Contacts of the helix formed by residues 350 - 362 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B THR* 3.6 1.6 - - - +
316B ASN* 3.8 18.9 - - - +
349B GLY* 1.3 73.5 - - - -
351B ALA* 1.3 65.4 + - - +
352B GLN* 3.3 6.2 + - - +
353B LYS* 3.6 20.8 + - - +
354B ILE* 3.4 24.6 + - - +
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Residues in contact with ALA 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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311B SER* 4.2 7.6 - - - +
312B PRO 3.3 18.8 - - - +
313B THR* 3.1 24.7 - - + +
317B ASP 3.5 13.4 + - - +
318B ILE* 3.6 18.8 - - + +
350B GLY* 1.3 79.4 - - - +
352B GLN* 1.3 57.3 + - - +
354B ILE* 3.4 0.6 + - - -
355B LEU* 2.9 34.3 + - + +
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Residues in contact with GLN 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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313B THR* 4.6 1.6 - - - +
341B ALA* 3.0 42.0 + - - +
342B PHE* 3.6 12.9 - - - -
343B GLY* 4.0 1.4 + - - +
350B GLY 3.3 3.4 - - - +
351B ALA* 1.3 76.3 - - - +
353B LYS* 1.3 65.9 + - + +
355B LEU* 3.4 5.8 + - - +
356B GLU* 2.8 55.6 + - - +
370B PRO* 5.2 2.0 - - + -
371B GLY 3.7 13.2 - - - +
372B PRO 3.6 17.2 - - - +
373B THR* 4.1 14.4 + - - +
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Residues in contact with LYS 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 GLY 6.3 0.4 - - - -
350B GLY* 3.6 18.9 + - - +
351B ALA 3.3 0.2 - - - -
352B GLN* 1.3 77.3 - - + +
354B ILE* 1.3 60.8 + - + +
356B GLU* 3.2 10.6 + - - +
357B GLU* 2.8 32.8 + - - +
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Residues in contact with ILE 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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327A ASP* 5.6 0.2 - - - +
316B ASN 4.1 4.0 - - - +
317B ASP* 2.9 51.1 - - - +
318B ILE* 3.9 16.4 - - + +
350B GLY 3.4 13.4 + - - +
351B ALA 3.4 5.1 + - - +
352B GLN 3.3 0.4 - - - -
353B LYS* 1.3 77.7 - - + +
355B LEU* 1.3 62.4 + - - +
357B GLU* 3.4 16.3 + - - +
358B ARG* 3.0 62.0 + - + +
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Residues in contact with LEU 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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309B VAL* 3.8 31.9 - - + +
311B SER* 4.0 17.9 - - - +
318B ILE* 4.0 12.6 - - + -
322B VAL* 4.2 6.1 - - + -
326B LEU* 3.6 28.2 - - + +
341B ALA* 3.6 19.5 - - + -
342B PHE 3.7 23.6 - - - +
351B ALA 2.9 25.4 + - - +
352B GLN* 3.8 5.2 - - - +
354B ILE* 1.3 77.9 - - - +
356B GLU* 1.3 58.7 + - - +
358B ARG* 3.4 2.1 + - - +
359B LEU* 2.9 32.9 + - + +
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Residues in contact with GLU 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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341B ALA* 4.1 5.3 + - + +
352B GLN* 2.8 56.5 + - - +
353B LYS* 3.9 7.5 - - - +
355B LEU* 1.3 72.7 - - - +
357B GLU* 1.3 67.0 + - - +
359B LEU* 3.8 3.6 - - - +
360B LYS* 2.9 42.3 + - - +
366B LEU* 3.1 30.3 - - + -
368B ALA 4.5 0.3 - - - +
369B GLU* 5.2 0.2 - - - -
370B PRO* 3.4 19.7 - - - +
371B GLY* 3.0 19.9 + - - -
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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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358A ARG* 6.0 0.2 + - - -
353B LYS 2.8 18.3 + - - +
354B ILE* 3.4 29.0 - - - +
356B GLU* 1.3 77.4 - - - +
358B ARG* 1.3 73.0 + - - +
360B LYS* 3.2 10.7 + - - +
361B ALA* 2.9 28.5 + - + +
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Residues in contact with ARG 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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327A ASP* 2.6 37.8 + - - -
358A ARG* 2.7 39.4 - - - +
318B ILE* 4.7 5.9 - - - +
323B SER* 4.3 5.9 + - - +
326B LEU* 4.0 32.7 - - + +
327B ASP* 3.4 16.3 + - - -
329B LEU* 5.8 0.2 - - - +
330B VAL* 3.4 19.6 - - + +
354B ILE* 3.0 51.1 + - + +
355B LEU 4.0 2.5 - - - +
357B GLU* 1.3 90.3 + - - +
359B LEU* 1.3 62.7 + - - +
361B ALA* 3.3 7.0 + - - -
362B ALA* 3.2 17.8 + - - +
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Residues in contact with LEU 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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307B VAL* 4.7 4.3 - - + +
309B VAL* 4.4 23.8 - - + -
326B LEU* 4.5 10.3 - - + -
329B LEU* 4.5 9.0 - - + -
339B GLY 5.1 0.2 - - - -
340B LEU 3.8 33.2 - - - +
341B ALA* 4.2 10.3 - - + -
355B LEU* 2.9 20.3 + - + +
356B GLU 3.8 3.8 - - - +
358B ARG* 1.3 76.5 - - - +
360B LYS* 1.3 62.2 + - - +
362B ALA* 3.2 9.1 + - + +
364B ILE* 3.1 58.7 + - + +
366B LEU* 4.0 19.5 - - + -
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Residues in contact with LYS 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 GLU* 2.9 35.3 + - - +
357B GLU* 3.6 7.2 - - - +
359B LEU* 1.3 72.7 - - - +
361B ALA* 1.3 55.1 + - - +
362B ALA 3.0 4.5 - - - -
363B LYS* 2.6 33.7 + - - +
364B ILE 4.1 9.6 - - - +
365B GLU* 6.0 0.4 - - - -
366B LEU* 3.9 27.7 - - + +
369B GLU* 4.5 14.5 + - - -
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Residues in contact with ALA 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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330B VAL* 3.7 29.5 - - + +
333B ARG* 5.7 1.2 - - - +
357B GLU* 2.9 15.2 + - + +
358B ARG* 3.5 13.2 - - - +
359B LEU 3.3 0.4 - - - -
360B LYS* 1.3 76.0 - - - +
362B ALA* 1.3 58.6 + - - +
363B LYS* 3.1 11.9 + - - +
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Residues in contact with ALA 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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329B LEU* 3.5 39.0 - - + +
330B VAL* 3.7 10.8 - - - +
333B ARG* 4.4 4.3 - - - +
334B PRO* 3.7 19.8 - - + +
358B ARG 3.2 10.1 + - - +
359B LEU* 3.6 10.1 - - - +
360B LYS 3.0 1.2 - - - -
361B ALA* 1.3 75.8 - - - +
363B LYS* 1.3 72.8 + - - +
364B ILE* 3.2 13.5 + - + +
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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