Contacts of the helix formed by residues 350 - 362 (chain D) in PDB entry 1YCH
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 350 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313D THR* 3.8 0.8 - - - +
316D ASN* 3.8 19.6 - - - +
349D GLY* 1.3 74.4 - - - -
351D ALA* 1.3 64.2 + - - +
352D GLN* 3.3 5.7 + - - +
353D LYS* 3.6 10.2 + - - +
354D ILE* 3.6 22.5 + - - +
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D SER* 4.1 10.1 - - - +
312D PRO 3.3 27.8 - - - +
313D THR* 3.6 14.3 - - + +
317D ASP 3.7 17.2 + - - +
318D ILE* 3.9 11.6 - - + +
350D GLY* 1.3 77.8 - - - +
352D GLN* 1.3 58.1 + - - +
354D ILE* 3.3 4.3 + - - +
355D LEU* 2.8 34.2 + - + +
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Residues in contact with GLN 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D SER 5.2 0.7 - - - +
313D THR* 5.0 1.4 - - - +
341D ALA* 2.7 35.7 + - - +
342D PHE* 3.4 23.9 - - - +
343D GLY* 3.7 6.4 + - - +
350D GLY 3.3 3.7 - - - +
351D ALA* 1.3 80.5 - - - +
353D LYS* 1.3 60.9 + - - +
355D LEU* 3.5 5.1 + - - +
356D GLU* 3.1 47.2 + - - +
370D PRO* 5.4 2.5 - - + -
371D GLY* 3.5 21.6 - - - +
372D PRO 4.0 1.8 - - - +
373D THR* 4.7 11.1 + - - +
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Residues in contact with LYS 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D GLY* 3.6 11.0 + - - +
351D ALA 3.3 0.4 - - - -
352D GLN* 1.3 78.2 - - - +
354D ILE* 1.3 61.2 - - + +
356D GLU* 3.3 8.1 + - - +
357D GLU* 2.9 39.9 + - + +
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Residues in contact with ILE 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ASP* 5.2 1.3 - - - +
316D ASN 4.3 2.9 - - - +
317D ASP* 3.1 43.5 - - - +
318D ILE* 4.2 17.7 - - + +
326D LEU* 5.3 1.8 - - + -
350D GLY 3.6 10.5 + - - +
351D ALA* 3.3 7.9 + - - +
353D LYS* 1.3 79.7 - - + +
355D LEU* 1.3 64.8 + - - +
357D GLU* 3.4 13.1 + - - +
358D ARG* 3.0 54.9 + - + +
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Residues in contact with LEU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D VAL* 3.8 30.7 - - + +
311D SER* 4.0 17.0 - - - +
318D ILE* 3.7 18.8 - - + -
322D VAL* 4.1 2.9 - - + -
326D LEU* 3.7 27.2 - - + +
341D ALA* 3.7 17.3 - - + -
342D PHE 3.7 22.4 - - - +
351D ALA 2.8 24.0 + - - +
352D GLN* 3.8 5.2 - - - +
354D ILE* 1.3 76.8 - - - +
356D GLU* 1.3 59.0 + - - +
358D ARG* 3.9 3.7 - - - +
359D LEU* 2.9 35.8 + - + +
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Residues in contact with GLU 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D ALA* 3.8 15.6 + - + +
352D GLN* 3.1 37.1 + - - +
353D LYS* 3.9 5.8 - - - +
355D LEU* 1.3 74.0 - - - +
357D GLU* 1.3 67.4 + - - +
359D LEU* 3.8 3.4 - - - +
360D LYS* 2.9 33.3 + - + +
366D LEU* 3.4 25.3 - - + +
368D ALA 4.1 2.6 - - - +
369D GLU* 3.5 20.5 - - - +
370D PRO* 3.5 10.9 - - - +
371D GLY* 3.1 28.8 + - - -
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Residues in contact with GLU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D LYS* 2.9 25.0 + - + +
354D ILE* 3.6 24.0 - - - +
356D GLU* 1.3 78.7 - - - +
358D ARG* 1.3 73.6 + - + +
360D LYS* 3.2 9.5 + - - +
361D ALA* 2.9 28.9 + - + +
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Residues in contact with ARG 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ASP* 2.4 44.7 + - - -
358C ARG* 3.1 24.2 - - - +
318D ILE* 5.2 1.2 - - - +
323D SER* 4.3 3.0 + - - +
326D LEU* 4.0 38.7 - - + +
327D ASP* 3.2 22.6 + - - -
330D VAL* 3.4 17.3 - - + +
354D ILE* 3.0 40.7 + - + +
355D LEU 4.0 2.7 - - - +
357D GLU* 1.3 86.6 + - + +
359D LEU* 1.3 65.1 + - - +
361D ALA* 3.4 6.9 + - - -
362D ALA* 3.2 18.0 + - - +
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D VAL* 4.7 4.3 - - + +
309D VAL* 4.2 26.0 - - + -
326D LEU* 4.5 10.5 - - + -
329D LEU* 4.3 9.2 - - + -
339D GLY* 5.1 0.9 - - - -
340D LEU 3.9 27.6 - - - +
341D ALA* 4.2 8.5 - - + -
355D LEU* 2.9 21.2 + - + +
356D GLU 3.9 3.4 - - - +
357D GLU 3.3 0.2 - - - -
358D ARG* 1.3 78.1 - - - +
360D LYS* 1.3 60.7 + - - +
362D ALA* 3.3 7.2 + - + +
364D ILE* 3.1 57.8 + - + +
366D LEU* 4.1 23.8 - - + -
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Residues in contact with LYS 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D GLU* 2.9 19.8 + - - +
357D GLU* 3.7 6.7 - - - +
359D LEU* 1.3 74.2 - - - +
361D ALA* 1.3 56.5 + - - +
362D ALA 3.0 2.0 - - - -
363D LYS* 2.7 33.0 + - - +
364D ILE 4.1 8.1 - - - +
365D GLU* 6.0 0.2 - - - -
366D LEU* 3.3 37.7 - - + +
369D GLU* 3.2 23.8 + - - +
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Residues in contact with ALA 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D VAL* 3.7 28.4 - - + +
333D ARG* 5.8 1.2 - - - +
357D GLU* 2.9 18.7 + - + +
358D ARG* 3.6 9.2 - - - +
359D LEU 3.3 0.4 - - - -
360D LYS* 1.3 75.6 - - - +
362D ALA* 1.3 56.5 + - - +
363D LYS* 3.0 16.9 + - - +
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Residues in contact with ALA 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D LEU* 3.5 35.9 - - + +
330D VAL* 3.7 11.2 - - - +
333D ARG* 4.4 3.4 - - - -
334D PRO* 3.4 21.6 - - + +
358D ARG 3.2 12.3 + - - +
359D LEU* 3.6 10.3 - - - +
360D LYS 3.0 0.6 - - - -
361D ALA* 1.3 74.9 - - - +
363D LYS* 1.3 72.0 + - - +
364D ILE* 3.2 12.8 + - + +
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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