Contacts of the helix formed by residues 269 - 275 (chain B) in PDB entry 2PQG
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 ASP 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B TRP* 3.6 12.1 - - + +
255B PRO 5.3 5.6 - - - +
267B ILE* 3.9 1.9 - - - +
268B LYS* 1.3 113.6 + - + +
270B LYS* 1.3 66.3 + - + +
271B ASN* 3.0 15.6 + - + +
272B GLU* 3.0 29.3 + - - +
273B ALA* 3.2 9.7 + - - +
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Residues in contact with LYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLY* 3.5 25.9 + - - -
57B ILE* 5.7 0.2 - - - +
58B PHE* 3.8 33.3 - - + +
59B GLN* 4.9 1.4 + - - -
248B ALA* 5.9 0.7 - - - -
251B TRP* 3.1 57.1 + - + +
255B PRO* 3.4 26.2 + - - +
269B ASP* 1.3 73.8 - - + +
271B ASN* 1.3 70.1 + - - +
273B ALA* 3.2 4.3 + - - +
274B ALA* 2.8 28.4 + - - +
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Residues in contact with ASN 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 4.6 10.8 - - - -
269B ASP* 3.0 13.2 + - - +
270B LYS* 1.3 93.8 - - - +
272B GLU* 1.3 62.8 + - + +
274B ALA* 3.0 22.0 + - - +
275B ARG* 3.5 10.1 + - - +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLY 3.4 8.9 - - - +
267B ILE* 3.2 20.6 + - + -
268B LYS* 2.8 46.3 + - + +
269B ASP* 3.0 18.9 + - - +
271B ASN* 1.3 76.9 - - + +
273B ALA* 1.3 60.5 + - - +
275B ARG* 3.3 14.2 + - - +
276B ILE* 3.3 22.5 - - + +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLN* 3.9 4.3 - - - +
244B ILE* 4.3 18.2 - - + +
248B ALA* 6.2 3.1 - - + -
251B TRP* 4.1 15.7 - - + -
262B MET* 6.0 0.4 - - - -
267B ILE* 3.3 17.0 - - + +
269B ASP 3.2 8.0 + - - +
270B LYS* 3.4 11.0 - - - +
271B ASN 3.1 0.6 - - - -
272B GLU* 1.3 74.2 - - - +
274B ALA* 1.3 61.0 + - - +
275B ARG 3.1 0.4 - - - -
276B ILE* 2.9 20.7 + - - +
277B VAL* 2.9 22.0 + - + +
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 3.8 27.6 - - + -
59B GLN* 3.5 13.3 - - - +
212B ASN* 3.1 14.7 - - - +
270B LYS 2.8 12.7 + - - +
271B ASN* 3.0 15.2 + - - +
273B ALA* 1.3 78.6 - - - +
275B ARG* 1.3 55.8 + - + +
276B ILE 3.5 0.5 + - - -
277B VAL 3.7 6.9 - - - +
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ASN* 3.4 8.4 - - - +
213B THR 3.9 1.2 + - - -
216B ARG* 3.0 73.7 + - - +
271B ASN 3.5 9.8 + - - +
272B GLU* 3.3 12.4 + - - +
273B ALA 3.1 0.6 - - - -
274B ALA* 1.3 78.4 - - + +
276B ILE* 1.3 61.5 + - + +
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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