Contacts of the helix formed by residues 271 - 276 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270C ILE* 1.3 74.3 - - - +
272C PRO* 1.3 77.2 - - - +
273C ARG 3.2 2.9 - - - -
274C GLU* 2.7 27.2 + - - -
275C ILE* 3.2 12.6 + - - +
281C MSE 3.6 9.9 - - - -
297C ILE* 4.5 0.9 - - - -
298C HIS 3.4 15.6 + - - -
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Residues in contact with PRO 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C SER* 3.1 15.7 + - - +
111C MSE 4.1 19.1 - - + -
271C GLY* 1.3 81.0 - - - +
273C ARG* 1.3 59.0 + - + +
275C ILE* 4.0 1.3 - - + -
276C GLY 2.8 27.2 + - - -
277C GLY* 2.9 33.4 + - - +
278C ILE* 5.3 0.4 - - + -
281C MSE 3.9 1.9 - - + -
297C ILE* 4.6 2.9 - - + -
298C HIS 4.6 0.2 - - - +
306C THR* 4.9 2.7 - - + -
310C GLU* 3.9 33.9 - - + +
313C ILE* 4.0 22.2 - - + -
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Residues in contact with ARG 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C THR* 3.5 41.0 + - + +
100C ARG 4.8 0.9 - - - +
103C ASN* 3.8 1.2 - - - +
104C GLN* 3.6 30.9 + - + +
107C SER* 3.4 12.0 + - - +
251C PHE* 4.6 5.7 - - - -
271C GLY 3.1 0.8 + - - -
272C PRO* 1.3 81.5 - - + +
274C GLU* 1.3 90.1 + - - +
298C HIS* 3.7 11.3 + - - -
299C SER 3.5 22.8 + - - -
300C SER* 3.5 23.4 - - - +
301C PHE* 5.5 2.0 - - - +
94H HIS 3.7 19.6 + - - -
95H GLY* 3.7 26.7 + - - -
96H ALA* 4.6 4.0 - - - +
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Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG 4.7 0.2 - - - +
103C ASN* 3.0 24.6 + - - +
247C ASP* 4.9 1.4 - - - +
250C ALA 4.4 2.8 - - - +
251C PHE* 3.1 66.8 - - + +
269C CYS 4.5 0.7 - - - +
270C ILE* 3.4 13.1 - - + +
271C GLY* 2.7 33.5 + - - +
273C ARG* 1.3 105.9 + - - +
275C ILE* 1.3 58.8 + - - +
298C HIS* 3.3 28.2 - - + +
299C SER 4.4 1.6 - - - +
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASN* 3.5 15.1 + - - +
251C PHE 3.1 14.8 - - - +
252C THR* 3.5 3.6 - - - -
253C LEU* 3.2 39.3 - - + +
270C ILE* 3.8 15.5 - - + -
271C GLY 3.2 13.9 + - - +
272C PRO 4.0 0.2 - - - +
274C GLU* 1.3 77.6 - - - +
276C GLY* 1.3 60.1 + - - +
277C GLY 3.6 9.6 - - - +
280C PRO* 3.4 31.0 - - + +
281C MSE 3.6 30.1 - - + +
284C ALA* 4.3 10.5 - - + -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ILE* 5.1 2.1 - - - +
103C ASN* 3.4 29.5 - - - +
106C PHE* 3.6 19.4 - - - +
107C SER* 3.6 6.5 - - - -
110C ASP* 3.9 4.7 - - - +
272C PRO 2.8 11.1 + - - -
274C GLU 3.4 2.8 - - - -
275C ILE* 1.3 79.9 - - - +
277C GLY* 1.3 55.2 + - - +
280C PRO* 3.6 12.4 - - - +
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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