Contacts of the helix formed by residues 352 - 359 (chain C) in PDB entry 4UEL
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 LEU 352 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A PHE* 3.6 32.5 - - + -
151A PHE* 3.7 10.5 - - + -
292A LEU* 5.4 0.7 - - + -
296A MET* 5.7 0.4 - - + -
343C PHE* 3.6 42.8 - - + +
346C ALA* 3.6 9.4 + - + -
347C LEU* 3.6 33.0 - - + +
350C GLY* 3.6 1.2 - - - -
351C GLN* 1.3 76.9 - - - +
353C GLY* 1.3 66.1 + - - +
354C PRO* 3.4 2.5 - - - -
355C LEU* 3.2 19.1 + - + +
356C MET* 2.8 40.6 + - + +
369C ALA* 5.2 1.2 + - + -
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Residues in contact with GLY 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C GLY 5.1 0.2 - - - -
351C GLN 3.4 1.0 - - - -
352C LEU* 1.3 76.8 - - - +
354C PRO* 1.3 65.7 - - - +
356C MET* 3.3 5.9 + - - +
357C CYS* 2.9 32.9 + - - +
366C VAL* 3.8 19.2 - - - +
369C ALA* 4.8 2.4 - - - +
370C ASN* 3.2 24.2 + - - -
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Residues in contact with PRO 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C GLN 4.1 10.8 - - - +
352C LEU 3.7 2.0 - - - -
353C GLY* 1.3 88.5 - - - +
355C LEU* 1.3 58.2 + - + +
357C CYS* 3.2 9.2 + - + +
358C GLN* 2.9 45.3 + - - +
370C ASN* 4.7 2.5 - - - +
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Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A MET 3.6 24.0 - - - +
149A PHE* 4.1 22.0 - - + -
150A GLU 5.6 0.4 - - - +
151A PHE* 4.9 6.1 - - + -
292A LEU* 3.9 13.5 - - + -
296A MET* 4.3 8.3 - - + -
351C GLN 5.5 0.2 + - - -
352C LEU* 3.2 20.2 + - + +
354C PRO* 1.3 79.9 - - + +
356C MET* 1.3 59.1 + - - +
358C GLN* 3.1 22.0 + - - +
359C PHE* 2.9 53.6 + - + -
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Residues in contact with MET 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A MET* 3.4 26.5 - - + -
343C PHE* 5.4 2.5 - - + -
347C LEU* 4.0 9.6 - - + -
352C LEU* 2.8 33.9 + - + +
353C GLY 3.7 3.1 - - - +
355C LEU* 1.3 73.3 - - - +
357C CYS* 1.3 66.7 + - - +
359C PHE* 3.1 8.6 + - - +
360C GLY 3.2 0.2 + - - -
361C LEU* 3.0 41.8 + - + +
365C ALA 4.2 3.4 - - - +
366C VAL* 4.3 5.6 - - + -
369C ALA* 3.4 28.7 - - + -
377C PHE* 2.9 48.0 - - + -
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Residues in contact with CYS 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C GLY 2.9 17.8 + - - +
354C PRO* 3.4 11.9 - - + +
356C MET* 1.3 74.5 - - - +
358C GLN* 1.3 58.7 + - + +
360C GLY* 3.0 19.9 + - - -
361C LEU 4.6 4.9 - - - +
366C VAL* 3.6 31.3 - - - +
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Residues in contact with GLN 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C PRO* 2.9 36.3 + - - +
355C LEU* 3.1 26.2 + - + +
357C CYS* 1.3 79.2 - - + +
359C PHE* 1.3 62.7 + - + +
360C GLY 3.2 2.9 + - - -
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Residues in contact with PHE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 3.7 30.3 - - + -
293A PRO* 4.0 31.6 - - + -
296A MET* 3.7 31.0 - - + -
300A LYS* 2.9 36.1 + - - +
313C TYR* 6.4 0.4 - + - -
355C LEU* 2.9 38.0 + - + +
356C MET 3.1 4.2 + - - +
358C GLN* 1.3 80.3 - - + +
360C GLY* 1.3 58.4 + - - +
361C LEU* 3.3 9.5 + - + +
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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