Contacts of the helix formed by residues 306 - 314 (chain A) in PDB entry 3H60
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 THR 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ARG* 3.7 8.5 - - - +
302A GLY 4.3 2.7 - - - +
303A ASN* 2.6 30.4 + - - +
304A HIS 3.2 1.2 + - - -
305A GLU* 1.3 82.8 - - - +
307A ASP* 1.3 68.1 + - - +
308A ASN* 4.5 5.4 + - - +
309A MET* 3.4 13.5 + - - +
310A ASN* 3.0 28.1 + - - -
335A PHE* 5.7 0.4 - - - -
374A GLN* 3.4 10.3 - - - +
375A PRO* 3.5 34.1 - - + -
385A LEU* 4.9 1.6 - - + -
386A TRP* 5.5 1.7 + - - +
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Residues in contact with ASP 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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306A THR* 1.3 69.6 - - - +
308A ASN* 1.3 61.6 + - - +
310A ASN* 3.1 1.6 + - - +
311A GLN* 2.4 56.1 + - + +
328A TYR* 3.4 8.8 + - - -
332A SER* 2.7 36.8 + - - -
335A PHE* 6.1 0.2 - - - -
374A GLN* 2.7 34.0 + - + +
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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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306A THR* 3.5 6.9 - - - +
307A ASP* 1.3 79.6 - - - +
309A MET* 1.3 76.5 + - + +
311A GLN* 3.6 11.5 + - - +
312A ILE* 3.7 20.7 + - + +
374A GLN* 4.6 0.6 + - - -
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Residues in contact with MET 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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274A ASP* 3.4 16.8 - - - +
303A ASN* 3.2 24.0 - - - +
304A HIS* 3.8 18.4 - - - +
306A THR* 3.4 12.0 + - - +
307A ASP 3.3 0.8 - - - -
308A ASN* 1.3 92.5 - - + +
310A ASN* 1.3 58.3 + - - +
312A ILE* 3.2 10.2 + - + -
313A TYR* 2.9 56.0 + - + -
386A TRP* 3.8 32.8 - - + -
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Residues in contact with ASN 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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273A VAL* 3.7 2.6 - - - +
274A ASP* 3.1 18.3 + - - -
304A HIS 2.8 26.1 + - - -
306A THR 3.0 22.5 + - - +
307A ASP* 3.1 0.7 + - - +
309A MET* 1.3 75.4 - - - +
311A GLN* 1.3 60.7 + - - +
312A ILE 3.4 0.3 + - - -
314A GLY 3.8 4.2 + - - -
315A PHE* 3.5 30.5 + - - +
316A GLU* 3.1 23.5 + - - +
317A GLY 4.5 0.2 + - - -
328A TYR* 3.0 33.7 + - + +
332A SER* 5.7 0.2 - - - -
335A PHE* 3.6 17.0 - - - -
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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 ASP* 2.4 48.2 + - + +
308A ASN* 4.0 7.9 - - - +
309A MET 3.2 0.4 - - - -
310A ASN* 1.3 77.1 - - - +
312A ILE* 1.3 60.6 + - + +
314A GLY 5.0 0.9 + - - -
316A GLU* 2.0 55.4 - - - +
328A TYR* 3.0 29.3 + - - -
490A ALA* 5.7 3.6 - - - -
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Residues in contact with ILE 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* 3.7 14.6 + - + +
309A MET* 3.2 10.2 + - + +
311A GLN* 1.3 80.7 - - + +
313A TYR* 1.3 98.1 + - + +
314A GLY 3.4 1.6 - - - -
487A MET* 5.2 0.5 - - - +
490A ALA* 3.4 20.8 - - - +
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Residues in contact with TYR 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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274A ASP* 3.5 25.5 - - + -
275A ARG* 2.8 61.9 + - - +
304A HIS* 3.6 13.5 - + + -
309A MET* 2.9 50.6 + - + -
311A GLN 3.8 0.2 - - - -
312A ILE* 1.3 99.3 - - + +
314A GLY* 1.3 57.5 + - - +
487A MET* 3.5 26.2 - - - +
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Residues in contact with GLY 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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274A ASP* 5.0 1.3 - - - -
275A ARG 4.9 0.9 - - - -
276A GLY 6.1 1.8 - - - -
279A SER* 5.7 0.2 - - - -
310A ASN 3.8 2.6 + - - -
311A GLN 5.0 0.6 + - - -
312A ILE 3.4 4.9 + - - -
313A TYR* 1.3 79.0 - - - +
315A PHE* 1.3 58.5 + - - +
316A GLU 3.5 1.8 - - - -
317A GLY 3.4 3.7 + - - -
318A GLU* 2.8 32.7 + - - +
487A MET* 4.5 3.1 - - - -
489A TYR* 3.5 6.1 - - - +
490A ALA* 3.9 24.7 - - - +
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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