Contacts of the helix formed by residues 260 - 270 (chain A) in PDB entry 2POZ
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 TYR 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLY 4.4 5.2 - - - +
86A GLY* 4.0 11.4 - - - -
87A ALA* 3.3 44.4 - - + +
90A PHE* 4.1 17.5 - - + -
257A GLU 4.1 1.3 - - - -
258A ARG* 3.4 42.5 - - - +
259A VAL* 1.3 83.2 - - - +
261A THR* 1.3 79.4 + - - +
264A GLY* 3.0 13.9 + - - -
265A PHE* 4.5 0.2 - - - -
283A THR* 3.4 40.4 - - - +
284A ALA* 4.4 1.8 - - - +
81F TRP* 3.6 14.8 + + - -
83F LYS 4.9 2.3 + - - -
84F ASN* 4.0 19.8 + - - +
85F GLY* 5.7 0.6 - - - -
237F PHE* 3.8 5.4 - - + -
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Residues in contact with THR 261 (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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72A TRP* 4.5 8.7 - - + -
90A PHE* 3.4 47.6 - - + -
260A TYR* 1.3 83.9 + - - +
262A ARG* 1.3 64.6 + - - +
263A PHE* 3.1 25.4 + - + +
264A GLY 3.4 2.3 + - - -
265A PHE* 3.0 19.6 + - - -
284A ALA* 2.9 26.4 + - - +
289A GLU* 3.5 10.5 - - - +
293A ILE* 3.5 11.1 - - - +
237F PHE* 3.6 4.7 - - + -
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Residues in contact with ARG 262 (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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72A TRP* 4.1 15.8 - - - -
261A THR* 1.3 71.6 - - - +
263A PHE* 1.3 82.4 + - + +
265A PHE* 3.8 2.7 - - - +
266A ARG* 2.9 29.6 + - - +
289A GLU* 2.7 44.2 + - - +
292A LYS* 3.9 33.1 - - + +
293A ILE* 3.7 18.2 - - + +
296A MSE 3.8 27.8 - - - +
295E ALA* 2.9 38.7 + - - +
298E GLU* 3.0 31.7 + - - +
299E ALA* 4.4 3.0 - - + +
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Residues in contact with PHE 263 (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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72A TRP* 5.0 5.8 - + - -
76A TYR* 3.7 30.5 - + - -
261A THR* 3.0 12.3 - - - +
262A ARG* 1.3 108.9 - - + +
264A GLY* 1.3 61.1 + - - +
266A ARG* 3.8 15.2 + - - +
267A LYS* 3.6 12.0 + - - +
298E GLU* 3.8 14.6 - - + -
299E ALA* 3.5 42.0 - - + +
175F ARG* 4.2 15.9 - - - -
237F PHE* 3.5 49.0 - + + +
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Residues in contact with GLY 264 (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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259A VAL* 3.4 17.2 - - - +
260A TYR 3.0 20.8 + - - -
261A THR 3.0 4.2 + - - -
263A PHE* 1.3 77.3 - - - +
265A PHE* 1.3 63.7 + - - +
267A LYS* 3.3 39.1 + - - +
268A ILE* 3.9 2.3 + - - +
237F PHE* 3.9 3.3 - - - -
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Residues in contact with PHE 265 (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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255A VAL 4.6 0.4 - - - -
256A GLY* 3.6 30.1 - - - -
259A VAL* 3.3 40.6 - - + -
260A TYR* 4.5 1.1 - - - -
261A THR 3.0 26.4 + - - +
262A ARG* 4.0 3.6 - - - +
264A GLY* 1.3 75.0 - - - +
266A ARG* 1.3 64.5 + - - +
268A ILE* 2.9 12.1 + - + +
269A PHE* 2.9 43.8 + + + -
277A ILE* 3.9 31.6 - - + -
279A PRO* 3.7 19.3 - - + -
284A ALA* 4.6 1.1 - - + -
293A ILE* 3.5 33.0 - - + -
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Residues in contact with ARG 266 (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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262A ARG 2.9 17.3 + - - +
263A PHE* 3.8 10.3 - - - +
264A GLY 3.2 0.4 - - - -
265A PHE* 1.3 75.9 - - - +
267A LYS* 1.3 65.6 + - + +
269A PHE* 3.7 11.5 - - - +
270A GLU* 3.0 44.5 + - - +
296A MSE 4.6 6.3 - - + -
272E GLN* 3.0 32.3 + - - +
299E ALA* 2.9 29.4 + - + -
300E TYR* 3.3 43.8 - - + +
238F ASP* 2.9 28.3 + - - +
240F GLY* 3.7 12.0 - - - +
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Residues in contact with LYS 267 (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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84A ASN* 4.5 6.5 + - - -
239A ASN* 3.9 16.0 + - - +
259A VAL* 5.9 0.4 - - - -
263A PHE 3.6 7.0 - - - +
264A GLY* 3.3 28.3 + - - +
265A PHE 3.1 0.6 - - - -
266A ARG* 1.3 81.2 - - + +
268A ILE* 1.3 61.7 + - + +
270A GLU* 4.0 7.2 + - - +
271A LEU* 3.1 28.9 + - - +
84F ASN* 5.4 8.7 + - - +
237F PHE* 3.8 34.7 + - - +
239F ASN* 5.6 4.9 - - - +
267F LYS* 4.6 26.3 - - + +
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Residues in contact with ILE 268 (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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239A ASN* 3.5 27.8 - - - +
242A LEU* 4.1 14.8 - - + -
255A VAL* 3.9 25.6 - - + -
259A VAL* 4.2 33.7 - - + -
264A GLY 4.3 1.3 - - - +
265A PHE* 2.9 15.3 + - + +
267A LYS* 1.3 76.5 - - + +
269A PHE* 1.3 69.4 + - + +
271A LEU* 3.0 20.0 + - - +
272A GLN* 3.5 4.0 + - - -
273A ALA 4.8 0.9 + - - -
274A CYS* 4.0 18.8 + - + -
277A ILE* 4.6 14.1 - - + -
302A MSE 4.6 3.5 - - + +
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Residues in contact with PHE 269 (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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265A PHE* 2.9 41.0 + + + +
266A ARG* 3.7 4.7 - - - +
268A ILE* 1.3 75.7 - - + +
270A GLU* 1.3 57.8 + - + +
272A GLN* 3.0 20.6 + - - +
277A ILE* 4.0 11.9 - - + -
293A ILE* 3.6 23.3 - - + -
296A MSE 3.4 47.6 - - + -
297A ALA* 3.6 21.5 - - + -
300A TYR* 3.4 45.1 - + + +
302A MSE 3.8 25.0 - - + +
300E TYR* 6.0 0.2 - - - +
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Residues in contact with GLU 270 (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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266A ARG* 3.0 40.5 + - - +
267A LYS* 4.4 6.9 - - - +
269A PHE* 1.3 75.7 - - + +
271A LEU* 1.3 62.7 + - + +
272A GLN* 3.3 6.1 + - - +
300A TYR* 4.4 11.2 - - - +
270E GLU* 4.6 17.2 - - - +
272E GLN* 5.7 0.9 + - - +
300E TYR* 3.0 34.3 + - - +
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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