Contacts of the helix formed by residues 271 - 276 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ILE* 1.3 75.8 - - - +
272A PRO* 1.3 75.4 - - - +
273A ARG 3.2 3.1 - - - -
274A GLU* 2.6 26.5 + - - +
275A ILE* 3.2 12.6 + - - +
281A MSE 3.6 8.7 - - - -
297A ILE* 4.6 0.4 - - - -
298A HIS 3.2 16.6 - - - -
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Residues in contact with PRO 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A SER* 3.0 14.8 + - - +
111A MSE 5.5 6.1 - - + -
271A GLY* 1.3 83.7 - - - +
273A ARG* 1.3 59.5 + - + +
275A ILE* 3.8 2.2 - - + -
276A GLY 2.9 11.5 + - - -
277A GLY* 2.9 50.8 + - - +
278A ILE* 4.4 1.6 - - + +
281A MSE 4.0 3.1 - - + -
297A ILE* 4.7 3.1 - - + -
306A THR* 4.9 5.8 - - + -
309A ALA* 5.3 3.8 - - + -
310A GLU* 3.6 39.3 - - + +
313A ILE* 4.0 18.8 - - + -
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A THR* 3.6 35.2 + - + +
100A ARG 4.9 0.7 - - - +
103A ASN* 3.7 2.8 - - - +
104A GLN* 3.6 31.9 + - + +
107A SER* 3.5 11.6 + - - +
251A PHE* 4.7 5.1 - - - -
271A GLY* 3.1 1.0 + - - -
272A PRO* 1.3 83.9 - - + +
274A GLU* 1.3 90.6 + - - +
298A HIS* 3.4 13.3 - - - +
299A SER 3.3 22.8 + - - +
300A SER* 3.5 30.0 - - - +
301A PHE* 5.3 1.6 - - - +
310A GLU* 5.5 1.5 + - - +
94G HIS 3.6 20.4 + - - -
95G GLY* 3.8 25.0 + - - -
96G ALA* 4.8 3.7 - - - +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 4.7 1.0 - - - +
103A ASN* 3.0 20.8 - - - +
247A ASP* 5.1 1.5 - - - +
250A ALA 4.2 4.8 - - - +
251A PHE* 3.0 74.8 - - + +
269A CYS 4.7 0.3 - - - +
270A ILE* 3.5 7.8 - - + -
271A GLY* 2.6 33.7 + - - +
273A ARG* 1.3 107.1 + - - +
275A ILE* 1.3 56.7 + - - +
298A HIS* 3.1 29.7 + - - +
299A SER 4.2 1.6 - - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 3.2 16.2 + - - +
251A PHE 3.2 15.5 - - - +
252A THR* 3.5 2.7 - - - +
253A LEU* 3.3 39.5 - - + +
270A ILE* 3.9 16.2 - - + -
271A GLY 3.2 15.0 + - - +
272A PRO* 3.8 1.1 - - + -
274A GLU* 1.3 76.3 - - - +
276A GLY* 1.3 60.3 + - - +
277A GLY 3.5 10.1 - - - +
280A PRO* 3.3 31.4 - - + +
281A MSE 3.5 29.8 - - + +
284A ALA* 4.1 10.1 - - + -
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 5.2 1.7 - - - +
103A ASN* 3.4 31.7 - - - +
106A PHE* 3.5 20.5 - - - +
107A SER* 3.5 6.7 - - - -
110A ASP* 3.8 5.0 - - - +
272A PRO 2.9 4.8 + - - -
274A GLU 3.5 2.2 - - - -
275A ILE* 1.3 79.3 - - - +
277A GLY* 1.3 58.9 + - - +
280A PRO* 3.6 13.6 - - - +
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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