Contacts of the helix formed by residues 355 - 367 (chain B) in PDB entry 2JGE
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 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ILE* 1.3 77.2 - - - +
356B ARG* 1.3 63.5 + - - +
357B ALA* 3.2 10.5 + - - +
358B GLN* 2.7 38.4 + - - +
359B PHE* 3.1 21.5 + - - +
389B GLU 5.8 1.1 - - - -
394B LEU* 3.7 4.8 - - - +
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Residues in contact with ARG 356 (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 SER* 1.3 73.4 - - - +
357B ALA* 1.3 63.7 + - - +
359B PHE* 3.0 18.5 + - - +
360B LEU* 3.1 29.2 + - + +
379B VAL* 3.5 17.6 - - - +
380B LEU* 4.4 3.8 - - - +
383B THR* 2.8 41.5 + - - +
385B TRP* 3.7 22.6 - - - -
388B PRO* 3.6 18.6 + - - +
389B GLU* 3.9 30.4 + - + +
394B LEU* 3.5 27.8 - - + +
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Residues in contact with ALA 357 (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 SER* 3.2 7.8 + - - +
356B ARG* 1.3 78.0 - - - +
358B GLN* 1.3 63.8 + - + +
360B LEU* 3.4 11.0 + - - +
361B ALA* 3.2 22.3 + - - +
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Residues in contact with GLN 358 (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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343B VAL* 5.1 1.6 - - - +
344B PRO* 4.2 18.7 - - + +
345B GLY* 3.5 29.3 - - - +
346B PHE* 5.7 0.7 - - - -
353B LEU 4.7 1.4 + - - +
354B ILE* 3.5 18.8 - - + +
355B SER* 2.7 46.0 + - - +
356B ARG 3.2 0.2 - - - -
357B ALA* 1.3 78.2 - - + +
359B PHE* 1.3 52.5 + - - +
361B ALA* 3.5 5.9 + - - +
362B GLY* 2.8 30.8 + - - -
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Residues in contact with PHE 359 (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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354B ILE* 3.8 12.3 - - + +
355B SER 3.1 11.9 + - - +
356B ARG* 3.0 9.9 + - - +
358B GLN* 1.3 76.6 - - - +
360B LEU* 1.3 77.1 + - + +
361B ALA 3.2 0.2 - - - -
362B GLY* 3.3 1.9 + - - +
363B VAL* 3.1 49.1 + - + +
379B VAL* 3.9 25.6 - - + -
382B TYR* 4.1 16.2 - - + -
383B THR* 4.1 11.2 - - - -
394B LEU* 3.6 36.3 - - + -
397B ALA* 3.9 16.4 - - + -
398B MET* 3.8 32.5 - - + -
401B VAL* 4.5 2.2 - - + -
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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
----------------------------------------------------------
356B ARG* 3.1 43.6 + - + +
357B ALA* 4.0 8.5 - - - +
359B PHE* 1.3 80.3 - - + +
361B ALA* 1.3 61.3 + - - +
363B VAL* 3.5 4.2 + - - +
364B ARG* 3.5 26.8 + - - +
376B GLU* 5.3 7.6 - - - +
379B VAL* 3.5 41.9 - - + +
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Residues in contact with ALA 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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344B PRO* 5.9 7.6 - - + -
357B ALA 3.2 16.1 + - - +
358B GLN* 3.7 7.4 - - - +
359B PHE 3.2 0.4 - - - -
360B LEU* 1.3 76.4 - - - +
362B GLY* 1.3 64.9 + - - +
364B ARG* 3.3 17.5 + - - +
365B ILE* 3.5 21.2 + - + +
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Residues in contact with GLY 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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343B VAL* 3.7 26.2 - - - +
344B PRO* 5.9 1.1 - - - +
358B GLN 2.8 18.2 + - - -
359B PHE 3.3 0.6 + - - -
361B ALA* 1.3 75.7 - - - +
363B VAL* 1.3 55.3 + - - +
365B ILE* 3.1 7.0 + - - +
366B GLY 2.9 24.9 + - - -
398B MET* 3.4 19.7 - - - +
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Residues in contact with VAL 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PHE* 3.1 45.8 + - + +
360B LEU 3.8 5.6 - - - +
361B ALA 3.2 0.6 - - - -
362B GLY* 1.3 72.1 - - - +
364B ARG* 1.3 59.3 + - - +
365B ILE 3.1 2.0 - - - -
366B GLY* 4.9 0.2 - - - -
367B VAL* 3.0 35.8 + - + +
370B ALA* 5.5 0.2 - - - +
375B ALA* 4.0 26.1 - - + +
378B VAL* 3.8 24.5 - - + -
379B VAL* 4.1 10.1 - - + -
398B MET* 4.1 11.7 - - + -
401B VAL* 4.6 8.1 - - + -
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Residues in contact with ARG 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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292B GLU 4.5 1.9 - - - +
360B LEU 3.5 16.6 + - - +
361B ALA* 3.3 10.8 + - - +
363B VAL* 1.3 77.4 - - - +
365B ILE* 1.3 60.0 + - + +
367B VAL 3.7 2.5 + - - +
368B PRO* 3.3 24.1 - - - +
370B ALA* 2.9 28.2 + - - +
371B SER* 3.6 5.1 - - - +
372B ASP* 2.6 36.5 + - - +
375B ALA* 3.5 29.4 - - - +
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Residues in contact with ILE 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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292B GLU* 3.3 44.4 - - + +
293B SER* 3.3 25.8 - - - +
294B ILE* 3.3 30.2 + - + +
342B GLY 3.7 20.2 - - - +
343B VAL* 4.5 4.9 - - + -
344B PRO* 4.1 15.3 - - + -
361B ALA* 3.7 16.4 - - + +
362B GLY* 3.1 9.3 + - - +
363B VAL 3.1 0.2 - - - -
364B ARG* 1.3 81.8 - - + +
366B GLY* 1.3 62.0 + - - +
367B VAL 3.3 0.4 - - - -
368B PRO* 3.5 6.8 - - - +
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Residues in contact with GLY 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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294B ILE* 3.9 22.3 - - - +
296B ARG* 4.6 1.4 + - - -
362B GLY 2.9 15.0 + - - -
363B VAL 4.1 1.1 - - - -
365B ILE* 1.3 76.7 - - - +
367B VAL* 1.3 63.5 + - - +
368B PRO* 3.3 7.8 - - - +
398B MET* 4.5 2.2 - - - -
401B VAL* 5.3 0.4 - - - -
402B VAL* 4.3 13.4 - - - +
405B HIS* 3.5 16.6 - - - +
406B ASN* 4.2 8.1 + - - -
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B VAL* 3.0 23.1 + - + +
364B ARG* 3.7 7.3 + - - +
366B GLY* 1.3 83.5 - - - +
368B PRO* 1.3 65.6 - - - +
369B GLN* 3.1 4.9 - - + +
370B ALA* 3.0 36.1 + - + +
378B VAL* 4.8 5.6 - - + -
401B VAL* 3.7 26.7 - - + -
405B HIS* 3.9 20.4 - - + +
532B TRP* 3.7 26.0 - - + -
536B LEU* 5.3 2.9 - - + -
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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