Contacts of the helix formed by residues 337 - 347 (chain C) in PDB entry 1Z6T
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 ARG 337 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331C LEU* 4.3 1.8 - - - +
334C PHE* 3.3 41.7 + - + +
335C PRO 3.4 3.2 - - - -
336C ASN* 1.3 87.6 - - - +
338C TRP* 1.3 58.6 + - - +
339C GLU 3.4 2.7 - - - -
340C TYR* 3.3 46.7 + - + +
341C TYR* 3.0 46.1 + - + -
374C MET* 3.4 32.5 - - - +
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Residues in contact with TRP 338 (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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295C LEU* 4.2 10.8 - - + -
299C VAL* 4.0 26.8 - - + +
301C MET* 4.3 10.0 - - + +
306C LEU* 4.1 12.6 - - + -
307C PRO* 3.3 35.4 - - + +
309C GLN* 3.9 18.8 - - + +
310C ALA* 3.5 39.0 - - + -
313C ILE* 3.5 27.1 - - + +
331C LEU* 3.5 36.6 - - + +
335C PRO 3.8 22.6 + - - -
336C ASN* 3.6 4.2 + - - -
337C ARG* 1.3 78.0 - - - +
339C GLU* 1.3 61.0 + - - +
341C TYR* 4.1 0.4 - - - -
342C LEU* 3.1 24.6 + - - +
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Residues in contact with GLU 339 (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 GLN* 2.6 42.0 + - - +
337C ARG 3.4 0.2 - - - -
338C TRP* 1.3 74.9 - - - +
340C TYR* 1.3 67.7 + - - +
342C LEU* 3.2 12.1 + - - +
343C LYS* 3.0 62.9 + - + +
346C GLN* 5.7 0.3 - - - +
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Residues in contact with TYR 340 (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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337C ARG* 3.3 54.4 + - + +
339C GLU* 1.3 79.8 - - - +
341C TYR* 1.3 85.0 + + - +
343C LYS* 3.6 7.4 + - + +
344C GLN* 3.0 63.7 + - + +
374C MET* 4.3 13.8 - - - +
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Residues in contact with TYR 341 (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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313C ILE* 5.0 8.7 - - + -
327C ILE* 5.2 9.4 - - + -
330C LEU* 3.9 34.9 - - + +
331C LEU* 4.1 15.3 - - + -
334C PHE* 3.1 32.6 - - + +
337C ARG* 3.0 37.8 + - + +
338C TRP 4.4 2.0 - - - +
340C TYR* 1.3 95.9 - + - +
342C LEU* 1.3 66.6 + - - +
344C GLN* 3.5 15.0 + - - +
345C LEU* 3.1 28.2 + - + +
370C ILE* 3.7 28.2 - - + +
374C MET* 3.5 16.4 - - + +
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLN* 4.0 19.1 - - + -
312C SER* 3.4 50.7 - - - +
313C ILE* 3.7 18.5 - - + +
316C GLU* 4.0 7.0 - - + -
338C TRP 3.1 20.2 + - - +
339C GLU* 3.2 13.7 + - - +
341C TYR* 1.3 77.0 - - - +
343C LYS* 1.3 56.7 + - - +
345C LEU* 3.2 4.3 + - + +
346C GLN* 3.0 50.5 + - - +
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Residues in contact with LYS 343 (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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339C GLU* 3.0 50.2 + - + +
340C TYR* 3.8 6.5 - - - +
342C LEU* 1.3 73.2 - - - +
344C GLN* 1.3 60.9 + - - +
346C GLN* 3.2 12.8 + - - +
347C ASN* 2.8 36.1 + - + +
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Residues in contact with GLN 344 (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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340C TYR* 3.0 58.7 + - + +
341C TYR* 3.5 14.2 - - - +
342C LEU 3.4 0.2 - - - -
343C LYS* 1.3 77.1 - - + +
345C LEU* 1.3 60.2 + - - +
347C ASN* 3.1 29.9 - - - +
349C GLN* 5.1 8.1 + - - +
366C GLU* 3.7 13.4 - - - +
370C ILE* 3.5 35.2 - - + +
373C GLU* 5.8 5.7 - - - +
374C MET* 5.5 1.1 - - - +
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Residues in contact with LEU 345 (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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313C ILE* 3.8 35.4 - - + +
316C GLU* 3.5 31.6 - - + +
317C CYS* 4.6 1.6 - - - -
323C VAL* 5.2 4.3 - - + -
327C ILE* 4.0 32.3 - - + -
341C TYR 3.1 18.4 + - - +
342C LEU* 3.2 7.8 + - - +
344C GLN* 1.3 76.4 - - - +
346C GLN* 1.3 57.9 + - - +
348C LYS* 2.9 36.3 - - - +
363C ALA* 4.7 6.3 - - - +
366C GLU* 4.6 7.9 - - + -
367C ALA* 4.5 14.1 - - + +
370C ILE* 4.5 9.9 - - + -
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Residues in contact with GLN 346 (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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312C SER* 4.7 5.3 - - - -
316C GLU* 3.6 30.5 + - + +
339C GLU* 5.7 0.2 - - - +
342C LEU* 3.0 47.4 + - - +
343C LYS* 3.2 15.4 + - - +
345C LEU* 1.3 77.3 - - - +
347C ASN* 1.3 59.1 + - - +
348C LYS* 3.5 6.7 + - - +
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Residues in contact with ASN 347 (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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343C LYS* 2.8 19.3 + - + +
344C GLN* 3.1 19.9 + - - +
346C GLN* 1.3 70.6 - - + +
348C LYS* 1.3 62.7 + - - +
349C GLN* 3.4 34.2 + - - +
366C GLU* 4.2 0.7 - - - +
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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