Contacts of the helix formed by residues 306 - 314 (chain A) in PDB entry 1KY5
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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279A ASP* 5.3 4.6 - - - +
281A ILE 3.0 20.5 + - - +
282A LEU* 4.2 19.0 - - + +
283A GLY 4.8 2.4 + - - -
286A PHE* 3.7 10.8 - - - -
303A VAL 4.8 2.4 + - - -
304A GLU 4.1 0.6 + - - -
305A ILE* 1.3 69.3 - - - +
307A VAL* 1.3 59.3 + - - +
308A LYS* 3.2 18.8 + - - +
309A TRP* 2.8 45.3 + - + +
310A LEU 3.7 3.5 + - - -
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASP* 4.6 2.7 - - - +
305A ILE* 2.8 25.5 + - + +
306A ASP* 1.3 71.6 - - - +
308A LYS* 1.3 75.2 + - - +
310A LEU* 3.3 9.8 + - + +
311A ASN* 2.8 42.0 + - - +
327A TYR* 4.3 7.4 - - - +
337A LEU* 3.9 22.2 - - + -
340A GLU* 3.8 27.4 - - + +
341A GLY* 4.0 13.9 - - - +
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Residues in contact with LYS 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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302A ASP* 3.4 28.7 + - - -
303A VAL* 4.1 16.0 - - - +
305A ILE 3.6 16.2 + - - -
306A ASP* 3.5 14.0 - - - +
307A VAL* 1.3 85.4 - - - +
309A TRP* 1.3 54.3 + - - +
311A ASN* 3.1 12.1 + - - +
312A GLU* 2.7 49.2 + - - +
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Residues in contact with TRP 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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283A GLY* 3.3 37.3 - - - +
286A PHE* 3.7 25.4 - + + -
287A GLU* 3.5 31.8 + - + -
306A ASP* 2.8 34.7 + - + +
308A LYS* 1.3 74.9 - - - +
310A LEU* 1.3 100.4 + - + +
312A GLU* 2.7 12.6 + - - -
313A ASN* 2.7 71.1 + - + +
329A LEU* 4.2 13.9 - - + -
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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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286A PHE* 3.3 45.8 - - + -
306A ASP 3.7 2.6 + - - +
307A VAL* 3.3 11.4 + - - +
309A TRP* 1.3 91.4 - - + +
311A ASN* 1.3 64.3 + - - +
314A ALA* 2.9 31.0 + - - +
327A TYR* 4.1 30.9 - - + -
329A LEU* 3.8 29.4 - - + -
335A ILE* 4.5 5.6 - - + -
337A LEU* 4.1 26.0 - - + -
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Residues in contact with ASN 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 VAL* 2.8 27.9 + - - +
308A LYS* 3.3 13.4 - - - +
310A LEU* 1.3 78.9 - - - +
312A GLU* 1.3 57.0 + - + +
313A ASN 3.8 0.2 + - - -
314A ALA 4.8 3.1 + - - +
317A LYS* 3.9 8.7 - - - +
327A TYR* 2.9 29.0 + - - -
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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 LYS* 2.7 35.9 + - - +
309A TRP* 2.7 11.7 + - - +
311A ASN* 1.3 73.9 - - + +
313A ASN* 1.3 80.7 + - - +
314A ALA 3.9 0.9 - - - -
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Residues in contact with ASN 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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309A TRP* 2.7 84.5 + - + +
312A GLU* 1.3 94.7 + - - +
314A ALA* 1.3 64.5 + - - +
315A VAL 3.8 0.5 + - - -
329A LEU* 5.2 0.5 - - - -
330A LYS* 3.6 36.5 + - - +
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Residues in contact with ALA 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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310A LEU* 2.9 18.3 + - - +
311A ASN 4.8 3.4 - - - +
312A GLU 5.4 0.3 - - - -
313A ASN* 1.3 78.3 + - - +
315A VAL* 1.3 66.3 + - - +
316A GLU* 3.2 5.5 + - - +
317A LYS* 5.8 0.2 - - + -
327A TYR* 3.7 31.9 - - + -
328A LEU 3.6 12.3 - - - +
329A LEU* 4.3 12.1 - - + +
330A LYS* 5.4 0.9 - - - -
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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