Contacts of the helix formed by residues 354 - 372 (chain B) in PDB entry 1L0N
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 ASN 354 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B SER* 1.3 80.9 + - - +
355B PRO* 1.3 70.9 - - + +
356B ASP 3.0 1.1 - - - -
357B VAL* 3.3 5.2 + - - +
358B GLN* 2.9 39.6 + - - +
407B ASP* 3.4 25.0 + - - +
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Residues in contact with PRO 355 (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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353B SER* 3.4 15.9 - - - +
354B ASN* 1.3 97.4 - - + +
356B ASP* 1.3 53.9 + - - +
358B GLN* 3.4 9.9 - - + +
359B ALA* 2.7 34.0 + - - +
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Residues in contact with ASP 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 4.4 11.5 - - + +
352B LEU* 4.5 13.2 - - + +
353B SER* 3.3 31.7 + - - +
354B ASN 3.0 1.2 - - - -
355B PRO* 1.3 77.8 - - - +
357B VAL* 1.3 55.3 + - - +
359B ALA* 3.2 7.3 + - - +
360B ALA* 2.8 34.1 + - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 3.9 14.8 - - + -
278B VAL* 4.4 3.4 - - + -
352B LEU* 3.7 35.4 - - + -
353B SER 4.3 3.4 - - - +
354B ASN 3.3 3.7 + - - +
356B ASP* 1.3 75.0 - - - +
358B GLN* 1.3 55.8 + - - +
360B ALA* 3.0 6.3 + - - +
361B LYS* 2.6 60.4 + - - +
407B ASP* 3.5 33.0 - - - +
410B VAL* 4.2 9.4 - - + -
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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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354B ASN* 2.9 35.2 + - - +
355B PRO* 3.4 11.9 - - + +
357B VAL* 1.3 75.1 - - - +
359B ALA* 1.3 59.0 + - - +
361B LYS* 3.3 22.3 + - - +
362B ASN* 2.9 45.5 + - - +
365B LYS* 5.7 1.0 + - - -
403B ASP* 5.0 3.8 - - - +
407B ASP* 5.9 0.2 + - - -
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 4.3 33.4 - - - +
292B THR* 5.8 4.3 - - + -
355B PRO 2.7 20.8 + - - +
356B ASP* 3.6 7.2 - - - +
358B GLN* 1.3 69.7 - - - +
360B ALA* 1.3 61.5 + - - +
362B ASN* 3.2 3.7 + - - +
363B LYS* 2.7 42.1 + - - +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 3.7 11.9 - - + +
277B HIS* 3.7 14.2 - - + +
278B VAL* 3.5 38.8 - - + +
356B ASP 2.8 14.5 + - - +
357B VAL 3.0 6.9 + - - +
359B ALA* 1.3 77.8 - - - +
361B LYS* 1.3 64.3 + - - +
363B LYS* 2.8 15.8 + - - +
364B LEU* 2.8 15.6 + - - +
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Residues in contact with LYS 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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274B VAL* 4.5 8.2 - - + +
357B VAL* 2.6 43.1 + - + +
358B GLN* 3.5 24.2 - - - +
360B ALA* 1.3 70.9 - - - +
362B ASN* 1.3 60.3 + - - +
364B LEU* 3.2 3.7 + - - +
365B LYS* 2.9 44.7 + - - +
402B ILE* 3.3 30.7 - - + +
403B ASP* 3.3 27.6 - - - +
405B VAL* 2.6 38.1 + - - +
406B ALA 5.0 0.2 - - - -
407B ASP* 5.2 0.6 + - - -
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Residues in contact with ASN 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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81A SER 3.6 21.7 - - - +
82A MET* 4.1 10.5 - - - +
83A GLY* 3.9 1.5 - - - -
102A LEU* 5.8 4.5 - - + +
358B GLN* 2.9 31.1 + - - +
359B ALA* 3.5 6.5 - - - +
361B LYS* 1.3 76.5 - - - +
363B LYS* 1.3 65.9 + - - +
365B LYS* 4.3 19.2 - - - +
366B ALA* 3.1 26.2 + - - +
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Residues in contact with LYS 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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80A GLU 3.3 26.5 - - - +
83A GLY* 3.8 8.3 - - - +
85A HIS* 6.0 1.0 - - - -
277B HIS* 3.6 41.6 + - + -
280B GLY* 5.7 3.0 - - - -
284B HIS* 3.3 35.5 + - + +
292B THR* 2.8 45.0 + - - +
293B SER* 4.7 3.0 - - - +
359B ALA* 2.7 32.9 + - - +
360B ALA* 2.8 3.7 + - - +
362B ASN* 1.3 72.0 - - - +
364B LEU* 1.3 57.6 + - - +
366B ALA* 3.8 1.4 - - - +
367B GLY* 3.0 26.2 + - - -
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Residues in contact with LEU 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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270B ASN* 4.9 0.7 - - - +
273B SER* 3.8 27.8 - - - -
274B VAL* 3.9 22.2 - - + -
276B GLN* 5.6 0.7 - - - +
277B HIS* 3.7 29.7 - - + +
360B ALA 2.8 14.7 + - - +
361B LYS 3.6 3.1 - - - +
363B LYS* 1.3 74.7 - - - +
365B LYS* 1.3 59.5 + - - +
367B GLY* 3.3 1.7 + - - -
368B TYR* 2.9 26.1 + - + +
402B ILE* 3.8 26.9 - - + -
1I MET* 3.8 30.1 - - + -
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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
----------------------------------------------------------
102A LEU* 5.9 4.0 - - + -
358B GLN* 5.7 1.4 + - - -
361B LYS* 2.9 39.8 + - - +
362B ASN* 4.3 16.4 - - - +
364B LEU* 1.3 68.9 - - - +
366B ALA* 1.3 67.7 + - - +
368B TYR* 3.0 12.7 + - - +
369B LEU* 3.0 21.1 + - + +
399B LEU* 3.6 43.6 - - + +
402B ILE* 3.9 20.0 - - + -
403B ASP* 2.7 38.9 + - - -
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Residues in contact with ALA 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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82A MET 4.1 5.2 - - - +
83A GLY 3.5 26.7 - - - +
101A ALA* 6.2 0.2 - - - -
102A LEU* 3.7 31.2 - - + +
362B ASN 3.1 19.4 + - - +
363B LYS 3.8 0.7 - - - +
365B LYS* 1.3 78.0 - - - +
367B GLY* 1.3 57.0 + - - +
369B LEU* 3.5 2.1 + - - +
370B MET* 3.0 37.5 + - - +
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Residues in contact with GLY 367 (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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83A GLY 5.1 0.4 + - - -
85A HIS* 5.6 4.3 - - - -
277B HIS* 6.1 0.9 - - - -
363B LYS 3.0 15.9 + - - -
364B LEU* 3.6 3.6 - - - -
365B LYS 3.1 0.2 - - - -
366B ALA* 1.3 74.9 - - - +
368B TYR* 1.3 53.8 + - - +
370B MET* 3.1 14.0 + - - +
371B SER* 2.7 35.3 + - - -
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Residues in contact with TYR 368 (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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364B LEU* 2.9 16.7 + - + +
365B LYS* 3.0 6.5 + - - +
367B GLY* 1.3 71.7 - - - +
369B LEU* 1.3 76.7 + - + +
371B SER* 2.9 21.7 + - - -
372B VAL* 3.3 22.6 + - + +
381B GLU* 2.6 47.0 + - + +
385B GLN* 3.8 5.7 + - - -
392B TYR* 5.6 1.0 - - - -
393B THR 4.3 3.8 + - - -
395B PRO* 4.4 17.5 - - + +
398B VAL* 3.7 36.8 - - + +
399B LEU* 4.8 4.5 - - + -
402B ILE* 5.4 1.1 - - + -
1I MET* 3.6 35.7 - - + -
2I LEU 5.2 0.4 - - - -
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Residues in contact with LEU 369 (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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33A PRO* 4.0 30.3 - - + +
34A THR* 3.6 18.4 + - - +
102A LEU* 3.9 22.4 - - + -
365B LYS* 3.0 17.3 + - + +
366B ALA 3.9 2.2 - - - +
368B TYR* 1.3 78.0 - - + +
370B MET* 1.3 63.0 + - - +
372B VAL* 3.1 23.2 + - + +
373B GLU* 3.5 6.6 + - - -
395B PRO* 3.8 30.1 - - + -
399B LEU* 3.8 32.5 - - + -
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Residues in contact with MET 370 (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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34A THR* 3.5 26.2 - - + -
83A GLY 4.5 5.6 - - - +
85A HIS* 3.2 37.9 - - + +
100A LYS* 3.6 37.9 - - + +
101A ALA* 4.9 3.1 - - - -
102A LEU* 6.1 0.2 - - - -
366B ALA* 3.0 27.1 + - - +
367B GLY* 3.4 8.7 - - - +
369B LEU* 1.3 77.4 - - - +
371B SER* 1.3 62.9 + - - +
372B VAL 3.1 1.0 + - - -
373B GLU* 3.1 31.3 + - - +
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Residues in contact with SER 371 (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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367B GLY 2.7 17.2 + - - -
368B TYR* 2.9 18.7 + - - -
370B MET* 1.3 73.6 - - - +
372B VAL* 1.3 62.9 + - - +
373B GLU 3.4 1.1 + - - -
374B SER* 5.0 0.9 + - - -
377B GLY* 3.4 23.4 + - - -
381B GLU* 5.6 1.9 + - - +
6I ALA* 4.1 24.3 - - - +
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Residues in contact with VAL 372 (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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32A GLN* 5.7 1.2 - - - +
368B TYR* 3.3 23.5 + - + +
369B LEU* 3.1 20.3 + - + +
371B SER* 1.3 84.4 - - - +
373B GLU* 1.3 62.6 + - - +
374B SER 3.2 7.2 + - - +
377B GLY 3.9 3.4 - - - +
378B PHE* 4.0 31.4 - - + +
381B GLU* 3.7 37.2 - - + -
395B PRO* 5.3 8.3 - - + -
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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