Contacts of the helix formed by residues 375 - 383 (chain E) in PDB entry 3KDO
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 ILE 375 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E LEU* 4.6 11.0 - - + -
371E HIS 3.0 21.5 - - - +
372E PRO* 3.5 18.8 + - + +
374E ASN* 1.3 81.7 - - - +
376E GLN* 1.3 59.7 + - - +
377E PRO 3.7 0.2 - - - -
378E VAL* 3.9 10.3 - - + -
379E ILE* 3.0 38.5 + - + +
388E LEU* 4.8 10.5 - - + -
390E LEU* 4.0 16.8 - - + -
408E VAL* 4.8 7.4 - - + +
411E ALA* 4.3 24.9 - - + +
412E ILE* 4.4 19.7 - - + -
415E ILE* 4.5 10.5 - - + -
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Residues in contact with GLN 376 (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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372E PRO 5.0 1.1 + - - +
373E GLY 6.2 0.4 - - - -
374E ASN* 5.2 1.1 - - - +
375E ILE* 1.3 76.4 - - - +
377E PRO* 1.3 67.9 - - + +
378E VAL 2.9 4.0 + - - -
379E ILE* 3.3 2.1 + - - +
380E GLU* 2.9 33.0 + - - +
415E ILE* 3.9 24.2 - - + +
440E HIS* 6.4 0.7 - - + +
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Residues in contact with PRO 377 (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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318E ALA* 4.8 6.8 - - - +
320E ALA* 4.5 14.8 - - + -
327E ARG* 4.9 4.3 + - - +
374E ASN* 3.9 20.4 - - + +
375E ILE 3.9 0.2 - - - -
376E GLN* 1.3 96.8 - - + +
378E VAL* 1.3 61.6 + - - +
380E GLU* 4.1 7.9 - - + +
381E ALA* 3.6 19.4 + - - +
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Residues in contact with VAL 378 (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 4.3 9.0 - - - +
318E ALA* 5.2 2.9 - - + -
320E ALA* 3.9 15.3 - - + -
366E SER* 3.5 29.4 - - - +
370E LEU* 3.9 17.5 - - + -
374E ASN 3.5 19.7 - - - +
375E ILE* 3.9 9.6 - - - +
376E GLN 2.9 1.0 - - - -
377E PRO* 1.3 76.6 - - - +
379E ILE* 1.3 61.5 + - - +
380E GLU 3.1 1.7 + - - -
381E ALA 3.4 1.0 + - - -
382E LEU* 3.0 42.6 + - + +
386E ILE* 4.1 10.5 - - + -
388E LEU* 4.3 8.5 - - + -
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Residues in contact with ILE 379 (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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156E PRO* 4.4 12.3 - - + -
375E ILE* 3.0 24.0 + - + +
376E GLN 4.2 0.7 - - - +
378E VAL* 1.3 78.4 - - + +
380E GLU* 1.3 62.8 + - - +
383E GLY* 3.0 38.2 + - - +
384E THR* 4.5 14.1 - - + -
386E ILE* 4.6 9.0 - - + -
388E LEU* 4.2 26.2 - - + -
412E ILE* 5.2 4.9 - - + -
415E ILE* 3.5 42.8 - - + -
416E MET* 6.1 1.8 - - - -
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Residues in contact with GLU 380 (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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327E ARG* 4.5 7.8 + - - +
376E GLN 2.9 20.3 + - - +
377E PRO* 4.1 8.1 - - + +
378E VAL 3.1 0.2 - - - -
379E ILE* 1.3 80.0 - - - +
381E ALA* 1.3 61.1 + - - +
383E GLY* 4.3 1.9 + - - -
415E ILE* 5.6 0.2 - - - +
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Residues in contact with ALA 381 (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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318E ALA* 4.8 2.0 - - + -
327E ARG* 3.4 45.5 - - + +
331E LEU* 3.5 25.7 - - + +
377E PRO 3.6 14.0 + - - +
378E VAL 3.4 2.1 + - - +
380E GLU* 1.3 82.6 - - - +
382E LEU* 1.3 72.2 + - + +
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Residues in contact with LEU 382 (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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315E VAL* 4.8 2.9 - - + -
316E GLY 4.5 2.0 - - - +
318E ALA* 4.5 8.1 - - + -
330E THR* 3.5 36.3 - - + -
331E LEU* 3.9 15.7 - - - +
334E VAL* 3.6 21.6 - - + +
338E ARG* 2.8 34.9 + - - -
366E SER* 4.1 16.6 - - - +
378E VAL* 3.0 31.8 + - + +
381E ALA* 1.3 89.5 - - + +
383E GLY* 1.3 59.9 + - - +
386E ILE* 3.8 19.2 - - + +
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Residues in contact with GLY 383 (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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338E ARG* 4.6 4.0 - - - -
379E ILE* 3.0 29.1 + - - +
380E GLU 4.3 1.9 + - - -
381E ALA 3.5 1.8 - - - -
382E LEU* 1.3 81.8 - - - +
384E THR* 1.3 65.5 + - - -
385E ASP 3.5 1.1 - - - -
386E ILE* 3.7 15.2 - - - +
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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