Contacts of the helix formed by residues 247 - 259 (chain E) in PDB entry 4KZZ
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 247 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246E LEU* 1.3 71.9 - - - +
248E ILE* 1.3 53.2 + - - +
249E ALA* 2.9 8.4 + - - +
250E GLU* 2.7 42.8 + - - +
251E GLU 2.6 32.6 + - - -
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Residues in contact with ILE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E LEU 3.5 1.4 + - - +
247E THR* 1.3 72.6 - - - +
249E ALA* 1.3 61.4 + - + +
251E GLU* 3.7 22.3 - - - +
252E ARG* 3.1 24.4 + - - +
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Residues in contact with ALA 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E THR* 2.8 8.1 + - - +
248E ILE* 1.3 81.4 - - + +
250E GLU* 1.3 65.8 + - + +
251E GLU 3.1 1.3 - - - -
252E ARG* 3.0 28.1 + - - +
253E ASP* 2.8 32.5 + - - +
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Residues in contact with GLU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E ARG 4.7 0.9 - - - +
246E LEU* 3.4 18.1 - - + +
247E THR* 2.7 46.1 + - - +
249E ALA* 1.3 75.6 - - + +
251E GLU* 1.3 61.2 + - - +
253E ASP* 3.0 19.8 + - - +
254E LYS* 2.9 40.6 + - - +
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Residues in contact with GLU 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LYS* 3.8 22.6 + - - -
246E LEU* 4.5 22.1 - - + +
247E THR 2.6 18.8 + - - +
248E ILE* 3.7 23.6 - - - +
250E GLU* 1.3 73.7 - - - +
252E ARG* 1.3 61.9 + - - +
254E LYS* 3.6 8.5 + - - +
255E ARG* 3.2 46.4 + - - +
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Residues in contact with ARG 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E ILE 3.1 15.2 + - - +
249E ALA* 3.0 33.5 + - - +
251E GLU* 1.3 75.8 - - - +
253E ASP* 1.3 94.7 + - - +
255E ARG* 3.2 15.7 + - + +
256E LEU* 3.2 36.3 + - + +
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Residues in contact with ASP 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E ALA* 2.8 21.6 + - - +
250E GLU* 3.0 14.5 + - - +
252E ARG* 1.3 106.4 + - - +
254E LYS* 1.3 65.4 + - + +
256E LEU* 3.9 10.5 - - - +
257E ALA* 3.1 28.9 + - - +
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Residues in contact with LYS 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E LEU* 4.4 23.3 - - + -
250E GLU* 2.9 37.7 + - - +
251E GLU* 3.8 7.6 - - - +
253E ASP* 1.3 79.6 - - - +
255E ARG* 1.3 60.0 + - - +
257E ALA* 4.6 2.5 - - - -
258E ALA* 3.0 35.3 + - - +
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Residues in contact with ARG 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E GLU* 3.2 48.4 + - - +
252E ARG* 3.2 8.2 + - - +
254E LYS* 1.3 77.0 - - - +
256E LEU* 1.3 59.9 + - - +
258E ALA* 4.5 1.3 - - - +
259E LYS* 3.5 16.5 + - - +
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Residues in contact with LEU 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E ARG* 3.2 39.6 + - + +
253E ASP* 3.9 11.4 - - - +
255E ARG* 1.3 77.6 - - - +
257E ALA* 1.3 87.5 + - + +
259E LYS* 3.4 17.7 + - - +
260E GLN* 4.9 3.7 - - - +
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E ASP 3.1 20.5 + - - +
254E LYS* 4.1 2.9 - - - +
256E LEU* 1.3 88.6 - - + +
258E ALA* 1.3 54.2 - - - +
259E LYS 3.2 0.6 + - - -
261E SER* 5.6 0.9 - - - -
262E SER* 2.2 32.1 + - - -
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Residues in contact with ALA 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E LYS* 3.0 18.8 + - + +
255E ARG* 4.8 1.6 - - - +
257E ALA* 1.3 73.7 - - - +
259E LYS* 1.3 71.1 + - + +
262E SER* 2.4 29.0 + - - +
263E GLY 4.3 2.1 - - - +
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Residues in contact with LYS 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E ARG 3.5 13.5 + - - +
256E LEU* 3.4 12.6 + - - +
257E ALA 3.2 3.8 - - - -
258E ALA* 1.3 90.7 - - + +
260E GLN* 1.3 132.4 + - - +
261E SER 4.1 1.6 - - - +
262E SER* 3.9 7.2 - - - +
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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