Contacts of the helix formed by residues 258 - 268 (chain A) in PDB entry 3IPA
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 ASN 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A PRO 2.9 25.5 + - - +
253A THR 5.1 0.7 - - - +
255A ARG* 2.9 22.2 + - - +
257A GLU* 1.3 83.1 - - - +
259A LYS* 1.3 64.6 + - - +
260A GLU 3.3 2.5 - - - -
261A LEU* 3.2 14.5 + - + +
262A VAL* 2.9 33.9 + - + +
277A LEU* 3.7 11.8 - - + +
313A ALA* 2.8 45.8 + - - +
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Residues in contact with LYS 259 (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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253A THR 5.8 2.0 - - - -
255A ARG 3.8 2.1 + - - -
256A PRO* 3.2 19.6 + - + +
257A GLU 3.4 1.2 - - - -
258A ASN* 1.3 77.5 - - - +
260A GLU* 1.3 61.3 + - - +
262A VAL* 3.4 4.4 + - - +
263A GLU* 2.7 60.0 + - + +
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Residues in contact with GLU 260 (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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257A GLU 5.0 2.1 + - - +
258A ASN 3.3 0.4 - - - -
259A LYS* 1.3 75.9 - - - +
261A LEU* 1.3 60.3 + - - +
263A GLU* 3.2 15.0 + - - +
264A LYS* 2.9 36.2 + - + +
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Residues in contact with LEU 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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28A GLN* 4.2 0.7 - - + -
32A ASP* 4.0 1.1 - - - +
257A GLU 5.4 1.5 + - - +
258A ASN* 3.2 26.9 + - + +
260A GLU* 1.3 79.8 - - - +
262A VAL* 1.3 63.3 + - + +
264A LYS* 3.2 35.1 + - - +
265A PHE* 3.1 45.3 + - + -
277A LEU* 3.7 25.1 - - + -
280A TYR* 3.7 39.7 - - + +
313A ALA* 4.5 2.0 - - + -
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Residues in contact with VAL 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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253A THR* 4.0 39.9 - - - +
258A ASN* 2.9 21.4 + - + +
259A LYS* 3.8 4.9 - - - +
261A LEU* 1.3 76.2 - - - +
263A GLU* 1.3 64.2 + - + +
265A PHE* 3.3 4.6 + - - +
266A LYS* 3.1 49.3 + - + +
272A PRO* 3.9 20.0 - - + -
277A LEU* 4.2 15.9 - - + -
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Residues in contact with GLU 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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259A LYS* 2.7 51.5 + - + +
260A GLU* 3.2 16.5 + - + +
262A VAL* 1.3 77.8 - - + +
264A LYS* 1.3 56.7 - - - +
266A LYS* 3.4 10.9 + - + +
267A ALA* 3.0 28.6 + - - +
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Residues in contact with LYS 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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28A GLN* 3.6 28.7 - - - +
32A ASP* 3.2 28.9 + - - -
260A GLU* 2.9 19.6 + - + +
261A LEU* 3.4 29.2 - - - +
262A VAL 3.2 0.2 - - - -
263A GLU* 1.3 74.5 - - - +
265A PHE* 1.3 65.5 + - - +
267A ALA* 3.2 8.2 + - + +
268A ALA* 3.1 21.1 + - + +
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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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24A LYS* 3.5 29.2 - - + -
25A GLY* 4.1 4.7 - - - -
28A GLN* 3.5 30.7 - - + -
261A LEU* 3.1 49.8 + - + -
262A VAL* 3.3 6.7 + - - +
264A LYS* 1.3 76.0 - - - +
266A LYS* 1.3 58.5 + - - +
268A ALA* 2.9 23.8 + - + +
269A GLY 3.1 0.5 + - - -
270A PHE* 3.0 46.6 + + + +
272A PRO* 3.6 21.3 - - + -
276A THR* 4.0 15.0 - - + -
277A LEU* 3.9 15.0 - - + -
280A TYR* 4.3 4.0 - + - -
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Residues in contact with LYS 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 VAL* 3.1 35.3 + - + +
263A GLU* 3.7 12.1 - - + +
264A LYS 3.3 0.2 - - - -
265A PHE* 1.3 79.6 - - - +
267A ALA* 1.3 57.3 + - - +
269A GLY* 3.0 18.1 + - - -
270A PHE 3.4 16.2 - - - +
271A ASN* 4.1 18.8 - - - -
272A PRO* 4.3 3.1 - - + -
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Residues in contact with ALA 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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263A GLU 3.0 17.8 + - - +
264A LYS* 3.6 9.4 - - + +
265A PHE 3.2 0.2 - - - -
266A LYS* 1.3 75.6 - - - +
268A ALA* 1.3 57.5 + - - +
269A GLY 3.3 1.3 + - - -
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Residues in contact with ALA 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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24A LYS* 5.5 4.7 + - - -
28A GLN* 5.6 5.6 - - - +
264A LYS* 3.1 10.3 + - + +
265A PHE* 2.9 14.5 + - + +
267A ALA* 1.3 77.9 - - - +
269A GLY* 1.3 59.7 - - - +
270A PHE* 3.5 3.5 - - + +
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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