Contacts of the helix formed by residues 306 - 314 (chain A) in PDB entry 5ICN
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 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A TYR* 3.5 18.3 - - + +
304A GLY 3.2 5.5 + - - -
305A LYS* 1.3 74.7 - - - +
307A PHE* 1.3 57.9 + - - +
308A THR* 3.3 19.8 + - - -
309A ASP* 3.0 29.6 + - - +
310A ILE* 3.0 26.5 + - - +
26B GLN* 3.8 20.7 + - - +
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Residues in contact with PHE 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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296A PHE* 4.1 8.1 - + - -
300A LEU* 5.1 1.3 - - + -
304A GLY 5.1 0.2 - - - -
305A LYS* 3.4 20.9 + - + -
306A ASP* 1.3 70.5 + - - +
308A THR* 1.3 62.6 + - - +
310A ILE* 3.8 22.0 - - + +
311A GLN* 3.3 17.0 + - - +
320A LEU* 3.4 17.6 - - + +
323A ILE* 4.1 20.0 - - + +
324A ILE* 3.5 31.6 - - + -
327A TYR* 3.3 58.1 - + + -
328A TYR* 6.1 0.2 - + - -
23B TYR* 3.7 40.3 - + + -
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Residues in contact with THR 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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306A ASP* 3.3 9.8 + - - -
307A PHE* 1.3 75.3 - - - +
309A ASP* 1.3 73.2 + - - +
311A GLN* 3.4 11.6 + - - +
312A GLN* 3.0 32.0 + - - +
320A LEU* 3.9 27.1 - - + -
81B PRO* 6.4 2.0 - - + -
104B ASP* 5.2 7.6 - - + +
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Residues in contact with ASP 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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303A TYR* 3.8 20.3 - - + -
306A ASP* 3.0 29.4 + - - +
308A THR* 1.3 84.1 + - - +
310A ILE* 1.3 65.8 + - - +
312A GLN* 4.1 8.7 - - - +
313A ASP* 3.0 33.1 + - - +
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Residues in contact with ILE 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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296A PHE* 4.4 21.1 - - + -
299A ALA* 3.4 42.6 - - + +
300A LEU* 3.7 7.2 - - + +
303A TYR* 4.0 11.9 - - + -
304A GLY 3.1 25.6 - - - +
306A ASP 3.0 19.4 + - - +
307A PHE* 3.9 26.0 - - + +
308A THR 3.3 0.4 - - - -
309A ASP* 1.3 76.9 - - - +
311A GLN* 1.3 56.4 + - - +
314A PHE* 3.0 33.3 + - + +
315A LEU* 3.1 7.7 + - + -
323A ILE* 4.7 8.3 - - + -
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Residues in contact with GLN 311 (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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307A PHE 3.3 7.4 + - - +
308A THR* 3.5 15.1 - - - +
309A ASP 3.2 0.2 - - - -
310A ILE* 1.3 77.6 - - - +
312A GLN* 1.3 79.3 + - + +
315A LEU 3.0 18.3 + - - +
316A PRO* 2.9 29.1 + - + -
318A LYS 2.7 29.7 + - - -
319A SER* 3.9 1.0 - - - +
320A LEU* 3.4 29.5 - - - +
323A ILE* 3.4 19.3 - - + +
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Residues in contact with GLN 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 THR* 3.0 18.2 + - - +
309A ASP* 3.8 9.0 - - - +
311A GLN* 1.3 92.5 - - + +
313A ASP* 1.3 71.5 + - - +
316A PRO* 3.7 17.6 - - - +
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Residues in contact with ASP 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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303A TYR* 2.9 26.1 + - + +
309A ASP* 3.0 17.1 + - - +
312A GLN* 1.3 91.5 + - - +
314A PHE* 1.3 78.4 + - + +
316A PRO* 4.9 2.9 - - - +
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Residues in contact with PHE 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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295A LEU* 3.5 47.8 - - + +
298A GLU* 4.4 22.2 - - + -
299A ALA* 3.5 36.8 - - + -
302A LYS* 4.3 20.9 - - + -
303A TYR* 3.8 33.7 - + - -
310A ILE 3.0 15.9 + - - +
311A GLN 3.2 0.2 + - - -
313A ASP* 1.3 89.3 - - + +
315A LEU* 1.3 64.5 + - + +
316A PRO* 3.5 9.7 - - - +
317A TRP* 4.0 4.2 - - - -
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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