Contacts of the helix formed by residues 343 - 362 (chain A) in PDB entry 3RU0
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 LEU 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 3.6 31.6 - - + -
338A CYS* 2.6 28.6 + - + +
341A LEU* 3.9 24.2 - - + +
342A GLY* 1.3 74.8 - - - +
344A LEU* 1.3 58.0 + - - +
345A GLU 3.5 2.0 - - - -
346A GLU* 3.5 16.8 + - + +
347A ALA 2.9 22.9 + - - -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 4.1 21.1 - - + +
342A GLY* 3.3 28.6 + - - +
343A LEU* 1.3 70.3 - - - +
345A GLU* 1.3 61.9 + - - +
347A ALA* 3.4 3.6 + - - +
348A LEU* 3.0 27.9 + - - +
379A LEU* 3.7 25.9 - - + +
382A HIS* 3.6 50.3 - - + +
383A GLN* 4.4 4.8 + - + +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU 3.5 0.2 - - - -
344A LEU* 1.3 76.1 - - - +
346A GLU* 1.3 62.5 + - - +
348A LEU* 3.3 6.4 + - + +
349A PHE* 3.0 21.0 + - - +
383A GLN* 3.7 32.0 + - - +
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 4.1 0.2 - - - +
310A GLN* 2.7 28.0 + - - -
338A CYS* 3.6 14.7 - - - -
343A LEU* 3.5 26.1 + - + +
344A LEU 3.4 0.2 - - - -
345A GLU* 1.3 75.7 - - - +
347A ALA* 1.3 65.6 + - - +
349A PHE* 3.1 20.1 + - + +
350A TYR* 2.7 57.3 + - + +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A MET* 3.5 24.0 - - + +
338A CYS* 3.5 18.1 - - + +
339A ILE* 3.8 11.2 - - + +
343A LEU 2.9 17.4 + - - +
344A LEU* 3.6 7.6 - - - +
345A GLU 3.2 0.2 - - - -
346A GLU* 1.3 75.6 - - - +
348A LEU* 1.3 58.8 + - - +
350A TYR* 3.3 1.6 + - - -
351A GLY* 2.9 25.3 + - - -
379A LEU* 3.7 17.6 - - + +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU 3.0 16.6 + - - +
345A GLU* 3.7 5.4 - - + +
346A GLU 3.3 0.2 - - - -
347A ALA* 1.3 74.4 - - - +
349A PHE* 1.3 66.7 + - - +
351A GLY* 4.4 0.7 - - - +
352A THR* 2.9 51.0 + - - +
376A VAL* 3.9 12.1 - - + -
379A LEU* 3.6 24.1 - - + +
380A GLN* 3.7 23.3 - - + -
383A GLN* 3.7 28.3 - - + +
385A MET* 3.7 24.7 - - + -
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Residues in contact with PHE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ILE* 5.3 1.3 - - + -
345A GLU 3.0 13.8 + - - +
346A GLU* 3.1 14.5 + - + +
348A LEU* 1.3 79.0 - - - +
350A TYR* 1.3 90.5 + + - +
352A THR* 4.2 3.8 - - - -
353A ARG* 3.5 59.8 + - + +
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Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 4.4 2.5 - - + -
310A GLN* 3.6 15.2 - - + +
313A ILE* 3.6 26.0 - - + +
331A LEU* 3.7 39.9 - - + +
334A ALA* 3.5 28.7 - - + -
335A MET* 3.9 5.4 - - - +
338A CYS* 3.8 8.3 - - - -
346A GLU* 2.7 54.9 + - + +
347A ALA 3.3 2.4 + - - +
349A PHE* 1.3 99.7 - + - +
351A GLY* 1.3 64.0 + - - +
353A ARG* 3.2 14.6 + - - +
354A THR* 3.4 16.0 + - - +
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Residues in contact with GLY 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A MET* 3.6 28.8 - - - +
347A ALA 2.9 16.8 + - - -
348A LEU 4.0 0.7 - - - -
350A TYR* 1.3 69.1 - - - +
352A THR* 1.3 66.7 + - - +
354A THR* 2.7 23.9 + - - -
355A MET* 3.6 7.8 + - - +
376A VAL* 3.7 13.4 - - - +
379A LEU* 5.6 0.2 - - - -
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Residues in contact with THR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 2.9 41.2 + - - +
349A PHE* 4.2 3.8 - - - -
351A GLY* 1.3 74.3 - - - +
353A ARG* 1.3 62.8 + - + +
355A MET* 3.2 27.0 + - + +
356A GLU 4.8 0.7 + - - -
376A VAL* 4.2 7.3 - - + +
380A GLN* 4.6 6.2 + - - +
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Residues in contact with ARG 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ILE* 3.6 30.3 + - - +
317A SER* 5.7 7.7 - - - +
320A LEU 5.8 0.2 + - - -
322A ASP* 2.8 51.7 + - - +
327A GLN* 5.0 3.8 - - - +
331A LEU* 3.9 21.7 - - + +
349A PHE* 3.5 52.7 + - + +
350A TYR 3.2 8.0 + - - +
351A GLY 3.2 1.2 - - - -
352A THR* 1.3 77.5 - - + +
354A THR* 1.3 60.5 + - - +
355A MET 3.3 0.2 - - - -
356A GLU 5.1 0.2 - - - -
357A PRO* 3.5 18.0 - - - +
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Residues in contact with THR 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 3.8 20.9 - - + -
331A LEU* 3.8 22.4 - - + -
332A ASP* 4.2 9.6 - - + +
350A TYR 3.4 15.5 - - - +
351A GLY* 2.7 19.4 + - - -
353A ARG* 1.3 76.4 - - - +
355A MET* 1.3 65.5 + - - +
357A PRO* 3.4 2.5 - - - +
358A TYR* 2.9 34.1 + - - +
372A GLN* 3.0 31.5 + - - +
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Residues in contact with MET 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLY 3.7 4.3 - - - +
352A THR* 3.2 24.8 + - + +
353A ARG 3.3 0.2 - - - -
354A THR* 1.3 84.0 - - - +
356A GLU* 1.3 63.3 + - - +
358A TYR* 3.3 6.5 + - + +
359A ARG* 3.1 21.7 + - - +
369A ARG* 5.0 2.9 + - - -
372A GLN* 3.4 40.4 - - + +
373A VAL* 3.9 23.6 - - + +
376A VAL* 3.6 32.8 - - + -
392A ASN* 4.7 11.4 - - - +
395A LEU* 6.2 0.2 - - - -
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Residues in contact with GLU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 6.4 0.9 - - + -
352A THR 4.8 1.0 + - - -
353A ARG 4.7 0.4 + - - -
355A MET* 1.3 74.6 - - - +
357A PRO* 1.3 72.1 - - + +
359A ARG* 2.5 53.5 + - - +
360A ILE* 3.1 30.7 + - + +
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Residues in contact with PRO 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ASP* 4.1 7.2 - - + +
323A ILE* 3.9 38.6 - - + +
328A LEU* 3.7 27.4 - - + -
353A ARG 3.5 19.3 - - - +
354A THR 3.4 8.7 - - - +
356A GLU* 1.3 92.5 - - + +
358A TYR* 1.3 56.1 + - - +
360A ILE* 3.2 5.6 + - + +
361A PHE* 2.9 37.3 + - + -
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 4.4 8.9 - - + +
328A LEU* 4.0 28.5 - - + -
332A ASP* 3.4 27.4 + - + +
354A THR* 2.9 30.1 + - + +
355A MET* 3.7 8.7 - - + +
357A PRO* 1.3 72.7 - - - +
359A ARG* 1.3 60.4 + - - +
362A PHE* 3.0 68.0 + + + +
368A VAL* 3.9 16.7 - - + +
369A ARG* 3.5 20.4 - - + +
372A GLN* 3.5 46.4 + - + -
373A VAL* 6.2 0.2 - - + -
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Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A MET 3.1 12.0 + - - +
356A GLU* 2.5 48.3 + - - +
358A TYR* 1.3 75.4 - - - +
360A ILE* 1.3 82.7 + - - +
362A PHE 4.2 10.4 - - - +
363A PRO* 4.3 5.7 - - - +
369A ARG* 3.5 38.2 + - - +
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Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LYS* 3.4 27.2 - - + -
274A ASP* 5.1 7.6 - - + -
323A ILE* 4.6 15.3 - - + -
356A GLU* 3.1 23.5 + - + +
357A PRO* 3.2 8.9 + - + +
359A ARG* 1.3 110.4 - - - +
361A PHE* 1.3 80.5 + - + +
362A PHE 3.6 0.3 + - - -
363A PRO* 4.0 6.2 - - - +
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A MET* 3.7 24.0 - - - +
243A LEU* 3.7 32.1 - - + -
265A ARG* 5.8 1.0 + - - -
271A LYS* 4.1 14.4 - - + +
274A ASP* 4.0 6.7 - - + -
275A MET* 3.5 51.6 - - + +
323A ILE* 3.3 46.7 - - + -
325A ILE* 3.9 7.6 - - + -
328A LEU* 3.8 10.5 - - + -
357A PRO* 2.9 22.8 + - + +
360A ILE* 1.3 84.9 - - + +
362A PHE* 1.3 61.5 + - + +
363A PRO* 3.3 12.0 - - - +
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Residues in contact with PHE 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP* 4.9 4.0 - - - -
242A MET* 3.5 37.0 - - + -
243A LEU* 3.7 31.4 - - + -
358A TYR* 3.0 54.8 + + - +
359A ARG 4.2 2.8 - - - +
361A PHE* 1.3 81.2 - - + +
363A PRO* 1.3 68.3 - - - +
364A GLY 3.8 4.5 + - - +
366A HIS* 3.6 27.4 + + + +
368A VAL* 3.6 33.2 - - + -
369A ARG* 3.7 30.4 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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