Contacts of the helix formed by residues 344 - 364 (chain A) in PDB entry 3NUI
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 GLY 344 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A VAL 3.7 0.2 + - - -
340A VAL 4.1 3.0 + - - -
341A MET 4.6 2.3 + - - -
342A ASN* 3.5 3.8 + - - +
343A GLU* 1.3 79.5 - - - +
345A LEU* 1.3 60.1 + - - +
346A ALA 3.6 1.6 - - - -
347A GLU* 3.4 24.6 + - - +
348A ASN* 2.9 28.6 + - - +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL 3.8 10.8 - - - +
61A ALA* 3.8 28.7 - - + -
65A HIS* 6.2 1.3 - - + -
339A VAL* 3.7 34.3 - - + +
340A VAL* 3.4 22.1 + - + -
343A GLU* 3.9 10.8 - - + +
344A GLY* 1.3 75.2 - - - +
346A ALA* 1.4 67.1 + - - +
348A ASN* 3.1 16.9 + - + +
349A VAL* 3.2 16.1 + - - +
427A PHE* 3.7 16.5 - - + +
428A ILE* 3.5 25.8 - - + -
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY* 4.6 15.1 - - - +
266A GLY* 5.6 0.3 - - - -
267A ASN 6.3 0.9 - - - -
268A THR* 6.3 0.9 - - - -
340A VAL* 3.0 33.8 + - + +
341A MET* 5.0 7.6 - - + +
345A LEU* 1.4 75.7 - - - +
347A GLU* 1.3 62.1 + - - +
349A VAL* 3.2 10.8 + - - +
350A ARG* 3.2 39.6 + - - +
427A PHE* 4.6 2.5 - - - -
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A VAL 4.7 0.4 + - - -
344A GLY* 3.4 22.0 + - - +
345A LEU 3.2 0.4 - - - -
346A ALA* 1.3 76.7 - - - +
348A ASN* 1.3 59.4 + - - +
349A VAL 3.3 0.2 + - - -
350A ARG* 3.4 30.7 + - + +
351A ARG* 2.9 76.2 + - - +
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Residues in contact with ASN 348 (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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344A GLY 2.9 18.0 + - - +
345A LEU* 3.1 11.0 + - + +
347A GLU* 1.3 72.7 - - - +
349A VAL* 1.3 57.4 + - - +
351A ARG* 3.7 6.9 - - - +
352A LEU* 2.8 49.9 + - - +
377A PHE* 4.5 3.2 - - - -
427A PHE 2.7 23.8 + - - +
428A ILE* 4.0 3.0 + - - +
429A LEU 2.8 25.3 + - - +
430A THR* 5.6 0.5 - - - -
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 3.5 19.1 - - - +
266A GLY* 4.3 6.3 - - - -
345A LEU 3.2 6.7 + - - +
346A ALA* 3.5 7.4 - - - +
347A GLU 3.2 0.6 - - - -
348A ASN* 1.3 78.1 - - - +
350A ARG* 1.3 57.6 - - - +
353A ALA* 2.9 30.0 + - - +
376A GLY* 4.0 9.2 - - - -
377A PHE* 3.8 41.8 - - + +
427A PHE* 3.4 48.2 - - + -
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Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY* 3.5 34.7 + - - +
267A ASN* 5.7 3.0 - - - +
346A ALA* 3.2 27.9 + - - +
347A GLU* 3.4 38.0 + - - +
349A VAL* 1.3 78.1 - - - +
351A ARG* 1.3 64.5 + - + +
353A ALA* 4.0 4.7 - - - +
354A PRO* 3.4 17.8 - - - +
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A GLU* 2.9 56.3 + - + +
348A ASN* 3.9 7.2 - - - +
350A ARG* 1.3 75.1 - - + +
352A LEU* 1.3 68.3 + - + +
354A PRO* 3.4 12.1 - - - +
355A ARG* 4.8 9.0 + - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 2.8 36.4 + - - +
351A ARG* 1.3 77.0 - - + +
353A ALA* 1.3 65.6 + - - +
354A PRO* 3.3 3.8 - - - -
355A ARG* 3.1 43.1 + - + +
356A PHE* 2.9 21.5 + - - +
377A PHE* 3.7 15.7 - - + -
429A LEU 3.3 26.2 - - - +
430A THR* 4.0 16.4 - - - -
431A GLU* 4.1 10.1 - - + +
434A MET* 3.8 17.6 - - + +
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Residues in contact with ALA 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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266A GLY* 6.4 0.4 - - - -
349A VAL 2.9 19.6 + - - +
350A ARG* 4.0 6.1 - - - +
352A LEU* 1.3 77.4 - - - +
354A PRO* 1.4 69.1 - - + +
356A PHE* 3.3 5.3 + - - +
357A GLU* 2.9 25.4 + - - +
376A GLY* 3.5 36.6 - - - +
377A PHE* 4.2 1.1 - - - -
379A TRP* 4.4 3.4 - - + -
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Residues in contact with PRO 354 (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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350A ARG 3.4 16.8 - - - +
351A ARG* 3.4 9.4 - - - +
352A LEU 3.3 5.2 - - - -
353A ALA* 1.4 91.2 - - + +
355A ARG* 1.3 57.2 + - + +
357A GLU* 3.3 7.9 + - + +
358A GLU* 2.9 28.2 + - - +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ARG* 4.8 8.5 + - - +
352A LEU* 3.1 36.6 + - - +
354A PRO* 1.3 77.2 - - + +
356A PHE* 1.3 68.0 + - - +
358A GLU* 3.9 7.3 - - - +
359A ARG* 3.0 25.3 + - - +
431A GLU* 3.7 36.1 - - - +
434A MET* 4.2 10.6 - - - +
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Residues in contact with PHE 356 (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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352A LEU 2.9 11.3 + - - +
353A ALA* 3.3 11.4 - - - +
355A ARG* 1.3 81.1 - - - +
357A GLU* 1.3 62.6 + - - +
359A ARG 3.4 0.2 + - - -
360A LEU* 3.3 31.4 + - + +
377A PHE* 3.7 23.6 - + - -
379A TRP* 3.4 32.5 - + - +
423A LEU* 3.9 19.7 - - + -
425A PRO* 3.7 37.9 - - + -
429A LEU* 5.2 0.4 - - + -
434A MET* 3.6 28.4 - - + -
437A MET* 4.6 5.2 - - - -
438A PHE* 3.4 28.0 - + - -
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Residues in contact with GLU 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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353A ALA 2.9 15.9 + - - +
354A PRO* 3.7 7.5 - - + +
356A PHE* 1.3 74.8 - - - +
358A GLU* 1.3 68.6 + - - +
360A LEU* 3.3 7.7 + - - +
361A LYS* 2.9 25.2 + - + +
372A TYR* 2.9 33.8 + - + +
379A TRP* 3.8 27.0 - - + -
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Residues in contact with GLU 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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354A PRO 2.9 17.4 + - - +
355A ARG* 3.9 7.9 - - - +
357A GLU* 1.3 80.3 - - - +
359A ARG* 1.3 62.7 + - - +
361A LYS* 3.4 11.6 + - + +
362A HIS* 3.0 21.5 + - - +
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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 ARG 3.0 16.4 + - - +
357A GLU 3.2 0.2 - - - -
358A GLU* 1.3 78.0 - - - +
360A LEU* 1.3 61.1 + - - +
362A HIS* 3.3 13.5 + - - +
363A ILE* 3.0 23.3 + - + +
435A ASP* 3.7 37.4 + - - +
438A PHE* 3.3 49.9 - - + +
439A ASP* 3.3 20.0 + - - -
442A GLU* 3.1 34.3 + - - -
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Residues in contact with LEU 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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356A PHE* 3.3 28.1 + - + +
357A GLU* 3.5 7.9 - - - +
359A ARG* 1.3 74.2 - - - +
361A LYS* 1.3 56.2 + - - +
363A ILE* 3.2 7.0 + - + +
364A ALA* 2.8 35.3 + - - +
372A TYR* 3.9 24.7 - - + +
379A TRP* 3.4 49.8 - - + -
380A ALA 5.2 0.9 - - - +
381A LEU* 3.7 30.9 - - + +
423A LEU* 4.9 5.6 - - + -
438A PHE* 3.5 22.0 - - + -
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Residues in contact with LYS 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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357A GLU* 2.9 22.3 + - + +
358A GLU* 3.5 12.8 - - + +
360A LEU* 1.3 71.0 - - - +
362A HIS* 1.3 66.0 + - - +
364A ALA* 3.3 10.8 + - - +
365A GLU* 3.5 15.4 + - + +
372A TYR* 3.7 34.7 - - + +
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Residues in contact with HIS 362 (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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358A GLU 3.0 14.1 + - - +
359A ARG* 3.6 14.4 - - - +
360A LEU 3.3 0.4 - - - -
361A LYS* 1.3 74.6 - - - +
363A ILE* 1.3 64.8 + - - +
365A GLU* 3.1 51.6 + - + +
366A ARG* 4.4 1.0 + - - +
442A GLU* 4.0 17.5 - - - -
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Residues in contact with ILE 363 (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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359A ARG* 3.0 12.7 + - + +
360A LEU* 3.2 8.7 + - - +
362A HIS* 1.3 75.3 - - - +
364A ALA* 1.3 57.3 + - - +
366A ARG* 3.0 42.0 + - - +
369A ILE* 3.6 6.1 - - + +
381A LEU* 4.0 21.5 - - + -
438A PHE* 3.7 33.7 - - + -
441A LEU* 4.2 12.6 - - + -
442A GLU* 3.4 37.5 - - + +
445A LEU* 3.7 23.8 - - + -
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU 2.8 18.8 + - - +
361A LYS* 3.7 6.5 - - - +
362A HIS 3.3 0.2 - - - -
363A ILE* 1.3 69.6 - - - +
365A GLU* 1.3 59.9 + - - +
366A ARG 3.2 2.5 - - - +
369A ILE* 3.7 28.1 - - + +
371A GLU* 4.6 2.9 - - - -
372A TYR* 3.7 27.6 - - + +
387A LYS* 3.1 19.9 + - - -
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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