Contacts of the helix formed by residues 306 - 314 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ARG* 3.6 18.4 - - - +
302B GLY 4.2 2.5 - - - +
303B ASN* 2.8 30.0 + - - +
304B HIS 3.1 1.8 + - - -
305B GLU* 1.3 83.1 - - - +
307B ASP* 1.3 61.9 + - - +
308B ASN* 4.4 4.6 + - - +
309B MET* 3.5 14.4 + - - +
310B ASN* 3.0 34.2 + - - -
335B PHE* 5.2 1.6 - - - -
374B GLN* 3.6 10.5 - - - +
375B PRO* 3.6 24.9 - - + -
385B LEU* 4.6 1.3 - - + -
386B TRP* 5.7 1.0 - - - +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B THR* 1.3 69.2 - - - +
308B ASN* 1.3 61.5 + - - +
310B ASN* 3.0 1.4 + - - -
311B GLN* 2.6 54.7 + - - +
328B TYR* 3.5 10.3 + - - -
329B GLU* 5.7 1.1 - - - +
332B SER* 2.7 35.4 + - - -
335B PHE* 6.1 0.2 - - - -
336B GLU* 5.2 0.3 - - - +
374B GLN* 2.8 31.1 + - + +
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Residues in contact with ASN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B THR* 4.4 5.6 + - - +
307B ASP* 1.3 79.0 - - - +
309B MET* 1.3 77.7 + - + +
311B GLN* 3.5 13.1 + - - +
312B ILE* 3.5 21.4 + - + +
374B GLN* 4.6 1.0 + - - -
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP* 3.2 16.6 - - - +
303B ASN 3.3 25.4 - - - +
304B HIS* 3.9 16.4 - - - +
306B THR* 3.5 11.7 + - - +
307B ASP 3.2 0.8 - - - -
308B ASN* 1.3 91.0 - - + +
310B ASN* 1.3 61.4 - - - +
312B ILE* 3.2 10.2 + - + -
313B TYR* 2.9 55.0 + - + +
386B TRP* 3.7 34.3 - - + -
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Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B VAL* 3.8 7.9 - - - +
274B ASP* 3.3 17.8 + - - -
304B HIS 2.8 26.5 + - - -
306B THR 3.0 20.8 + - - +
307B ASP* 3.0 1.2 + - - +
309B MET* 1.3 75.9 - - - +
311B GLN* 1.3 61.2 + - - +
312B ILE 3.4 0.2 + - - -
314B GLY 3.6 4.3 + - - -
315B PHE* 3.5 26.0 + - - +
316B GLU* 3.2 22.6 + - - +
317B GLY 4.7 0.2 + - - -
328B TYR* 2.8 37.0 + - + +
332B SER* 5.7 0.3 - - - -
335B PHE* 3.7 14.4 - - - -
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ASP* 2.6 56.8 + - + +
308B ASN* 3.8 9.9 - - - +
310B ASN* 1.3 77.7 - - - +
312B ILE* 1.3 62.4 + - + +
314B GLY 4.9 0.9 + - - -
316B GLU* 2.4 47.4 - - - +
328B TYR* 3.4 21.6 + - - -
490B ALA* 5.7 2.8 - - - +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ASN* 3.5 16.6 - - + +
309B MET* 3.2 11.7 + - + +
311B GLN* 1.3 82.1 - - + +
313B TYR* 1.3 97.6 - - + +
314B GLY 3.5 1.8 + - - -
487B MET* 5.1 0.9 - - - +
490B ALA* 3.6 16.7 - - - +
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP* 3.4 27.0 - - + -
275B ARG* 2.8 66.4 + - + +
304B HIS* 3.7 14.6 - + - -
309B MET* 2.9 39.0 + - + +
311B GLN 3.7 0.2 - - - -
312B ILE* 1.3 103.8 - - + +
314B GLY* 1.3 57.4 + - - +
487B MET* 3.7 20.8 - - - +
490B ALA* 4.5 0.2 - - - -
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASP* 5.1 0.7 - - - -
275B ARG 5.0 0.9 - - - -
276B GLY 6.2 0.2 - - - -
279B SER* 5.9 0.4 - - - -
310B ASN 3.6 3.0 + - - -
311B GLN 4.9 0.8 + - - -
312B ILE 3.5 4.4 + - - -
313B TYR* 1.3 79.0 - - - +
315B PHE* 1.3 52.5 + - - +
316B GLU 3.5 2.2 - - - -
317B GLY* 3.3 7.2 + - - -
318B GLU* 2.8 35.6 + - - +
487B MET* 5.4 3.6 - - - -
489B TYR* 3.7 6.7 - - - +
490B ALA* 4.1 22.4 - - - +
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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