Contacts of the helix formed by residues 318 - 326 (chain E) in PDB entry 6UWZ
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 SER 318 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316E SER* 3.7 9.7 + - - -
317E LEU* 1.3 80.7 - - - +
319E GLU* 1.3 65.9 + - - +
320E LYS* 4.0 8.7 - - - -
321E ILE* 3.4 21.7 + - - +
322E LYS* 3.4 25.8 + - - +
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Residues in contact with GLU 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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317E LEU 4.3 0.2 + - - -
318E SER* 1.3 74.1 - - - +
320E LYS* 1.3 60.3 + - + +
322E LYS* 3.4 19.9 + - - +
323E HIS* 2.9 56.2 + - + +
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Residues in contact with LYS 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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318E SER* 3.2 7.4 - - - -
319E GLU* 1.3 80.5 - - + +
321E ILE* 1.3 59.7 + - + +
323E HIS* 3.3 8.4 + - - +
324E LEU* 2.9 31.3 + - + +
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Residues in contact with ILE 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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328A THR* 5.5 7.9 - - + -
511A POV 5.9 2.5 - - - -
316E SER 4.6 5.4 - - - +
317E LEU* 4.1 11.7 - - + -
318E SER* 3.4 33.6 + - - +
319E GLU 3.3 0.6 - - - -
320E LYS* 1.3 79.7 - - + +
322E LYS* 1.3 63.9 + - - +
324E LEU* 3.0 5.8 + - - -
325E PHE* 3.0 40.6 + - + +
440E TRP* 4.6 1.6 - - + -
443E ILE* 4.4 6.1 - - + -
451E P1L 3.2 48.0 - - + -
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Residues in contact with LYS 322 (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 LEU* 3.6 37.8 - - + +
318E SER 3.4 12.8 + - - +
319E GLU* 3.8 21.7 + - - +
321E ILE* 1.3 76.4 - - - +
323E HIS* 1.3 63.5 + - + +
326E LEU* 2.7 63.6 + - + +
327E GLY 3.3 0.9 + - - -
436E GLU* 6.0 0.4 + - - -
439E ASN* 4.2 17.6 + - - +
443E ILE* 4.4 4.0 - - + -
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Residues in contact with HIS 323 (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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319E GLU* 2.9 41.3 + - + +
320E LYS* 3.8 7.3 - - - +
322E LYS* 1.3 83.3 - - + +
324E LEU* 1.3 57.9 + - - +
327E GLY* 3.9 8.0 + - - +
328E PHE* 3.3 26.2 + - - +
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Residues in contact with LEU 324 (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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320E LYS* 2.9 17.6 + - + +
321E ILE* 3.0 7.8 + - - +
323E HIS* 1.3 79.7 - - - +
325E PHE* 1.3 84.3 + - + +
328E PHE* 3.1 39.5 - - + -
329E LEU* 3.5 8.7 + - + +
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Residues in contact with PHE 325 (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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321E ILE* 3.0 37.7 + - + +
324E LEU* 1.3 101.7 - - + +
326E LEU* 1.3 61.2 + - - +
327E GLY 3.2 1.6 - - - -
328E PHE 4.3 0.2 - - - -
329E LEU* 4.0 26.3 - - + +
330E PRO* 3.1 28.9 - - - +
443E ILE* 4.2 25.1 - - + -
446E VAL* 4.1 14.9 - - + +
447E ILE* 3.5 35.9 - - + -
451E P1L 3.9 31.4 - - + -
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Residues in contact with LEU 326 (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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322E LYS* 2.7 49.3 + - + +
325E PHE* 1.3 72.4 - - - +
327E GLY* 1.3 54.3 + - - -
330E PRO* 4.5 10.0 - - - +
439E ASN* 4.3 20.0 - - + +
442E LEU* 4.0 20.2 - - + +
443E ILE* 3.9 39.7 - - + +
446E VAL* 4.8 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