Contacts of the helix formed by residues 344 - 364 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B VAL 4.3 2.0 + - - -
341B MET 4.8 3.0 + - - -
342B ASN* 3.5 4.4 + - - +
343B GLU* 1.3 77.4 - - - +
345B LEU* 1.3 60.1 + - - +
346B ALA 3.5 2.0 - - - -
347B GLU* 3.5 15.1 - - - +
348B ASN* 2.8 29.0 + - - +
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Residues in contact with LEU 345 (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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60B VAL 3.8 10.5 - - - +
61B ALA* 3.6 37.0 - - + -
65B HIS* 5.4 4.0 - - + +
339B VAL* 3.8 28.9 - - + +
340B VAL* 3.5 16.7 + - + +
343B GLU* 3.4 14.8 - - + +
344B GLY* 1.3 80.1 - - - +
346B ALA* 1.3 63.5 + - - +
348B ASN* 3.1 16.8 + - - +
349B VAL* 3.2 10.2 + - - +
427B PHE* 3.6 26.6 - - + +
428B ILE* 3.8 22.0 - - + -
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Residues in contact with ALA 346 (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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263B GLY* 4.7 14.6 - - - +
266B GLY* 5.4 1.3 - - - -
267B ASN 6.1 1.8 - - - -
268B THR* 6.1 2.0 - - - +
340B VAL* 2.9 34.7 + - + +
341B MET* 4.8 8.3 - - + +
345B LEU* 1.3 75.6 - - - +
347B GLU* 1.3 62.2 + - - +
349B VAL* 3.3 16.4 + - - +
350B ARG* 3.4 19.4 + - - +
427B PHE* 4.6 6.3 - - - -
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Residues in contact with GLU 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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340B VAL 4.8 0.2 + - - -
341B MET 5.8 1.0 + - - +
344B GLY* 3.4 18.7 + - - +
345B LEU 3.2 0.2 - - - -
346B ALA* 1.3 77.3 - - - +
348B ASN* 1.3 60.4 + - - +
350B ARG* 3.1 25.7 + - - +
351B ARG* 2.8 39.4 + - + +
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Residues in contact with ASN 348 (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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344B GLY 2.8 18.2 + - - +
345B LEU* 3.1 10.3 + - - +
347B GLU* 1.3 73.9 - - - +
349B VAL* 1.3 57.0 + - - +
351B ARG* 4.3 7.8 - - - +
352B LEU* 2.9 50.1 + - - +
377B PHE* 4.2 3.3 - - - -
427B PHE 2.7 23.4 + - - +
428B ILE* 3.9 3.2 - - - +
429B LEU 2.8 27.5 + - - +
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Residues in contact with VAL 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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263B GLY 3.5 20.2 - - - +
264B ARG 3.9 0.2 - - - +
266B GLY* 4.0 7.4 - - - +
345B LEU 3.2 6.9 + - - +
346B ALA* 3.4 9.0 - - - +
348B ASN* 1.3 75.5 - - - +
350B ARG* 1.3 62.9 + - - +
353B ALA* 3.0 28.5 + - - +
376B GLY* 3.9 8.7 - - - -
377B PHE* 3.7 40.8 - - + +
427B PHE* 3.3 49.6 - - + -
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Residues in contact with ARG 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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266B GLY* 2.8 45.2 + - - +
267B ASN* 3.2 20.0 + - - +
346B ALA* 3.4 14.8 + - - +
347B GLU* 3.1 30.2 + - - +
349B VAL* 1.3 77.2 - - - +
351B ARG* 1.3 65.0 + - - +
353B ALA* 4.0 4.9 - - - +
354B PRO* 3.5 17.3 - - - +
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Residues in contact with ARG 351 (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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347B GLU* 2.8 26.7 + - + +
348B ASN* 3.9 9.4 - - - +
350B ARG* 1.3 78.4 - - - +
352B LEU* 1.3 68.7 + - + +
354B PRO* 3.5 13.2 - - - +
355B ARG* 3.1 46.6 + - - +
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Residues in contact with LEU 352 (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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348B ASN* 2.9 33.2 + - - +
351B ARG* 1.3 81.9 - - + +
353B ALA* 1.3 59.8 + - - +
354B PRO* 3.4 3.6 - - - -
355B ARG* 3.1 36.8 + - + +
356B PHE* 3.0 25.6 + - - +
377B PHE* 3.8 17.9 - - + -
429B LEU* 3.3 27.6 - - + +
430B THR* 3.9 18.8 - - - +
431B GLU* 4.0 13.9 - - + +
434B MET* 4.2 12.2 - - + +
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Residues in contact with ALA 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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349B VAL 3.0 17.8 + - - +
350B ARG* 4.0 5.4 - - - +
352B LEU* 1.3 76.5 - - - +
354B PRO* 1.4 68.4 - - + +
356B PHE* 3.1 6.4 + - - +
357B GLU* 3.0 23.8 + - - +
376B GLY* 3.5 36.8 - - - +
377B PHE* 4.3 0.8 - - - -
379B TRP* 4.1 4.4 - - + -
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Residues in contact with PRO 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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350B ARG 3.5 16.8 - - - +
351B ARG 3.5 12.8 - - - +
352B LEU 3.5 0.9 - - - -
353B ALA* 1.4 89.7 - - + +
355B ARG* 1.3 57.7 + - + +
357B GLU* 3.3 8.4 + - + +
358B GLU* 3.0 37.4 + - + +
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Residues in contact with ARG 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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351B ARG* 3.1 43.4 + - - +
352B LEU* 3.1 34.0 + - - +
354B PRO* 1.3 77.0 - - + +
356B PHE* 1.3 67.4 + - - +
358B GLU* 3.6 20.9 - - - +
359B ARG* 3.3 22.7 + - - +
431B GLU* 3.3 31.2 + - - +
434B MET* 3.9 20.7 - - + +
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Residues in contact with PHE 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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352B LEU 3.0 10.4 + - - +
353B ALA 3.2 10.1 - - - +
355B ARG* 1.3 77.1 - - - +
357B GLU* 1.3 63.2 + - - +
359B ARG* 3.4 2.8 + - - +
360B LEU* 3.2 29.7 + - + +
376B GLY 4.0 0.2 - - - -
377B PHE* 3.9 28.0 - + - -
379B TRP* 3.5 38.8 - + - +
423B LEU* 4.0 15.9 - - + -
425B PRO* 3.7 33.7 - - + -
429B LEU* 5.2 1.1 - - + -
434B MET* 3.8 14.9 - - - -
437B MET* 3.6 19.7 - - + -
438B PHE* 3.3 30.7 - + - -
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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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353B ALA 3.0 13.0 + - - +
354B PRO* 3.9 7.2 - - + +
355B ARG 3.2 0.2 - - - -
356B PHE* 1.3 74.5 - - - +
358B GLU* 1.4 65.9 - - - +
360B LEU* 3.1 7.0 + - - +
361B LYS* 2.8 24.7 + - + +
372B TYR* 2.5 37.8 + - + +
379B TRP* 3.5 28.7 - - + -
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Residues in contact with GLU 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 PRO* 3.0 19.7 + - + +
355B ARG* 3.6 32.1 + - - +
357B GLU* 1.4 75.3 - - - +
359B ARG* 1.3 64.3 + - + +
361B LYS* 3.4 9.5 + - - +
362B HIS* 3.1 21.8 + - - +
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Residues in contact with ARG 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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355B ARG 3.3 14.2 + - - +
356B PHE 3.8 3.6 - - - +
357B GLU 3.2 0.6 - - - -
358B GLU* 1.3 80.3 - - - +
360B LEU* 1.3 60.1 + - - +
362B HIS* 3.3 13.0 + - - +
363B ILE* 3.0 32.0 + - - +
434B MET* 5.3 2.5 - - + -
435B ASP* 3.8 25.6 + - - +
438B PHE* 3.4 49.2 - - + +
439B ASP* 2.9 29.1 + - - +
442B GLU* 3.1 35.6 + - - +
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Residues in contact with LEU 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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356B PHE* 3.2 22.4 + - + +
357B GLU* 3.4 7.4 - - - +
359B ARG* 1.3 76.6 - - - +
361B LYS* 1.3 59.6 + - - +
363B ILE* 3.1 8.1 + - + +
364B ALA* 2.8 30.3 + - - +
372B TYR* 3.9 25.6 - - + +
379B TRP* 3.4 50.3 - - + -
380B ALA 5.4 1.1 - - - +
381B LEU* 4.1 23.4 - - + +
423B LEU* 4.4 5.2 - - + -
438B PHE* 3.2 31.0 - - + -
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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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357B GLU* 2.8 17.8 + - + +
358B GLU* 3.5 10.5 - - - +
360B LEU* 1.3 76.2 - - - +
362B HIS* 1.3 62.2 + - - +
364B ALA* 3.2 15.8 + - - +
365B GLU* 3.6 11.0 + - - +
372B TYR* 3.7 32.4 - - + +
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Residues in contact with HIS 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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358B GLU 3.1 10.4 + - - +
359B ARG* 3.6 15.9 - - - +
360B LEU 3.2 0.2 - - - -
361B LYS* 1.3 75.9 - - - +
363B ILE* 1.3 65.3 + - - +
365B GLU* 3.2 47.2 + - - +
366B ARG* 4.6 1.2 + - - +
442B GLU* 4.3 16.6 - - - -
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Residues in contact with ILE 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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359B ARG* 3.0 17.3 + - + +
360B LEU* 3.1 9.2 + - + +
362B HIS* 1.3 75.9 - - - +
364B ALA* 1.3 57.4 + - - +
365B GLU 3.0 5.4 + - - -
366B ARG* 3.1 31.5 + - - +
369B ILE* 3.7 6.4 - - + +
381B LEU* 4.1 22.2 - - + -
438B PHE* 3.6 33.7 - - + -
441B LEU* 4.2 11.7 - - + -
442B GLU* 3.3 39.0 - - + +
445B LEU* 3.6 24.9 - - + -
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Residues in contact with ALA 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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360B LEU 2.8 12.6 + - - +
361B LYS 3.2 11.6 + - - +
363B ILE* 1.3 72.6 - - - +
365B GLU* 1.3 58.7 + - - +
366B ARG 3.1 3.7 - - - +
369B ILE* 3.7 26.4 - - + +
370B GLY 5.7 0.2 - - - -
371B GLU* 4.6 2.7 - - - -
372B TYR* 4.1 24.5 - - + +
387B LYS* 2.9 23.4 + - - -
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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
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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