Contacts of the helix formed by residues 271 - 276 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E ILE* 1.3 75.2 - - - +
272E PRO* 1.3 76.7 - - - +
273E ARG 3.2 2.9 - - - -
274E GLU* 2.6 26.3 + - - +
275E ILE* 3.2 13.7 + - - +
281E MSE 3.6 9.9 - - - -
297E ILE* 4.6 0.7 - - - -
298E HIS 3.2 15.8 + - - -
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Residues in contact with PRO 272 (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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107E SER* 3.1 14.7 + - - +
111E MSE 4.0 20.4 - - + -
271E GLY* 1.3 82.2 - - - +
273E ARG* 1.3 58.5 + - + +
275E ILE* 4.0 1.1 - - + -
276E GLY 2.9 26.9 + - - -
277E GLY 3.0 33.4 + - - +
278E ILE* 5.6 0.4 - - + -
281E MSE 4.0 1.9 - - + -
297E ILE* 4.7 2.2 - - + -
306E THR* 4.7 2.5 - - + -
309E ALA* 5.2 0.2 - - + -
310E GLU* 3.5 39.7 - - + +
313E ILE* 4.1 17.3 - - + -
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Residues in contact with ARG 273 (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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94D HIS 3.5 21.6 + - - -
95D GLY* 3.6 27.2 + - - -
96D ALA* 4.5 3.4 - - - +
52E THR* 3.6 42.0 - - + +
100E ARG 5.0 0.9 - - - +
103E ASN* 3.8 2.6 - - - +
104E GLN* 3.7 28.3 + - + +
107E SER* 3.5 11.4 + - - -
251E PHE* 4.7 5.1 - - - -
271E GLY 3.2 0.8 + - - -
272E PRO* 1.3 82.7 - - + +
274E GLU* 1.3 84.3 + - - +
298E HIS* 3.4 28.5 - - - +
299E SER 3.6 10.1 + - - -
300E SER* 3.6 22.8 - - - +
301E PHE* 5.5 4.2 - - - +
310E GLU* 6.1 0.2 - - - +
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Residues in contact with GLU 274 (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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100E ARG* 4.9 0.2 - - - -
103E ASN* 2.9 25.3 + - - +
247E ASP* 5.3 1.5 - - - +
250E ALA 4.2 5.1 - - - +
251E PHE* 2.9 67.4 - - + +
269E CYS 4.9 0.2 - - - +
270E ILE* 3.5 6.6 - - + -
271E GLY 2.6 33.8 + - - +
273E ARG* 1.3 109.6 + - - +
275E ILE* 1.3 59.5 + - - +
298E HIS* 3.2 28.8 + - + +
299E SER 4.6 0.5 - - - +
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Residues in contact with ILE 275 (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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103E ASN* 3.5 12.7 + - - +
251E PHE 3.1 15.5 - - - +
252E THR* 3.4 4.0 - - - +
253E LEU* 3.2 39.9 - - + +
270E ILE* 4.0 14.6 - - + -
271E GLY 3.2 9.3 + - - +
272E PRO 4.0 0.2 - - - +
274E GLU* 1.3 78.4 - - - +
276E GLY* 1.3 59.2 + - - +
277E GLY 3.5 9.9 - - - +
280E PRO* 3.3 31.1 - - + +
281E MSE 3.4 37.5 - - + +
284E ALA* 4.2 10.3 - - + -
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Residues in contact with GLY 276 (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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83E ILE* 5.2 1.9 - - - +
103E ASN* 3.4 32.1 - - - +
106E PHE* 3.6 19.2 - - - +
107E SER* 3.6 7.0 - - - -
110E ASP* 3.8 4.3 - - - +
272E PRO 2.9 5.0 + - - -
274E GLU 3.4 3.0 - - - -
275E ILE* 1.3 79.7 - - - +
277E GLY* 1.3 58.4 + - - +
280E PRO* 3.5 14.3 - - - +
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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