Contacts of the helix formed by residues 258 - 271 (chain A) in PDB entry 1IN5
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ARG* 2.8 30.7 + - - +
250A LEU 5.7 0.9 - - - +
251A ASN 4.0 2.2 - - - -
252A ILE* 3.5 23.3 - - + -
256A GLY 3.5 1.6 + - - -
257A LEU* 1.3 75.6 - - - +
259A GLU* 1.3 65.9 + - + +
260A PHE* 3.2 7.5 + - - +
261A ASP* 2.8 27.3 + - - +
262A ARG* 3.1 24.8 + - - +
297A TYR* 4.2 10.6 + - - -
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Residues in contact with GLU 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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251A ASN* 4.2 18.7 + - + +
258A ASP* 1.3 77.5 - - + +
260A PHE* 1.3 58.9 + - - +
262A ARG* 3.4 22.8 + - - +
263A LYS* 3.0 30.8 + - + +
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Residues in contact with PHE 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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258A ASP* 3.2 8.0 + - - +
259A GLU* 1.3 77.3 - - + +
261A ASP* 1.3 67.0 + - - +
263A LYS* 3.0 19.0 + - + +
264A ILE* 2.9 39.0 + - + +
286A LEU* 4.1 31.6 - - + -
288A VAL* 3.8 38.4 - - + -
292A THR* 5.6 1.1 - - + -
293A LEU* 4.0 5.4 - - + -
297A TYR* 3.5 50.0 - + + +
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Residues in contact with ASP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 3.1 36.6 + - - -
257A LEU* 3.5 26.8 - - + -
258A ASP* 2.8 31.5 + - - +
260A PHE* 1.3 74.4 - - - +
262A ARG* 1.3 64.1 + - - +
264A ILE* 3.2 16.0 + - - +
265A LEU* 3.3 19.3 + - - +
297A TYR* 3.7 18.7 - - - +
300A TYR* 5.8 0.9 - - - +
301A LEU* 3.8 20.5 - - + +
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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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251A ASN* 3.0 43.2 + - - +
253A ASP* 3.7 27.7 + - - +
257A LEU* 2.8 35.9 + - + -
258A ASP 3.1 8.6 + - - +
259A GLU* 3.6 21.4 - - - +
261A ASP* 1.3 80.0 - - - +
263A LYS* 1.3 57.6 + - - +
265A LEU* 3.3 8.1 + - - +
266A LYS* 2.8 60.4 + - - +
324A LEU* 4.1 21.1 - - + -
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Residues in contact with LYS 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 GLU* 3.0 20.9 + - + +
260A PHE* 3.0 27.5 + - + +
262A ARG* 1.3 76.9 - - - +
264A ILE* 1.3 56.3 + - - +
266A LYS* 4.0 6.5 - - - +
267A THR* 2.7 45.0 + - - +
285A SER 6.0 0.4 - - - -
286A LEU* 4.0 24.0 - - + +
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Residues in contact with ILE 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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260A PHE* 2.9 30.4 + - + +
261A ASP* 3.4 7.9 - - - +
262A ARG 3.2 0.2 - - - -
263A LYS* 1.3 77.3 - - - +
265A LEU* 1.3 64.7 + - - +
267A THR* 3.4 2.4 + - - -
268A ILE* 3.1 39.4 + - + +
282A LEU* 4.5 11.3 - - + +
286A LEU* 3.9 14.8 - - + -
293A LEU* 3.5 31.2 - - + -
297A TYR* 3.6 26.5 - - + -
298A GLU* 5.3 1.8 - - + +
301A LEU* 4.1 22.4 - - + -
307A LEU* 4.4 7.4 - - + -
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Residues in contact with LEU 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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257A LEU* 4.1 25.4 - - + -
261A ASP 3.3 16.5 + - - +
262A ARG* 3.8 2.9 - - - +
264A ILE* 1.3 74.8 - - - +
266A LYS* 1.3 58.7 + - - +
268A ILE* 3.3 3.5 + - - +
269A ILE* 3.0 36.0 + - + +
301A LEU* 4.3 11.7 - - + -
306A PHE* 4.1 28.5 - - + +
307A LEU* 3.9 32.5 - - + -
316A VAL* 3.9 9.6 - - + +
320A ALA* 4.5 7.6 - - + -
324A LEU* 3.6 26.5 - - + -
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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 ARG* 2.8 50.7 + - + +
263A LYS* 4.1 5.4 - - - +
265A LEU* 1.3 69.6 - - - +
267A THR* 1.3 57.2 + - - +
269A ILE* 4.3 6.5 - - - -
270A GLU* 2.8 44.2 + - - +
324A LEU* 3.9 24.7 - - + -
326A TYR* 3.4 30.3 - - - +
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Residues in contact with THR 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 LYS* 2.7 31.9 + - - +
264A ILE 3.6 4.3 - - - -
266A LYS* 1.3 77.0 - - - +
268A ILE* 1.3 57.6 + - - +
270A GLU* 5.1 0.4 - - - -
271A ILE* 2.9 46.5 + - + +
272A TYR* 3.5 10.1 + - + -
282A LEU* 3.9 19.5 - - + -
285A SER* 4.4 12.3 - - - +
286A LEU* 3.5 20.3 - - + +
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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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264A ILE* 3.1 19.8 + - + +
265A LEU 3.7 1.6 - - - +
267A THR* 1.3 75.1 - - - +
269A ILE* 1.3 55.5 + - - +
272A TYR* 3.2 11.9 + - - -
273A ARG 3.2 8.1 + - - -
274A GLY 2.8 42.3 + - - +
275A GLY* 3.7 7.2 - - - +
277A VAL* 4.1 8.7 - - + -
282A LEU* 3.7 36.1 - - + -
307A LEU* 3.4 31.0 - - + -
314A ARG* 4.5 10.5 - - + +
316A VAL* 3.4 24.7 - - + +
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Residues in contact with ILE 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 LEU 3.0 21.9 + - - +
266A LYS* 3.6 4.3 - - - +
268A ILE* 1.3 77.4 - - - +
270A GLU* 1.3 59.8 + - + +
273A ARG* 3.2 24.3 + - - +
274A GLY 3.5 6.4 + - - +
316A VAL* 4.1 20.9 - - + -
321A TYR* 3.7 40.6 + - + -
324A LEU* 4.1 15.9 - - + -
326A TYR* 3.7 48.9 - - + -
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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 LYS* 2.8 24.2 + - - +
267A THR* 5.1 0.2 - - - -
269A ILE* 1.3 75.2 - - + +
271A ILE* 1.3 75.3 + - + +
273A ARG* 4.2 5.2 + - - +
326A TYR* 2.7 39.4 + - + +
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Residues in contact with ILE 271 (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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267A THR* 2.9 30.9 + - + +
270A GLU* 1.3 84.5 - - + +
272A TYR* 1.3 88.4 + - + +
273A ARG* 3.6 1.7 + - - +
285A SER* 5.0 4.7 - - - +
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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