Contacts of the helix formed by residues 358 - 367 (chain C) in PDB entry 3JXI
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 358 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312C HIS* 3.3 4.0 - - - -
349C GLU* 3.5 14.6 - - - -
352C LEU* 3.9 14.9 - - - +
356C GLY 4.0 1.4 + - - -
357C LEU* 1.3 74.0 - - - +
359C PRO* 1.3 81.6 - - - +
360C LEU* 3.7 8.1 + - - +
361C MET* 3.3 30.7 + - - +
362C MET* 3.0 17.5 + - - +
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Residues in contact with PRO 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C THR* 4.7 1.1 - - - +
311C LEU* 3.5 34.3 - - + +
312C HIS* 3.4 24.7 - - + +
315C VAL* 3.6 25.1 - - + +
332C TYR* 3.4 20.6 - - + +
348C LEU 5.0 0.4 - - - +
349C GLU* 3.6 19.7 - - + +
351C LEU 4.5 1.6 - - - +
358C SER* 1.3 89.6 - - - +
360C LEU* 1.3 50.6 + - - +
362C MET* 3.1 3.7 + - + +
363C ALA 2.9 29.8 + - - -
375C ILE* 4.6 0.2 - - - -
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Residues in contact with LEU 360 (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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332C TYR* 4.6 0.4 + - - -
358C SER* 3.2 7.1 + - - +
359C PRO* 1.3 79.7 - - - +
361C MET* 1.3 80.5 + - + +
363C ALA* 3.2 2.4 + - - +
364C ALA 3.0 22.9 + - - -
372C PHE* 3.3 54.2 - - + +
375C ILE* 3.6 39.3 - - + +
376C ILE* 3.8 21.3 - - + -
379C GLU* 5.8 5.4 - - + +
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Residues in contact with MET 361 (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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357C LEU* 4.3 18.2 - - + +
358C SER* 3.3 27.1 + - - +
360C LEU* 1.3 116.6 - - + +
362C MET* 1.3 59.4 + - - +
363C ALA 3.3 0.2 - - - -
364C ALA* 3.8 7.0 - - + +
365C LYS* 3.0 28.4 + - - +
372C PHE* 4.4 9.2 - - + -
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Residues in contact with MET 362 (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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306C ARG* 6.2 1.6 - - - +
308C ASN* 3.7 14.1 - - - +
312C HIS* 3.7 37.2 - - - +
315C VAL* 3.8 12.1 - - + -
316C ALA* 4.8 6.7 - - + -
353C ASN* 3.1 26.5 - - - +
355C ASP* 5.5 3.8 - - - +
357C LEU* 4.0 23.5 - - + +
358C SER 3.0 13.2 + - - +
359C PRO 3.4 7.4 - - - +
361C MET* 1.3 73.5 - - - +
363C ALA* 1.3 58.2 + - - +
365C LYS* 4.4 1.3 - - - -
366C THR* 2.5 47.8 + - + +
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Residues in contact with ALA 363 (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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315C VAL* 3.4 23.9 - - + +
359C PRO 2.9 10.0 + - - +
360C LEU* 3.5 11.2 - - - +
362C MET* 1.3 76.2 - - - +
364C ALA* 1.3 56.1 + - - +
366C THR* 3.9 1.1 - - - -
367C GLY* 2.9 10.4 + - - -
368C LYS* 2.8 46.1 + - - +
371C ILE* 3.8 11.4 - - + -
372C PHE* 3.8 10.5 - - + -
375C ILE* 5.1 0.7 - - + -
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Residues in contact with ALA 364 (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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360C LEU 3.0 10.4 + - - +
361C MET* 3.8 12.8 - - + +
362C MET 3.4 0.2 - - - -
363C ALA* 1.3 75.5 - - - +
365C LYS* 1.3 62.4 + - - +
367C GLY* 3.4 11.3 + - - -
369C ILE* 5.6 5.4 - - - +
372C PHE* 3.5 33.3 - - + -
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Residues in contact with LYS 365 (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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355C ASP* 5.6 6.7 + - - +
357C LEU* 3.9 28.9 - - + +
361C MET 3.0 19.6 + - - +
362C MET* 3.8 5.8 - - - +
363C ALA 3.3 0.2 - - - -
364C ALA* 1.3 76.8 - - - +
366C THR* 1.3 66.3 + - + +
367C GLY 3.7 0.2 + - - -
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Residues in contact with THR 366 (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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315C VAL* 4.3 2.9 - - - +
362C MET* 2.5 34.2 + - + +
365C LYS* 1.3 82.9 - - + +
367C GLY* 1.3 60.1 + - - +
368C LYS* 3.5 35.8 + - - +
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Residues in contact with GLY 367 (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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320C ASN* 3.2 14.7 - - - +
363C ALA 2.9 5.8 + - - -
364C ALA 3.4 10.2 + - - -
365C LYS 3.4 0.8 + - - -
366C THR* 1.3 79.0 - - - +
368C LYS* 1.3 61.0 + - - +
369C ILE* 3.0 25.4 + - - +
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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