Contacts of the helix formed by residues 315 - 321 (chain E) in PDB entry 3KC3
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 315 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246E MET* 4.1 4.7 - - - -
313E ARG 4.6 4.5 - - - +
314E MET* 1.3 76.8 - - - +
316E ILE* 1.4 58.7 + - - +
317E THR* 3.9 8.3 + - - -
318E GLU* 3.1 34.4 + - - +
319E PHE* 2.7 33.6 + - - +
281J MET* 4.6 6.5 + - - -
308J THR* 4.5 19.2 - - + +
309J GLU* 5.9 2.9 - - + -
312J GLN* 4.8 9.9 - - - +
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Residues in contact with ILE 316 (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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171E GLY* 4.0 7.9 - - - +
174E ILE* 3.6 27.1 - - + -
175E GLN* 3.9 22.7 - - + +
178E HIS* 2.7 47.8 - - + +
242E LYS* 5.3 1.1 - - + -
246E MET* 3.3 23.8 - - + -
249E LEU* 4.8 1.6 - - + -
315E THR* 1.4 68.1 - - - +
317E THR* 1.3 61.4 + - - +
319E PHE* 3.9 13.0 - - + -
320E MET* 2.7 44.7 + - + +
281J MET* 5.0 9.0 - - + -
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Residues in contact with THR 317 (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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175E GLN* 4.7 13.4 + - - +
315E THR* 3.3 4.2 + - - -
316E ILE* 1.3 80.1 - - - +
318E GLU* 1.3 65.9 + - - +
320E MET* 3.3 3.2 + - - +
321E ASN* 3.0 39.2 + - - +
281J MET* 2.8 41.4 + - - +
282J GLY 3.9 15.0 - - - +
283J GLN* 3.7 27.2 - - + +
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Residues in contact with GLU 318 (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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313E ARG 4.5 0.7 - - - +
314E MET* 3.3 32.8 - - + +
315E THR* 3.1 37.8 + - - +
317E THR* 1.3 80.1 - - - +
319E PHE* 1.3 63.9 + - - +
321E ASN* 3.0 18.6 + - - +
322E HIS* 3.4 7.6 + - - +
307J LYS* 3.0 35.7 + - - +
308J THR 5.9 0.3 + - - -
312J GLN* 4.7 3.5 + - - +
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Residues in contact with PHE 319 (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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167E MET* 4.0 12.6 - - + -
171E GLY* 4.1 0.7 - - - -
246E MET* 5.0 0.4 - - - -
249E LEU* 3.5 33.4 - - + -
253E MET* 3.2 31.2 - - + -
301E LEU* 4.0 7.9 - - + -
305E LEU* 3.6 21.3 - - + -
314E MET* 3.7 16.5 - - + +
315E THR 2.7 18.6 + - - +
316E ILE* 2.9 13.2 + - + +
318E GLU* 1.3 72.0 - - - +
320E MET* 1.3 99.7 + - + +
322E HIS* 3.2 19.1 + - - +
325E ILE* 3.4 32.6 - - + +
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Residues in contact with MET 320 (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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167E MET 4.1 0.7 - - - +
168E LYS* 3.9 14.2 + - - +
171E GLY* 3.1 30.5 - - - +
172E GLU* 4.2 9.6 - - - +
175E GLN* 3.8 24.0 - - - +
316E ILE* 2.7 29.7 + - + +
317E THR* 3.8 4.9 - - - +
319E PHE* 1.3 107.5 - - + +
321E ASN* 1.3 57.5 + - - +
322E HIS 3.1 5.2 + - - -
325E ILE* 3.5 26.5 - - + +
326E MET* 3.1 21.5 - - - +
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Residues in contact with ASN 321 (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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317E THR* 3.0 37.9 + - - +
318E GLU* 3.0 10.2 + - - +
320E MET* 1.3 76.8 - - - +
322E HIS* 1.3 63.7 + - - +
323E PRO* 3.5 5.2 - - - +
326E MET* 3.5 29.3 - - - +
284J TYR 5.5 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