Contacts of the helix formed by residues 346 - 360 (chain B) in PDB entry 1JLH
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 ARG 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ARG* 3.7 24.0 - - - +
381A GLU* 3.2 35.8 + - - +
161B LEU* 4.7 8.6 - - + +
164B LEU* 3.8 30.6 - - + +
165B MET* 3.4 22.3 - - + +
168B GLU* 4.8 1.1 - - + -
343B TYR 4.7 0.6 + - - -
344B LEU 3.1 0.8 - - - -
345B HIS* 1.3 117.1 + - + +
347B PHE* 1.3 58.5 + - - +
348B ALA 3.5 2.2 - - - -
349B ALA* 3.5 29.7 + - + +
350B TYR* 3.0 22.0 + - - +
381B GLU* 5.1 3.8 + - - -
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Residues in contact with PHE 347 (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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165B MET* 3.9 20.5 - - + +
337B MET* 3.6 26.0 - - + -
339B PRO* 4.3 18.6 - - + -
344B LEU* 2.9 41.1 + - + +
345B HIS 3.5 0.2 - - - -
346B ARG* 1.3 75.5 - - - +
348B ALA* 1.3 67.6 + - - +
350B TYR* 3.2 12.3 + - - +
351B PHE* 3.2 40.9 + + - -
406B LEU* 4.2 17.0 - - + -
486B LEU* 4.5 7.4 - - + -
489B LEU* 4.7 12.3 - - + -
490B VAL* 4.2 16.8 - - + -
493B TYR* 4.1 17.0 - + - -
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B MET* 3.6 39.5 - - + +
339B PRO* 5.2 2.8 - - + +
344B LEU 4.7 0.4 + - - -
345B HIS 5.1 2.5 + - - +
347B PHE* 1.3 79.2 - - - +
349B ALA* 1.3 64.0 + - - +
351B PHE* 3.2 3.8 + - - +
352B GLN* 2.9 23.1 + - - +
378B VAL* 4.3 5.2 - - + +
379B TRP* 4.2 5.8 - - - -
380B GLY* 3.9 28.7 - - - +
381B GLU* 5.5 0.7 - - - -
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Residues in contact with ALA 349 (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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381A GLU* 4.4 6.1 - - - +
389A ALA* 5.6 2.3 - - - +
161B LEU* 4.0 13.7 - - + +
345B HIS 5.4 0.6 + - - +
346B ARG* 3.5 50.6 + - - +
347B PHE 3.2 0.4 - - - -
348B ALA* 1.3 78.9 - - - +
350B TYR* 1.3 61.7 + - - +
352B GLN* 3.1 28.2 - - - +
353B GLN* 3.7 2.9 + - - +
380B GLY 5.5 0.2 + - - -
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Residues in contact with TYR 350 (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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161B LEU* 3.4 19.7 - - + +
162B GLY* 3.3 38.1 - - - -
165B MET* 3.8 22.4 - - + -
272B ARG* 3.3 26.8 + - - -
273B TYR* 4.7 1.4 - - - -
275B LEU* 3.4 21.8 + - + +
346B ARG 3.0 15.3 + - - +
347B PHE 3.4 7.6 - - - +
348B ALA 3.2 0.4 - - - -
349B ALA* 1.3 78.1 - - - +
351B PHE* 1.3 93.8 + + - +
353B GLN* 3.2 11.0 + - - +
354B GLY* 3.1 22.0 + - - -
490B VAL* 4.1 10.0 - - + +
494B GLU* 4.3 9.8 + - + -
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Residues in contact with PHE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B MET* 3.7 37.9 - - + -
347B PHE* 3.2 41.5 + + - +
348B ALA 3.2 5.5 + - - +
350B TYR* 1.3 94.8 - + - +
352B GLN* 1.3 60.4 + - - +
353B GLN 3.0 2.0 - - - -
354B GLY* 3.6 6.7 - - - +
355B ASP* 2.7 35.7 + - + +
378B VAL* 4.3 3.2 - - - +
490B VAL* 3.5 28.5 - - + -
493B TYR* 3.3 32.8 - + + -
494B GLU* 4.1 11.2 - - + -
497B ILE* 4.0 18.8 - - + -
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TRP* 3.8 19.5 - - - +
380A GLY 5.1 3.8 + - - +
381A GLU* 4.2 14.4 - - - +
389A ALA* 4.6 1.9 - - + +
390A PHE* 3.5 32.5 - - + +
348B ALA 2.9 11.1 + - - +
349B ALA* 3.1 21.9 - - - +
350B TYR 3.1 0.2 - - - -
351B PHE* 1.3 78.3 - - - +
353B GLN* 1.3 56.5 + - - +
356B MET* 2.8 46.4 - - - +
378B VAL* 2.8 35.2 + - - +
379B TRP* 3.9 11.5 - - - +
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Residues in contact with GLN 353 (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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388A HIS 3.5 14.2 + - - +
389A ALA* 3.2 31.8 - - + +
157B GLY* 3.5 23.0 + - - -
158B GLY* 3.3 21.8 + - - +
161B LEU* 3.8 19.3 - - + +
272B ARG* 3.8 19.0 + - + +
349B ALA 3.7 2.6 + - - +
350B TYR* 3.2 10.7 + - - +
352B GLN* 1.3 80.0 - - - +
354B GLY* 1.3 67.3 + - - +
357B GLU* 2.8 47.3 + - - +
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Residues in contact with GLY 354 (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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272B ARG* 4.2 20.4 - - - -
273B TYR* 4.0 4.5 + - - -
350B TYR* 3.1 14.6 + - - -
351B PHE* 3.4 8.9 + - - -
353B GLN* 1.3 79.1 - - - +
355B ASP* 1.3 56.5 + - - +
358B SER* 2.7 30.0 + - - -
497B ILE* 3.6 13.0 - - - +
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Residues in contact with ASP 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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335B HIS* 5.3 1.2 - - - -
337B MET* 5.9 1.6 - - - +
351B PHE* 2.7 24.4 + - + +
354B GLY* 1.3 71.4 - - - +
356B MET* 1.3 61.4 + - - +
358B SER* 3.2 3.5 + - - -
359B ASN* 2.8 37.2 + - - +
375B GLY* 4.7 0.3 - - - -
376B PRO* 3.9 21.9 - - - +
378B VAL* 3.6 25.0 - - + +
496B LYS* 4.6 12.1 + - - +
497B ILE* 3.5 27.8 - - + +
500B GLN* 4.4 9.3 - - - +
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Residues in contact with MET 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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379A TRP* 3.7 29.4 - - + -
390A PHE* 3.7 18.8 - - + +
393A LEU* 3.7 35.5 + - + +
394A ILE* 5.6 0.2 - - + -
352B GLN* 2.8 45.7 + - - +
355B ASP* 1.3 74.5 - - - +
357B GLU* 1.3 59.3 + - - +
359B ASN 5.2 0.2 - - - -
360B GLY* 2.8 30.8 + - - +
375B GLY* 6.0 0.2 - - - -
376B PRO 3.5 18.2 - - - +
377B ILE* 3.9 15.5 - - + -
378B VAL* 3.5 17.9 - - + +
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Residues in contact with GLU 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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387A GLN 5.7 0.2 - - - +
388A HIS* 4.0 15.8 - - - +
389A ALA 3.5 15.6 + - - +
390A PHE* 4.9 0.4 - - - +
392A GLN* 3.4 34.3 + - + +
271B GLY* 6.0 0.2 - - - -
272B ARG* 2.7 36.9 + - - +
352B GLN 4.2 0.2 + - - -
353B GLN* 2.8 40.2 + - + +
356B MET* 1.3 75.1 - - - +
358B SER* 1.3 60.4 + - - +
361B LYS* 3.4 9.4 + - - -
510B ASP 3.9 0.5 - - - +
511B GLN* 4.2 11.2 - - + +
514B VAL* 4.4 14.9 - - - +
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Residues in contact with SER 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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272B ARG* 2.8 17.6 + - - +
273B TYR* 2.8 15.2 + - - -
354B GLY 2.7 25.6 + - - -
355B ASP 3.2 3.3 + - - -
356B MET 3.1 0.6 - - - -
357B GLU* 1.3 81.5 - - - +
359B ASN* 1.3 62.4 + - - +
360B GLY 3.6 0.2 - - - -
361B LYS* 2.7 25.8 + - - +
497B ILE* 3.6 16.6 - - - -
508B SER* 3.2 25.3 + - - -
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Residues in contact with ASN 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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393A LEU* 5.0 0.2 - - - -
355B ASP* 2.8 18.7 + - - +
358B SER* 1.3 74.7 - - - +
360B GLY* 1.3 54.9 + - - +
361B LYS* 2.8 13.7 + - - -
374B THR* 3.4 5.0 + - - -
375B GLY* 3.0 27.3 + - - -
497B ILE* 3.1 36.3 + - - +
500B GLN* 3.9 6.5 + - - +
501B GLY* 3.8 1.2 - - - +
504B TRP* 3.4 33.1 - - + -
506B ILE* 3.7 12.4 - - + +
508B SER* 2.7 28.2 + - - -
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Residues in contact with GLY 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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392A GLN* 3.0 30.8 + - - +
393A LEU* 3.7 27.1 - - - +
396A GLN 3.4 6.1 - - - +
397A GLY* 3.8 9.0 - - - -
356B MET 2.8 25.3 + - - -
357B GLU 4.5 0.6 - - - -
358B SER 3.6 1.6 - - - -
359B ASN* 1.3 69.6 - - - +
361B LYS* 1.3 57.8 + - - -
374B THR* 4.8 0.7 - - - -
375B GLY 5.2 0.2 - - - -
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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