Contacts of the helix formed by residues 271 - 276 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270F ILE* 1.3 74.7 - - - +
272F PRO* 1.3 75.7 - - - +
273F ARG 3.3 2.7 - - - -
274F GLU* 2.7 26.2 + - - +
275F ILE* 3.3 13.5 + - - +
281F MSE 3.7 9.0 - - - -
297F ILE* 4.4 0.7 - - - -
298F HIS 3.2 17.0 + - - -
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Residues in contact with PRO 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F SER* 3.0 14.1 + - - +
111F MSE 4.2 18.6 - - + -
271F GLY* 1.3 82.5 - - - +
273F ARG* 1.3 58.8 + - + +
275F ILE* 4.1 0.7 - - + -
276F GLY 2.8 26.3 + - - -
277F GLY* 2.9 36.0 + - - +
278F ILE* 4.6 0.4 - - + +
281F MSE 4.0 3.5 - - + -
297F ILE* 4.6 2.9 - - + -
306F THR* 4.8 2.2 - - + -
310F GLU* 3.6 37.9 - - + +
313F ILE* 4.1 17.9 - - + -
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Residues in contact with ARG 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS 3.5 21.6 + - - -
95B GLY* 3.8 24.0 + - - -
96B ALA* 5.2 3.4 - - - +
52F THR* 3.5 42.4 + - + +
100F ARG 4.9 0.9 - - - +
103F ASN* 3.8 0.5 - - - +
104F GLN* 3.5 31.6 + - + +
107F SER* 3.4 12.3 + - - +
251F PHE* 4.7 5.2 - - - -
271F GLY 3.2 0.8 + - - -
272F PRO* 1.3 82.3 - - + +
274F GLU* 1.3 93.5 + - - +
298F HIS* 3.4 11.5 - - - -
299F SER 3.3 20.4 + - - -
300F SER* 3.5 23.6 - - - +
301F PHE* 5.3 3.4 - - - +
310F GLU* 6.1 0.4 - - - +
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Residues in contact with GLU 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F ARG* 4.7 0.3 - - - +
103F ASN* 2.9 19.9 + - - +
247F ASP* 5.1 2.4 - - - +
250F ALA 4.2 3.7 - - - +
251F PHE* 2.9 72.0 - - + +
269F CYS 4.8 0.2 - - - +
270F ILE* 3.6 8.2 - - + +
271F GLY* 2.7 36.0 + - - +
273F ARG* 1.3 106.2 + - - +
275F ILE* 1.3 58.9 + - - +
276F GLY 3.4 0.2 - - - -
298F HIS* 3.0 29.2 + - - +
299F SER 4.3 0.9 - - - +
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Residues in contact with ILE 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASN* 3.3 16.8 + - - +
251F PHE 3.1 11.0 - - - +
252F THR* 4.6 0.4 - - - -
253F LEU* 4.0 28.7 - - + +
270F ILE* 4.0 12.6 - - + -
271F GLY 3.3 13.2 + - - +
272F PRO* 4.1 0.2 - - + -
274F GLU* 1.3 75.0 - - - +
276F GLY* 1.3 59.3 + - - +
277F GLY 3.8 5.6 - - - +
280F PRO* 3.3 26.9 - - + +
281F MSE 3.6 32.8 - - + +
284F ALA* 3.3 35.2 - - + +
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Residues in contact with GLY 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ILE* 5.1 2.3 - - - +
103F ASN* 3.4 31.0 - - - +
106F PHE* 3.7 17.9 - - - +
107F SER* 3.6 6.3 - - - -
110F ASP* 3.8 5.4 - - - +
272F PRO 2.8 8.0 + - - -
274F GLU 3.4 2.6 - - - -
275F ILE* 1.3 80.3 - - - +
277F GLY* 1.3 55.0 + - - +
280F PRO* 3.6 13.3 - - - +
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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