Contacts of the helix formed by residues 355 - 373 (chain J) in PDB entry 5LN3
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192J PRO 4.6 4.7 + - - -
193J GLY 5.0 0.3 + - - -
194J THR* 4.0 20.0 + - - +
320J PRO* 4.6 9.0 - - - -
325J ARG* 6.4 0.2 - - - -
354J ALA* 1.3 79.1 - - - +
356J GLY* 1.4 59.7 + - - +
357J ALA* 3.2 11.2 + - - +
358J GLU* 3.0 35.7 + - - +
359J VAL* 3.1 15.2 + - - +
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Residues in contact with GLY 356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J ILE* 5.9 1.6 - - - -
194J THR* 3.8 19.1 - - - +
320J PRO* 5.2 3.0 - - - +
325J ARG* 6.5 0.4 - - - -
328J ILE* 3.0 36.7 - - - +
354J ALA 4.1 0.2 + - - -
355J SER* 1.4 70.3 + - - +
357J ALA* 1.3 64.9 + - - +
359J VAL* 3.4 13.9 + - - +
360J LYS* 3.7 4.9 + - - -
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Residues in contact with ALA 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J GLY 4.8 8.7 - - - +
194J THR 3.8 11.4 + - - +
254J ILE* 5.4 8.1 - - + -
355J SER* 3.9 9.6 + - - +
356J GLY* 1.3 78.1 - - - +
358J GLU* 1.3 64.4 + - + +
360J LYS* 3.0 40.2 + - + +
361J GLY 3.6 2.8 + - - -
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Residues in contact with GLU 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354J ALA* 5.0 6.1 - - + -
355J SER* 3.0 29.7 + - - +
357J ALA* 1.3 81.0 - - + +
359J VAL* 1.4 64.8 + - - +
360J LYS 3.3 0.4 + - - -
361J GLY* 3.5 9.3 + - - +
362J VAL* 3.5 14.4 + - - +
390J VAL* 4.1 21.6 - - + +
393J LYS* 4.8 15.1 - - - +
394J ASP* 5.7 4.3 - - - +
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Residues in contact with VAL 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325J ARG* 4.6 12.8 - - + +
328J ILE* 4.3 20.9 - - + -
329J LEU* 3.9 37.2 - - + -
332J HIS* 6.1 0.4 - - + -
351J MET* 4.3 25.4 - - + -
354J ALA* 5.3 3.6 - - + +
355J SER 3.1 14.7 + - - +
356J GLY* 3.5 14.6 - - - +
358J GLU* 1.4 72.6 - - - +
360J LYS* 1.3 64.5 + - - +
362J VAL* 2.9 26.7 + - - +
363J CYS* 3.7 5.4 + - - -
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Residues in contact with LYS 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J MET* 5.4 5.6 - - - -
151J ILE* 3.6 31.1 - - - +
194J THR 4.8 3.4 + - - -
198J LEU* 4.8 10.2 - - - +
328J ILE* 3.8 3.4 - - + +
332J HIS* 3.7 42.4 - - + +
356J GLY 3.7 17.2 + - - +
357J ALA* 3.0 23.0 + - + +
359J VAL* 1.3 73.5 - - - +
361J GLY* 1.3 59.9 + - - +
362J VAL 3.2 1.0 + - - -
363J CYS* 3.3 12.0 + - - +
364J THR* 2.9 21.7 + - - +
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Residues in contact with GLY 361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J ALA 3.6 4.4 + - - -
358J GLU* 3.5 8.4 + - - -
359J VAL 3.1 0.8 - - - -
360J LYS* 1.3 78.6 - - - +
362J VAL* 1.4 55.2 + - - +
364J THR* 2.9 10.8 + - - -
365J GLU* 2.9 40.1 + - - +
390J VAL* 4.6 2.7 - - - -
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Residues in contact with VAL 362 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329J LEU* 5.2 3.8 - - + -
351J MET* 5.0 10.3 - - + -
358J GLU 3.5 12.9 + - - +
359J VAL* 2.9 23.3 + - + +
361J GLY* 1.4 74.0 - - - +
363J CYS* 1.3 65.8 + - - +
365J GLU* 3.3 1.0 + - - -
366J ALA* 3.1 19.6 + - - +
383J PHE* 4.3 17.5 - - + -
386J ALA* 3.4 20.1 - - + +
387J VAL* 3.8 31.2 - - + +
390J VAL* 3.7 27.8 - - + +
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Residues in contact with CYS 363 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329J LEU* 3.9 27.1 - - - -
332J HIS* 3.9 31.2 - - + -
333J SER* 5.1 2.2 - - - -
336J MET* 3.8 24.6 - - + +
359J VAL* 3.9 13.9 - - - -
360J LYS* 3.3 8.5 - - - +
362J VAL* 1.3 80.1 - - - +
364J THR* 1.4 60.2 + - - +
366J ALA* 3.3 20.1 + - - +
367J GLY* 3.6 5.4 + - - -
383J PHE* 4.6 8.1 - - - -
196K ILE* 4.5 3.2 - - - +
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Residues in contact with THR 364 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360J LYS* 2.9 16.5 + - - +
361J GLY* 2.9 11.2 + - - -
363J CYS* 1.4 72.1 - - - +
365J GLU* 1.4 67.4 + - - +
366J ALA 3.4 0.2 + - - -
367J GLY* 3.6 8.0 + - - -
368J MET* 3.5 19.5 + - + +
196K ILE* 4.5 25.0 - - + +
329K ARG* 4.6 17.5 - - - +
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Residues in contact with GLU 365 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J GLY* 2.9 20.3 + - - +
362J VAL 3.9 3.8 - - - +
364J THR* 1.4 79.7 - - - +
366J ALA* 1.4 59.5 + - - +
368J MET* 3.1 21.0 + - - +
369J TYR* 3.1 43.8 + - + +
386J ALA* 4.2 4.2 - - + +
389J LYS* 3.8 15.8 - - - +
390J VAL* 3.1 31.0 - - - +
393J LYS* 3.4 17.7 + - - -
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Residues in contact with ALA 366 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336J MET* 4.8 4.5 - - + -
362J VAL 3.1 13.1 + - - +
363J CYS* 3.5 12.3 - - - +
364J THR 3.3 0.4 - - - -
365J GLU* 1.4 71.6 - - - +
367J GLY* 1.4 65.4 + - - +
368J MET 3.4 0.2 + - - -
369J TYR* 3.4 9.8 + - - +
370J ALA* 3.4 17.7 + - - +
378J VAL* 4.1 12.6 - - + +
382J ASP* 3.9 10.6 - - - +
383J PHE* 4.0 31.0 - - + -
386J ALA* 4.1 10.5 - - + -
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Residues in contact with GLY 367 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336J MET* 5.4 1.7 - - - +
363J CYS 3.6 3.0 + - - -
364J THR 3.6 3.2 + - - -
365J GLU 3.3 0.6 - - - -
366J ALA* 1.4 78.6 - - - +
368J MET* 1.4 54.1 + - - +
370J ALA* 3.2 8.0 + - - +
371J LEU* 3.0 37.3 + - - +
378J VAL* 5.0 3.4 - - - -
194K ILE* 4.9 8.0 - - - +
196K ILE* 3.8 26.0 - - - -
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Residues in contact with MET 368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J THR* 3.5 19.7 + - - +
365J GLU* 3.1 12.4 + - - +
367J GLY* 1.4 72.2 - - - +
369J TYR* 1.4 72.1 + - + +
371J LEU* 3.8 16.9 - - + +
372J ARG* 3.1 26.5 + - - +
179K GLU* 3.8 40.1 - - + +
180K ALA* 6.1 0.4 - - - -
183K LEU* 5.9 2.9 - - + -
191K TYR* 4.0 26.0 - - + +
196K ILE* 6.6 0.2 - - - -
329K ARG* 5.9 5.4 - - - -
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Residues in contact with TYR 369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365J GLU* 3.1 52.8 + - + +
366J ALA* 3.4 9.7 + - - +
367J GLY 3.4 0.4 - - - -
368J MET* 1.4 82.2 - - + +
370J ALA* 1.4 64.1 + - - +
372J ARG* 3.3 24.3 + - - +
373J GLU* 3.0 27.8 + - + +
382J ASP* 3.9 25.6 - - + +
385J MET* 4.6 28.0 - - + -
386J ALA* 4.3 15.3 - - - -
389J LYS* 3.5 21.3 - - + +
179K GLU* 5.8 0.2 - - - -
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Residues in contact with ALA 370 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366J ALA 3.4 6.3 + - - +
367J GLY 3.2 8.4 + - - +
369J TYR* 1.4 79.0 - - - +
371J LEU* 1.4 58.5 + - - +
373J GLU* 3.2 13.0 + - - +
375J ARG* 3.0 42.3 + - + +
378J VAL* 4.0 28.5 - - + -
382J ASP* 3.3 18.4 + - - +
194K ILE* 4.9 3.6 - - + -
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Residues in contact with LEU 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367J GLY* 3.0 25.7 + - - +
368J MET* 3.8 14.6 - - + +
370J ALA* 1.4 72.7 - - - +
372J ARG* 1.3 67.2 + - - +
374J ARG* 3.0 21.5 + - - +
375J ARG 5.0 2.0 - - - +
183K LEU* 6.2 4.3 - - + -
190K LEU* 3.6 41.2 - - + +
191K TYR* 4.0 38.4 - - + +
194K ILE* 3.4 32.5 - - + -
196K ILE* 5.8 6.1 - - + +
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Residues in contact with ARG 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J MET* 3.1 16.1 + - - +
369J TYR* 3.6 22.0 - - - +
371J LEU* 1.3 82.6 - - - +
373J GLU* 1.4 62.0 + - + +
374J ARG* 3.3 12.4 + - - +
175K GLN* 3.9 28.2 - - - +
179K GLU* 3.0 42.6 + - + +
183K LEU* 5.7 13.2 - - + -
226Q LYS* 5.7 1.2 + - - -
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Residues in contact with GLU 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369J TYR* 3.0 16.9 + - + +
370J ALA* 3.2 9.3 + - - +
372J ARG* 1.4 78.3 - - + +
374J ARG* 1.4 63.0 - - - +
375J ARG* 3.7 48.5 + - + +
381J GLU* 5.1 0.8 - - - +
382J ASP* 4.4 16.6 - - - +
187Q ARG* 3.5 24.9 + - - -
218Q HIS* 4.1 3.5 + - - -
227Q THR* 3.9 15.4 - - + +
231Q TYR* 3.0 25.5 + - - +
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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