Contacts of the helix formed by residues 346 - 360 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C LEU* 4.5 8.8 - - + +
164C LEU* 3.9 30.3 - - + +
165C MET* 3.2 24.3 - - + +
168C GLU* 4.7 2.0 - - + +
343C TYR 4.8 0.6 + - - -
344C LEU 3.1 1.2 - - - -
345C HIS* 1.3 119.5 + - + +
347C PHE* 1.3 58.7 + - - +
348C ALA 3.5 1.8 - - - -
349C ALA* 3.5 27.0 + - + +
350C TYR* 3.1 21.0 + - - +
381C GLU* 5.1 2.8 + - - -
346D ARG* 3.7 24.2 - - - +
381D GLU* 3.4 34.5 + - - +
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Residues in contact with PHE 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C MET* 3.8 24.5 - - + +
337C MET* 3.7 25.8 - - + -
339C PRO* 4.3 19.5 - - + -
344C LEU* 3.1 37.3 + - + +
345C HIS 3.5 0.4 - - - -
346C ARG* 1.3 75.6 - - - +
348C ALA* 1.3 67.4 + - - +
350C TYR* 3.2 12.1 + - - +
351C PHE* 3.3 41.2 + + - -
406C LEU* 4.2 20.4 - - + -
486C LEU* 4.5 7.4 - - + -
489C LEU* 4.8 13.7 - - + -
490C VAL* 4.0 18.2 - - + -
493C TYR* 4.2 10.8 - + - -
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Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C MET* 3.7 37.5 - - + +
339C PRO* 5.2 3.3 - - + +
344C LEU 4.7 0.6 + - - -
345C HIS 5.1 2.6 + - - +
347C PHE* 1.3 79.4 - - - +
349C ALA* 1.3 62.9 + - - +
351C PHE* 3.3 3.5 + - - +
352C GLN* 3.0 23.5 + - - +
378C VAL* 4.0 5.9 - - + +
379C TRP* 4.1 12.8 - - - +
380C GLY* 3.9 22.0 - - - +
381C GLU* 5.5 0.4 - - - -
382C PRO* 6.4 0.4 - - + -
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Residues in contact with ALA 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C LEU* 4.0 14.9 - - + +
345C HIS 5.4 0.6 + - - +
346C ARG* 3.5 46.9 + - - +
347C PHE 3.3 0.4 - - - -
348C ALA* 1.3 77.6 - - - +
350C TYR* 1.3 62.8 + - - +
352C GLN* 3.1 27.4 - - - +
353C GLN* 3.7 3.5 + - - +
381D GLU* 4.4 7.9 - - - +
389D ALA* 5.5 2.6 - - - +
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Residues in contact with TYR 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLY* 6.5 0.4 - - - -
161C LEU* 3.6 19.9 - - + +
162C GLY* 3.4 38.4 - - - -
165C MET* 3.7 18.8 - - + -
272C ARG* 3.2 28.4 + - - -
273C TYR* 4.7 1.0 - - - -
275C LEU* 3.3 21.4 + - + +
346C ARG 3.1 15.4 + - - +
347C PHE 3.4 8.3 - - - +
348C ALA 3.2 0.2 - - - -
349C ALA* 1.3 76.9 - - - +
351C PHE* 1.3 96.8 + + - +
353C GLN* 3.2 10.1 + - - +
354C GLY* 3.0 21.7 + - - -
490C VAL* 4.0 10.4 - - + +
494C GLU* 4.2 10.0 + - - +
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Residues in contact with PHE 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C MET* 3.9 34.5 - - + -
347C PHE* 3.3 45.8 + + - +
348C ALA 3.3 2.0 + - - +
350C TYR* 1.3 97.8 - + - +
352C GLN* 1.3 59.8 + - - +
353C GLN 3.1 1.6 - - - -
354C GLY* 3.6 5.4 - - - +
355C ASP* 2.7 39.3 + - + +
378C VAL* 4.1 3.3 - - - +
490C VAL* 3.5 30.1 - - + -
493C TYR* 3.3 31.2 - + + -
494C GLU* 4.1 10.5 - - + -
497C ILE* 3.9 21.3 - - + -
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Residues in contact with GLN 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C ALA 3.0 10.1 + - - +
349C ALA* 3.1 22.6 - - - +
350C TYR 3.1 0.2 - - - -
351C PHE* 1.3 78.3 - - - +
353C GLN* 1.3 56.7 + - - +
356C MET* 2.8 47.9 + - - +
378C VAL* 2.8 36.5 + - - +
379C TRP* 3.9 10.9 - - - +
379D TRP* 3.8 18.0 - - - +
380D GLY 5.1 3.6 + - - +
381D GLU* 4.1 13.9 - - - +
389D ALA* 5.1 0.8 - - + +
390D PHE* 3.5 32.8 - - + +
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Residues in contact with GLN 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C GLY* 3.6 22.8 + - - -
158C GLY* 3.4 17.6 + - - +
161C LEU* 3.9 18.9 - - + +
272C ARG* 3.8 17.6 + - + +
349C ALA 3.7 3.0 + - - +
350C TYR* 3.2 9.9 + - - +
352C GLN* 1.3 78.6 - - - +
354C GLY* 1.3 68.9 + - - +
357C GLU* 2.8 51.6 + - + +
388D HIS 3.5 13.5 + - - +
389D ALA* 3.1 34.4 - - + +
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Residues in contact with GLY 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ARG* 3.8 19.2 - - - -
273C TYR* 4.1 4.4 + - - -
350C TYR* 3.0 18.6 + - - -
351C PHE* 3.6 11.0 + - - -
353C GLN* 1.3 78.9 - - - +
355C ASP* 1.3 55.3 + - - +
358C SER* 2.7 30.0 + - - -
497C ILE* 3.7 10.6 - - - +
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Residues in contact with ASP 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C HIS* 5.4 2.1 - - - -
337C MET* 5.9 1.5 - - - +
351C PHE* 2.7 26.8 + - + +
354C GLY* 1.3 71.3 - - - +
356C MET* 1.3 60.2 + - - +
358C SER* 3.1 3.8 + - - -
359C ASN* 2.9 35.9 + - - +
375C GLY* 4.7 0.3 - - - -
376C PRO* 3.9 22.2 - - - +
378C VAL* 3.7 23.4 - - + +
496C LYS* 4.8 10.6 + - - +
497C ILE* 3.5 31.3 - - + +
500C GLN* 4.4 8.5 - - - +
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Residues in contact with MET 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C GLN* 2.8 43.3 + - - +
355C ASP* 1.3 81.3 - - - +
357C GLU* 1.3 56.9 + - - +
359C ASN 5.2 0.2 - - - -
360C GLY* 2.9 30.3 + - - +
375C GLY* 6.0 0.2 - - - -
376C PRO 3.5 16.8 - - - +
377C ILE* 3.9 17.0 - - + -
378C VAL* 3.5 22.2 - - + +
379D TRP* 3.6 29.6 - - + -
390D PHE* 3.7 17.3 - - + +
392D GLN* 4.3 0.2 - - - +
393D LEU* 3.8 36.2 + - + +
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Residues in contact with GLU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C GLY* 5.9 0.2 - - - -
272C ARG* 2.8 43.3 + - - +
353C GLN* 2.8 43.9 + - + +
356C MET* 1.3 74.6 - - - +
358C SER* 1.3 60.6 + - - +
361C LYS* 3.5 18.5 + - - -
510C ASP 3.9 0.5 - - - +
511C GLN* 4.2 12.6 - - + +
514C VAL* 4.4 15.6 - - - +
388D HIS* 4.0 12.5 - - - +
389D ALA 3.4 19.0 + - - +
390D PHE* 5.3 0.2 - - - +
392D GLN* 3.5 22.3 + - + +
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Residues in contact with SER 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ARG* 2.7 21.8 + - - +
273C TYR* 2.8 13.6 + - - -
354C GLY 2.7 21.4 + - - -
355C ASP 3.1 3.0 + - - -
357C GLU* 1.3 78.8 - - - +
359C ASN* 1.3 62.6 + - - +
361C LYS* 2.8 25.6 + - - +
497C ILE* 3.7 17.5 - - - -
508C SER* 3.2 25.8 + - - -
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Residues in contact with ASN 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ASP* 2.9 14.5 + - - +
358C SER* 1.3 77.6 - - - +
360C GLY* 1.3 55.6 + - - +
361C LYS* 2.9 13.4 + - - -
374C THR* 3.3 4.2 + - - -
375C GLY* 2.8 33.4 + - - -
497C ILE* 3.0 37.0 + - - +
500C GLN* 3.9 6.3 + - - +
501C GLY* 3.8 6.6 - - - +
504C TRP* 3.6 30.8 - - + -
506C ILE* 3.7 8.6 - - + +
508C SER* 2.5 28.4 + - - -
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Residues in contact with GLY 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C MET 2.9 19.7 + - - -
357C GLU 4.5 0.4 - - - -
358C SER 3.5 2.0 - - - -
359C ASN* 1.3 75.2 - - - +
361C LYS* 1.3 57.8 + - - -
374C THR* 4.7 1.1 - - - -
375C GLY 5.2 0.2 - - - -
392D GLN* 2.9 32.2 + - - +
393D LEU* 3.8 26.9 - - - +
396D GLN 3.4 8.4 - - - +
397D GLY* 3.9 4.5 - - - -
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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