Contacts of the helix formed by residues 306 - 316 (chain A) in PDB entry 1N3Y
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 ILE 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A PHE* 3.9 20.0 - - + -
267A ILE* 4.1 19.7 - - + -
295A PHE* 3.8 46.4 - - + -
296A LYS 5.6 0.9 - - - +
297A VAL* 3.7 26.2 - - + -
302A ALA 4.5 0.9 - - - +
303A LEU* 3.0 19.8 + - + +
305A ASP* 1.3 80.4 - - + +
307A GLN* 1.3 59.4 + - - +
308A ASN 3.4 2.2 - - - -
309A GLN* 3.2 16.4 + - - +
310A LEU* 2.8 31.7 + - + +
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Residues in contact with GLN 307 (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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153A ASN 5.4 0.2 - - - -
154A PHE* 3.5 32.9 - - + -
157A ALA* 3.4 33.3 + - - +
158A VAL* 4.5 11.6 - - + +
161A GLN* 5.8 9.0 - - + +
304A LYS* 3.3 36.6 + - - +
305A ASP 3.5 0.2 - - - -
306A ILE* 1.3 78.7 - - - +
308A ASN* 1.3 64.4 + - - +
310A LEU* 3.3 3.3 + - - +
311A LYS* 2.9 30.6 + - - +
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Residues in contact with ASN 308 (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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161A GLN* 5.4 1.2 - - - +
304A LYS 5.0 2.8 + - - -
305A ASP 5.2 4.5 + - - +
306A ILE 3.4 0.4 - - - -
307A GLN* 1.3 80.7 + - - +
309A GLN* 1.3 59.2 + - + +
311A LYS* 3.4 26.8 + - - +
312A GLU* 2.9 39.2 + - + +
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Residues in contact with GLN 309 (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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295A PHE* 3.7 23.3 - - + -
305A ASP 3.4 21.0 + - - +
306A ILE* 3.2 17.5 + - - +
308A ASN* 1.3 79.3 - - + +
310A LEU* 1.3 62.3 + - - +
312A GLU* 3.3 7.8 + - - +
313A LYS* 3.1 31.6 + - + +
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Residues in contact with LEU 310 (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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135A PHE* 5.0 0.7 - - + -
154A PHE* 3.9 26.5 - - + -
158A VAL* 4.2 20.0 - - + -
236A ILE* 4.4 13.5 - - + -
265A TYR* 4.3 23.6 - - + -
267A ILE* 4.2 13.9 - - + -
295A PHE* 3.9 27.7 - - + -
306A ILE* 2.8 18.6 + - + +
307A GLN 3.7 4.0 - - - +
309A GLN* 1.3 76.2 - - - +
311A LYS* 1.3 64.1 + - - +
313A LYS* 3.1 3.9 + - - +
314A ILE* 3.1 40.0 + - + +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 5.6 3.1 - - + +
161A GLN* 3.4 48.6 + - + +
162A PHE* 4.4 13.2 - - + -
307A GLN 2.9 16.6 + - - +
308A ASN* 3.6 25.6 + - - +
310A LEU* 1.3 78.4 - - - +
312A GLU* 1.3 76.1 + - - +
314A ILE* 3.2 2.8 + - - +
315A PHE* 2.9 59.4 + - + -
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Residues in contact with GLU 312 (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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308A ASN* 2.9 24.1 + - + +
309A GLN* 3.6 7.2 - - - +
310A LEU 3.3 0.2 - - - -
311A LYS* 1.3 96.8 + - - +
313A LYS* 1.3 64.5 + - + +
315A PHE* 3.5 9.9 + - - +
316A ALA* 3.2 23.0 + - - +
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Residues in contact with LYS 313 (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 TYR* 3.7 24.6 + - + +
291A GLN 5.5 0.9 - - - -
292A GLU* 3.7 39.2 + - + +
295A PHE* 4.0 24.7 - - + -
309A GLN* 3.1 18.0 + - - +
310A LEU* 3.4 6.7 - - - +
312A GLU* 1.3 78.1 - - + +
314A ILE* 1.3 61.9 + - - +
316A ALA* 3.3 18.2 + - - +
317A ILE* 3.5 11.1 - - - +
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Residues in contact with ILE 314 (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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131A GLN* 2.8 32.4 + - - +
133A ILE* 3.6 22.9 - - + -
158A VAL* 4.9 2.5 - - + -
162A PHE* 3.5 40.2 - - + -
169A PHE* 5.9 0.4 - - + -
234A ILE* 4.1 8.7 - - + -
236A ILE* 3.8 28.5 - - + -
265A TYR* 4.5 13.2 - - + -
310A LEU* 3.1 30.5 + - + +
311A LYS 3.7 1.3 - - - +
313A LYS* 1.3 71.5 - - - +
315A PHE* 1.3 59.6 + - - +
316A ALA 3.0 1.8 - - - -
317A ILE* 2.9 20.8 + - + +
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Residues in contact with PHE 315 (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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131A GLN* 4.6 4.1 + - - +
161A GLN 3.7 22.2 - - - -
162A PHE* 3.8 24.9 - + - -
311A LYS* 2.9 51.2 + - + +
312A GLU* 3.9 12.6 - - - +
313A LYS 3.4 0.2 - - - -
314A ILE* 1.3 76.9 - - - +
316A ALA* 1.3 58.2 + - - +
317A ILE 3.2 4.8 + - - -
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Residues in contact with ALA 316 (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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312A GLU 3.2 12.1 + - - +
313A LYS* 3.4 14.1 - - - +
314A ILE 3.0 0.8 - - - -
315A PHE* 1.3 76.1 - - - +
317A ILE* 1.3 63.1 + - - +
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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