Contacts of the helix formed by residues 331 - 342 (chain E) in PDB entry 1KYZ
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 331 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ARG* 6.1 0.2 - - - +
104A ARG* 6.3 0.9 - - - +
299E ILE* 4.1 0.7 - - - -
300E LEU* 3.3 31.6 - - + +
301E PRO 4.3 4.5 - - - +
302E VAL* 4.3 24.7 - - + -
330E ARG* 1.3 77.6 - - - +
332E GLN* 1.3 65.0 + - - +
333E LYS* 3.8 7.5 + - - +
334E GLU* 2.6 42.9 + - - +
335E PHE* 3.2 23.6 + - - -
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Residues in contact with GLN 332 (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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299E ILE* 3.7 24.3 - - + +
300E LEU 4.3 1.0 + - - -
331E THR* 1.3 74.9 - - - +
333E LYS* 1.3 57.3 + - - +
335E PHE* 3.3 8.7 + - - +
336E GLU* 3.0 33.4 + - - +
347E PHE* 3.9 21.2 - - + -
349E VAL* 3.7 28.8 - - + +
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Residues in contact with LYS 333 (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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100A GLY 4.3 15.0 + - - -
102A VAL* 6.3 0.4 - - - +
331E THR* 3.2 7.5 - - - +
332E GLN* 1.3 80.2 - - - +
334E GLU* 1.3 58.1 + - + +
336E GLU* 3.3 9.6 + - + +
337E ASP* 2.9 49.9 + - - +
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Residues in contact with GLU 334 (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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273E ASP* 5.9 1.1 - - - +
300E LEU* 5.1 1.4 - - - +
328E LYS* 4.2 17.2 + - - +
329E GLU 4.2 1.8 - - - +
330E ARG* 3.1 26.9 - - + +
331E THR* 2.6 51.0 + - - +
333E LYS* 1.3 78.3 - - + +
335E PHE* 1.3 57.6 + - - +
337E ASP* 3.3 9.3 + - - +
338E LEU* 3.0 30.9 + - - +
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Residues in contact with PHE 335 (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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268E CYS* 4.3 14.6 - - + -
269E HIS* 5.8 2.7 - - + -
295E VAL* 4.5 3.1 - - + -
297E GLU* 3.6 31.2 - - + -
298E CYS 3.6 14.1 - - - -
299E ILE* 4.3 4.5 - - + -
329E GLU* 5.9 0.7 - - - -
330E ARG* 3.6 41.7 - - + -
331E THR 3.2 24.2 + - - -
332E GLN* 3.6 7.2 - - - +
334E GLU* 1.3 73.0 - - - +
336E GLU* 1.3 61.4 + - - +
338E LEU* 3.0 15.2 + - + +
339E ALA* 2.9 23.9 + - - +
347E PHE* 4.1 5.2 - - + -
359E MET* 3.7 37.9 - - + -
361E PHE* 3.6 19.9 - + + -
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Residues in contact with GLU 336 (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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332E GLN* 3.0 19.8 + - - +
333E LYS* 3.6 13.1 - - + +
334E GLU 3.2 0.2 - - - -
335E PHE* 1.3 77.9 - - - +
337E ASP* 1.3 60.7 - - - +
339E ALA* 3.3 1.7 + - - +
340E LYS* 2.9 45.2 + - + +
347E PHE* 3.7 45.8 - - + -
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Residues in contact with ASP 337 (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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277E LEU* 5.0 0.3 - - - +
333E LYS* 2.9 42.0 + - - +
334E GLU* 3.7 7.4 - - - +
335E PHE 3.2 0.2 - - - -
336E GLU* 1.3 81.7 - - - +
338E LEU* 1.3 58.6 + - - +
340E LYS* 3.9 9.2 - - - +
341E GLY* 2.9 24.6 + - - -
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Residues in contact with LEU 338 (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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268E CYS* 5.0 3.4 - - - -
273E ASP* 4.2 24.2 - - + +
276E CYS* 4.1 26.9 - - + -
277E LEU* 3.7 18.4 - - + +
280E LEU* 4.2 15.1 - - + +
330E ARG* 3.6 36.1 - - - +
334E GLU 3.0 14.8 + - - +
335E PHE* 3.0 21.1 + - + +
337E ASP* 1.3 76.5 - - - +
339E ALA* 1.3 65.9 + - - +
341E GLY 3.3 0.5 + - - -
342E ALA* 3.0 25.8 + - - +
361E PHE* 4.6 2.7 - - + -
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Residues in contact with ALA 339 (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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335E PHE 2.9 12.1 + - - +
336E GLU 3.5 8.1 - - - +
338E LEU* 1.3 77.0 - - - +
340E LYS* 1.3 64.1 + - + +
342E ALA 3.2 6.9 + - - -
343E GLY 3.3 0.2 + - - -
344E PHE* 3.1 33.8 + - + +
346E GLY 4.6 5.8 - - - +
347E PHE* 4.2 11.2 - - + -
361E PHE* 3.7 41.2 - - + -
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Residues in contact with LYS 340 (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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336E GLU* 2.9 33.8 + - + +
337E ASP* 3.9 9.9 - - - +
339E ALA* 1.3 77.1 - - + +
341E GLY* 1.3 57.6 + - - +
343E GLY* 2.9 21.3 + - - -
344E PHE 4.0 16.0 + - - +
345E GLN* 4.9 9.2 - - - +
346E GLY* 6.3 1.1 - - - -
347E PHE* 6.3 1.3 - - + -
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Residues in contact with GLY 341 (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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277E LEU* 3.4 16.1 - - - +
281E LYS* 2.9 21.3 + - - -
337E ASP 2.9 19.1 + - - -
338E LEU 3.3 1.1 + - - -
340E LYS* 1.3 77.4 - - - +
342E ALA* 1.3 58.0 + - - +
343E GLY 3.2 1.0 + - - -
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Residues in contact with ALA 342 (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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277E LEU* 3.6 4.5 - - + +
280E LEU* 3.8 27.8 - - + -
281E LYS* 4.1 17.9 - - + +
284E TYR* 4.0 20.6 - - - +
338E LEU 3.0 16.7 + - - +
339E ALA 3.7 1.6 - - - +
340E LYS 3.1 0.4 - - - -
341E GLY* 1.3 76.5 - - - +
343E GLY* 1.3 58.7 + - - +
344E PHE* 3.5 23.7 + - + -
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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