Contacts of the helix formed by residues 350 - 362 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313C THR* 3.6 1.4 + - - -
316C ASN* 3.8 18.2 - - - +
349C GLY* 1.3 75.1 - - - -
351C ALA* 1.3 65.0 + - - +
352C GLN* 3.3 6.3 + - - +
353C LYS* 3.5 23.6 - - - +
354C ILE* 3.6 11.8 + - - +
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C SER* 4.2 9.6 - - - +
312C PRO 3.3 27.8 - - - +
313C THR* 3.2 15.3 + - - +
317C ASP 3.6 13.7 - - - +
318C ILE* 3.7 18.8 - - + +
350C GLY* 1.3 75.0 - - - +
352C GLN* 1.3 60.3 + - - +
354C ILE* 3.4 0.7 + - - -
355C LEU* 2.9 32.8 + - - +
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Residues in contact with GLN 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C SER 5.3 0.3 - - - +
313C THR* 4.7 1.0 + - - -
341C ALA* 3.0 31.8 + - - +
342C PHE* 3.5 25.1 + - - +
343C GLY* 3.9 2.8 + - - +
350C GLY 3.3 3.9 - - - +
351C ALA* 1.3 79.5 - - - +
353C LYS* 1.3 61.3 + - - +
355C LEU* 3.6 4.4 - - - +
356C GLU* 3.0 40.5 + - - +
370C PRO* 5.2 2.9 - - + -
371C GLY* 3.3 33.7 - - - +
372C PRO 4.1 2.0 - - - +
373C THR* 4.8 12.7 - - + +
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Residues in contact with LYS 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C GLY* 3.5 15.3 + - - +
352C GLN* 1.3 75.8 - - - +
354C ILE* 1.3 68.5 - - + +
356C GLU* 3.3 6.8 + - - +
357C GLU* 2.9 26.9 + - + +
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Residues in contact with ILE 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C ASN 4.3 3.1 - - - +
317C ASP* 2.9 47.6 - - - +
318C ILE* 3.8 26.2 - - + +
350C GLY 3.6 11.6 + - - +
351C ALA 3.4 2.1 + - - +
353C LYS* 1.3 82.8 - - + +
355C LEU* 1.3 64.4 + - - +
357C GLU* 3.3 13.5 + - - +
358C ARG* 2.9 53.0 + - + +
327D ASP* 4.8 2.0 - - - +
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Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C VAL* 3.6 41.3 - - + +
311C SER* 4.0 17.0 - - - +
318C ILE* 4.3 8.3 - - + -
322C VAL* 4.3 7.2 - - + -
326C LEU* 3.9 22.4 - - + +
341C ALA* 3.6 17.0 - - + -
342C PHE 3.6 24.7 - - - +
351C ALA 2.9 20.5 + - - +
352C GLN* 3.6 7.4 - - - +
354C ILE* 1.3 77.3 - - - +
356C GLU* 1.3 57.9 + - - +
358C ARG* 3.4 2.1 + - - +
359C LEU* 2.9 34.4 + - + +
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Residues in contact with GLU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ALA* 3.8 15.5 + - + +
352C GLN* 3.0 30.0 + - - +
353C LYS* 4.0 4.3 - - - +
355C LEU* 1.3 77.1 - - - +
357C GLU* 1.3 65.2 + - - +
359C LEU* 3.8 4.1 - - - +
360C LYS* 3.0 31.5 + - - +
366C LEU* 3.4 20.5 - - + +
368C ALA 3.7 5.7 - - - +
369C GLU* 3.3 30.4 - - - +
370C PRO* 3.2 10.7 - - - +
371C GLY* 3.0 28.3 + - - -
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Residues in contact with GLU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C LYS* 2.9 19.9 + - + +
354C ILE* 3.6 23.6 - - - +
356C GLU* 1.3 76.9 - - - +
358C ARG* 1.3 67.5 + - + +
360C LYS* 3.2 11.7 + - - +
361C ALA* 2.9 30.2 + - + +
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Residues in contact with ARG 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ILE* 4.3 6.2 - - - +
323C SER* 3.9 11.3 + - - +
326C LEU* 4.0 35.2 - - + +
327C ASP* 3.3 25.2 + - - -
330C VAL* 3.5 19.0 - - + +
354C ILE* 2.9 40.8 + - + +
355C LEU 3.9 2.7 - - - +
357C GLU* 1.3 87.0 + - + +
359C LEU* 1.3 62.5 + - - +
361C ALA* 3.4 6.1 + - - -
362C ALA* 3.2 18.5 + - - +
327D ASP* 2.6 37.2 + - - -
358D ARG* 3.1 25.9 - - - +
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Residues in contact with LEU 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C VAL* 4.7 6.1 - - + +
309C VAL* 4.4 17.3 - - + -
326C LEU* 4.2 18.2 - - + -
329C LEU* 4.5 5.8 - - + -
339C GLY* 4.8 2.0 - - - -
340C LEU 4.0 29.4 - - - +
341C ALA* 4.3 7.6 - - + +
355C LEU 2.9 20.3 + - - +
356C GLU* 3.8 4.9 - - - +
357C GLU 3.2 0.2 - - - -
358C ARG* 1.3 77.5 - - - +
360C LYS* 1.3 62.6 + - - +
362C ALA* 3.3 7.3 + - + +
364C ILE* 3.1 53.8 + - + +
366C LEU* 3.7 27.6 - - + -
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Residues in contact with LYS 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C GLU 3.0 22.3 + - - +
357C GLU* 3.7 7.0 - - - +
359C LEU* 1.3 72.1 - - - +
361C ALA* 1.3 55.1 + - - +
362C ALA 3.0 4.9 - - - -
363C LYS* 2.6 35.0 + - - +
364C ILE 4.1 8.5 - - - +
366C LEU* 3.5 31.9 - - + +
369C GLU* 3.0 30.1 + - - +
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Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C VAL* 3.8 29.2 - - + +
333C ARG* 5.9 1.0 - - - +
357C GLU* 2.9 19.0 + - + +
358C ARG* 3.6 10.1 - - - +
360C LYS* 1.3 76.2 - - - +
362C ALA* 1.3 56.8 + - - +
363C LYS* 3.1 13.9 + - - +
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Residues in contact with ALA 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C LEU* 3.6 28.3 - - + +
330C VAL* 3.7 16.8 - - - +
333C ARG* 4.4 4.2 - - - +
334C PRO* 3.8 17.5 - - + +
358C ARG 3.2 10.6 + - - +
359C LEU* 3.7 9.4 - - - +
360C LYS 3.0 1.2 - - - -
361C ALA* 1.3 75.4 - - - +
363C LYS* 1.3 71.3 + - - +
364C ILE* 3.3 21.5 + - + +
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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