chain D) in PDB entry 2PGW
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 GLY 271 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270D ILE* 1.3 74.7 - - - +
272D PRO* 1.3 75.3 - - - +
273D ARG 3.2 2.7 - - - -
274D GLU* 2.6 25.4 + - - +
275D ILE* 3.2 14.7 + - - +
281D MSE 3.6 9.4 - - - +
297D ILE* 4.6 0.9 - - - -
298D HIS* 3.3 15.8 - - - +
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Residues in contact with PRO 272 (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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107D SER* 2.8 16.8 + - - +
111D MSE 5.4 6.5 - - + -
271D GLY* 1.3 82.5 - - - +
273D ARG* 1.3 59.0 + - + +
275D ILE* 3.9 0.9 - - + -
276D GLY 2.9 11.1 + - - -
277D GLY* 2.8 51.6 + - - +
278D ILE* 4.5 2.0 - - + +
281D MSE 4.0 1.5 - - + -
297D ILE* 4.7 2.0 - - + -
306D THR* 4.8 7.6 - - + -
309D ALA* 5.4 3.8 - - + -
310D GLU* 3.7 37.5 - - + +
313D ILE* 4.0 16.6 - - + -
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Residues in contact with ARG 273 (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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52D THR* 3.6 40.7 + - + +
100D ARG 4.9 0.7 - - - +
103D ASN 3.7 0.5 - - - +
104D GLN* 3.5 33.0 + - + +
107D SER* 3.4 10.7 + - - -
251D PHE* 4.6 5.2 - - - -
271D GLY 3.2 1.0 + - - -
272D PRO* 1.3 83.8 - - + +
274D GLU* 1.3 89.5 + - - +
298D HIS* 3.7 11.3 + - - +
299D SER 3.4 23.0 + - - -
300D SER* 3.5 24.6 - - - +
301D PHE* 5.5 1.4 - - - +
94E HIS 3.6 20.6 + - - -
95E GLY* 3.6 26.5 + - - -
96E ALA* 4.5 4.2 - - - +
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Residues in contact with GLU 274 (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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100D ARG* 4.7 0.9 - - - +
103D ASN* 3.0 23.9 + - - +
247D ASP* 5.0 1.6 - - - +
250D ALA 4.2 4.3 - - - +
251D PHE* 3.1 69.4 - - + +
269D CYS 4.8 0.3 - - - +
270D ILE* 3.5 6.2 - - + -
271D GLY 2.6 33.0 + - - +
273D ARG* 1.3 106.9 + - - +
275D ILE* 1.3 58.6 + - - +
298D HIS* 3.1 32.3 - - + +
299D SER 4.3 1.6 - - - +
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Residues in contact with ILE 275 (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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103D ASN* 3.4 14.4 + - - +
251D PHE 3.1 10.3 - - - +
252D THR* 3.5 7.9 - - - +
253D LEU* 3.2 41.1 - - + +
270D ILE* 4.0 8.7 - - + -
271D GLY 3.2 15.4 + - - +
272D PRO* 3.9 0.4 - - + -
274D GLU* 1.3 78.3 - - - +
276D GLY* 1.3 59.4 + - - +
277D GLY 3.6 9.6 - - - +
280D PRO* 3.3 31.6 - - + +
281D MSE 3.6 30.7 - - + +
284D ALA* 4.1 14.8 - - + -
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Residues in contact with GLY 276 (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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83D ILE* 5.3 1.4 - - - +
103D ASN* 3.4 29.5 - - - +
106D PHE* 3.8 12.2 - - - +
107D SER* 3.6 11.6 + - - -
110D ASP* 3.9 4.3 - - - +
272D PRO 2.9 7.5 + - - -
274D GLU 3.3 2.6 - - - -
275D ILE* 1.3 80.9 - - - +
277D GLY* 1.3 58.8 + - - +
280D PRO* 3.4 15.0 - - - +
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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