Contacts of the helix formed by residues 358 - 366 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B HIS* 3.5 2.9 - - - -
349B GLU 3.5 13.2 - - - -
350B ALA* 4.8 1.8 - - - -
351B LEU 4.0 1.1 - - - -
352B LEU* 3.6 18.6 - - - +
357B LEU* 1.3 75.3 - - - +
359B PRO* 1.4 71.0 - - - +
360B LEU* 3.8 7.5 + - - +
361B MET* 3.3 29.9 + - - +
362B MET* 2.9 27.9 + - - +
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Residues in contact with PRO 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 4.8 0.9 - - - +
311B LEU* 3.7 24.9 - - + +
312B HIS* 3.5 27.1 - - + +
315B VAL* 3.7 15.3 - - + +
332B TYR* 3.5 29.4 - - + +
348B LEU 4.9 0.9 - - - +
349B GLU* 3.4 24.7 - - - +
351B LEU 3.8 4.3 - - - +
358B SER* 1.4 79.8 - - - +
360B LEU* 1.3 59.1 + - - +
362B MET* 3.3 1.9 + - + +
363B ALA* 2.9 31.7 + - - +
375B ILE* 4.6 0.9 - - - -
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B TYR* 4.5 1.2 + - - +
349B GLU* 5.4 1.8 + - - +
358B SER* 3.4 8.2 + - - +
359B PRO* 1.3 80.6 - - - +
361B MET* 1.3 77.5 + - + +
363B ALA* 3.3 3.9 + - - +
364B ALA* 3.0 22.7 + - - +
372B PHE* 3.4 55.7 - - + +
375B ILE* 3.8 27.4 - - + +
376B ILE* 3.7 16.6 - - + -
379B GLU* 3.6 29.2 - - - +
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Residues in contact with MET 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B LEU* 4.1 20.6 - - + +
358B SER* 3.3 23.4 + - - +
360B LEU* 1.3 101.3 - - + +
362B MET* 1.3 61.8 + - - +
364B ALA* 3.6 11.4 - - - +
365B LYS* 3.0 27.9 + - - +
372B PHE* 5.6 3.1 - - + -
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Residues in contact with MET 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B ARG* 6.4 0.4 - - - +
308B ASN* 4.5 10.5 - - - +
312B HIS* 3.4 50.0 - - - +
315B VAL* 4.2 8.3 - - + -
316B ALA* 3.8 24.7 - - + +
353B ASN* 4.0 10.1 - - - +
357B LEU* 4.0 25.7 - - + +
358B SER 2.9 16.4 + - - +
359B PRO 3.7 2.9 - - - +
361B MET* 1.3 75.6 - - - +
363B ALA* 1.3 54.5 + - - +
365B LYS* 3.2 0.8 + - - -
366B THR* 2.7 52.0 + - + +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B VAL* 3.5 21.6 - - + +
359B PRO 2.9 13.6 + - - +
360B LEU* 3.3 11.9 - - - +
362B MET* 1.3 76.7 - - - +
364B ALA* 1.3 61.5 + - - +
366B THR* 3.8 1.7 - - - -
367B GLY* 3.1 3.6 + - - -
368B LYS* 2.9 29.9 + - - +
371B ILE* 4.0 15.0 - - + -
372B PHE* 4.0 21.5 - - + -
375B ILE* 4.9 1.1 - - + -
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B LEU 3.0 9.2 + - - +
361B MET* 3.6 17.0 - - - +
362B MET 3.3 0.2 - - - -
363B ALA* 1.3 76.9 - - - +
365B LYS* 1.3 63.2 + - - +
367B GLY* 3.4 9.2 + - - -
372B PHE* 3.7 30.2 - - + -
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASP* 4.8 11.1 + - - +
357B LEU* 4.1 28.3 - - + +
361B MET 3.0 18.0 + - - +
362B MET* 3.8 4.5 - - - +
364B ALA* 1.3 76.5 - - - +
366B THR* 1.3 67.3 + - + +
367B GLY 3.3 0.6 + - - -
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Residues in contact with THR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B VAL* 4.2 4.3 - - - +
357B LEU* 6.2 0.2 - - + -
362B MET* 2.7 41.1 + - + +
363B ALA* 3.9 0.2 - - - -
365B LYS* 1.3 86.9 - - + +
367B GLY* 1.3 61.1 + - - +
368B LYS* 3.5 36.7 + - - +
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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