Contacts of the helix formed by residues 350 - 362 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A THR* 3.7 1.2 - - - +
316A ASN* 3.9 17.8 - - - +
349A GLY* 1.3 74.7 - - - -
351A ALA* 1.3 66.4 + - - +
352A GLN* 3.3 5.5 + - - +
353A LYS* 3.6 16.2 + - - +
354A ILE* 3.3 23.7 + - - +
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Residues in contact with ALA 351 (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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311A SER* 4.2 8.5 - - - +
312A PRO 3.3 27.4 - - - +
313A THR* 3.3 15.6 - - + +
317A ASP 3.7 12.5 + - - +
318A ILE* 3.8 17.7 - - + -
350A GLY* 1.3 75.8 - - - +
352A GLN* 1.3 61.8 + - - +
354A ILE* 3.4 1.4 + - - +
355A LEU* 2.8 37.0 + - + +
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Residues in contact with GLN 352 (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 THR* 4.7 1.8 - - - +
341A ALA* 2.7 50.0 + - - +
342A PHE* 3.8 9.1 - - - -
343A GLY* 3.9 0.9 + - - +
350A GLY* 3.3 4.6 - - - +
351A ALA* 1.3 79.1 - - - +
353A LYS* 1.3 58.0 + - + +
355A LEU* 3.7 5.1 - - - +
356A GLU* 3.0 53.6 + - - +
370A PRO* 5.3 2.5 - - + -
371A GLY* 3.9 13.2 - - - +
372A PRO 3.3 11.4 - - - +
373A THR* 3.3 25.4 + - - +
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Residues in contact with LYS 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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350A GLY* 3.7 17.5 - - - +
351A ALA 3.3 0.2 - - - -
352A GLN* 1.3 78.3 - - + +
354A ILE* 1.3 60.7 + - + +
356A GLU* 3.3 9.2 + - - +
357A GLU* 2.9 32.3 + - - +
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Residues in contact with ILE 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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316A ASN 3.9 4.5 - - - +
317A ASP* 3.2 42.8 - - - +
318A ILE* 3.7 18.8 - - + +
350A GLY 3.3 17.7 - - - +
351A ALA 3.7 5.2 - - - +
353A LYS* 1.3 78.8 - - + +
355A LEU* 1.3 61.1 + - - +
357A GLU* 3.4 9.1 + - - +
358A ARG* 3.0 63.5 + - + +
327B ASP* 5.0 0.4 - - - +
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Residues in contact with LEU 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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309A VAL* 4.1 25.6 - - + +
311A SER* 3.9 21.8 - - - +
318A ILE* 4.0 11.4 - - + -
322A VAL* 4.3 6.5 - - + -
326A LEU* 3.5 30.6 - - + +
341A ALA* 3.6 17.3 - - + -
342A PHE 3.8 22.9 - - - +
351A ALA 2.8 32.6 + - - +
352A GLN* 3.7 5.6 - - - +
354A ILE* 1.3 73.6 - - - +
356A GLU* 1.3 58.4 + - - +
358A ARG* 3.4 1.7 + - - +
359A LEU* 2.8 35.9 + - + +
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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
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341A ALA* 3.9 12.8 + - + +
352A GLN* 3.0 40.1 + - - +
353A LYS* 3.9 8.3 - - - +
355A LEU* 1.3 71.5 - - - +
357A GLU* 1.3 67.7 + - - +
359A LEU* 3.6 4.1 - - - +
360A LYS* 2.9 34.5 + - + +
366A LEU* 3.4 25.1 - - + -
368A ALA 4.5 1.2 - - - +
369A GLU* 3.8 17.5 - - - +
370A PRO* 3.6 9.3 - - - +
371A GLY* 3.2 28.2 + - - -
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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 LYS 2.9 18.3 + - - +
354A ILE* 3.6 8.9 - - - +
356A GLU* 1.3 75.7 - - - +
358A ARG* 1.3 87.8 + - - +
360A LYS* 3.1 16.8 + - - +
361A ALA* 2.8 31.0 + - + +
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Residues in contact with ARG 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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318A ILE* 4.7 2.4 - - - +
323A SER* 4.6 2.4 + - - +
326A LEU* 4.1 36.5 - - + +
327A ASP* 3.7 21.7 + - - -
330A VAL* 3.6 16.5 - - + +
354A ILE* 3.0 36.0 + - + +
355A LEU 3.9 2.5 - - - +
357A GLU* 1.3 99.0 + - - +
359A LEU* 1.3 61.3 + - - +
361A ALA* 3.3 10.5 + - - +
362A ALA* 3.2 18.7 + - - +
327B ASP* 2.6 42.2 + - - -
358B ARG* 2.7 29.2 - - - +
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Residues in contact with LEU 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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307A VAL* 5.0 4.3 - - + +
309A VAL* 4.5 24.7 - - + +
326A LEU* 4.5 12.6 - - + -
329A LEU* 5.0 4.5 - - + -
340A LEU 4.0 22.4 - - - +
341A ALA* 4.0 15.7 - - + -
355A LEU* 2.8 21.9 + - + +
356A GLU 3.6 4.5 - - - +
358A ARG* 1.3 78.5 - - - +
360A LYS* 1.3 61.4 + - - +
362A ALA* 3.3 7.7 + - + +
364A ILE* 3.1 64.0 + - + +
366A LEU* 3.9 21.1 - - + -
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Residues in contact with LYS 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 GLU* 2.9 26.7 + - + +
357A GLU* 3.5 14.1 - - - +
359A LEU* 1.3 71.8 - - - +
361A ALA* 1.3 59.6 + - - +
362A ALA 3.0 1.8 - - - -
363A LYS* 2.6 27.3 + - - +
364A ILE 4.2 8.5 - - - +
366A LEU* 4.0 14.1 - - + +
369A GLU* 2.8 32.7 + - - +
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Residues in contact with ALA 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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330A VAL* 3.6 17.0 - - + +
333A ARG* 3.1 28.5 + - - +
357A GLU* 2.8 17.5 + - + +
358A ARG* 3.4 15.3 - - - +
360A LYS* 1.3 77.9 - - - +
362A ALA* 1.3 55.7 + - - +
363A LYS* 3.1 3.9 + - - +
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Residues in contact with ALA 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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329A LEU* 3.4 37.5 - - + +
330A VAL* 3.6 9.9 - - - +
333A ARG* 3.9 4.9 - - - +
334A PRO* 3.8 19.2 - - + +
358A ARG 3.2 10.6 + - - +
359A LEU* 3.7 9.6 - - - +
360A LYS 3.0 1.2 - - - -
361A ALA* 1.3 74.3 - - - +
363A LYS* 1.3 75.2 + - - +
364A ILE* 3.3 12.2 + - + +
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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