Contacts of the helix formed by residues 347 - 358 (chain C) in PDB entry 5Q1B
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 347 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345C PRO 3.4 0.4 + - - -
346C SER* 1.3 74.6 + - - +
348C HIS* 1.4 60.9 + - - +
349C SER 3.3 3.5 - - - +
350C ASP* 3.3 21.9 + - - +
351C LEU* 3.2 21.6 + - - +
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Residues in contact with HIS 348 (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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278C LEU* 3.5 25.0 - - + +
344C LEU* 3.6 19.6 - - + +
345C PRO* 3.1 58.0 + - + +
346C SER 3.7 6.2 + - - -
347C GLY* 1.4 75.1 - - - +
349C SER* 1.3 57.4 + - - +
351C LEU* 3.4 6.4 + - - -
352C LEU* 2.9 29.6 + - - +
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Residues in contact with SER 349 (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 PHE* 5.0 14.2 + - - -
342C LYS 4.5 4.7 + - - -
343C LYS* 5.4 0.7 - - - -
344C LEU* 3.9 28.1 + - - +
345C PRO 4.5 1.2 + - - -
347C GLY 3.3 1.6 - - - +
348C HIS* 1.3 76.6 - - - +
350C ASP* 1.3 62.9 + - - +
352C LEU* 3.9 8.5 - - - +
353C GLU* 3.2 26.9 + - - +
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Residues in contact with ASP 350 (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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347C GLY* 3.5 22.0 + - - +
348C HIS 3.3 0.2 - - - -
349C SER* 1.3 82.6 + - - +
351C LEU* 1.4 58.6 + - - +
353C GLU* 3.5 8.0 + - - +
354C ALA* 3.2 26.7 + - - +
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Residues in contact with LEU 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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278C LEU* 3.8 22.2 - - + +
347C GLY 3.2 9.8 + - - +
348C HIS* 3.4 9.4 + - - +
350C ASP* 1.4 76.5 - - - +
352C LEU* 1.4 58.9 + - - +
354C ALA* 3.4 8.7 + - + +
355C ARG* 2.9 67.8 + - + +
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Residues in contact with LEU 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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274C THR* 4.0 32.5 - - + -
277C ILE* 4.0 26.9 - - + -
278C LEU* 3.6 15.0 - - + +
339C ILE 5.0 0.4 - - - +
340C PHE* 4.4 20.6 - - + +
344C LEU* 4.5 10.5 - - + -
348C HIS 2.9 18.3 + - - +
349C SER* 3.9 6.3 - - - +
350C ASP 3.4 0.2 - - - -
351C LEU* 1.4 75.1 - - - +
353C GLU* 1.3 61.5 + - - +
355C ARG* 3.3 5.4 + - - +
356C ILE* 3.1 34.5 + - + +
501C 9N7 3.8 30.5 - - - -
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Residues in contact with GLU 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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340C PHE* 3.8 20.5 - - + -
349C SER 3.2 16.1 + - - +
350C ASP* 3.6 9.0 - - - +
352C LEU* 1.3 76.9 - - - +
354C ALA* 1.4 56.5 + - - +
356C ILE 3.3 2.3 + - - -
357C ARG* 2.9 53.4 + - - +
370C PHE* 3.5 29.3 - - + -
374C LYS* 3.4 29.2 + - - -
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Residues in contact with ALA 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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350C ASP 3.2 14.5 + - - +
351C LEU* 3.7 12.1 - - + +
353C GLU* 1.4 74.4 - - - +
355C ARG* 1.3 63.4 + - - +
357C ARG* 3.4 11.2 + - - +
358C ASN* 3.1 24.8 + - - +
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Residues in contact with ARG 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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277C ILE* 3.4 31.0 + - + +
278C LEU* 2.9 41.3 + - - +
279C LYS 5.2 0.4 + - - -
280C GLU* 3.9 5.8 - - - +
281C ALA* 3.6 41.9 - - - +
282C PHE 5.3 0.4 - - - +
287C ASN* 4.9 3.5 + - - -
351C LEU* 2.9 49.5 + - + +
352C LEU* 3.3 6.0 + - - +
354C ALA* 1.3 71.9 - - - +
356C ILE* 1.3 65.4 + - - +
358C ASN* 3.3 7.1 + - - +
359C SER* 3.3 19.9 + - - -
501C 9N7 5.8 0.2 - - - -
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Residues in contact with ILE 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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277C ILE* 4.7 7.4 - - + -
340C PHE* 4.4 8.5 - - + -
352C LEU* 3.1 34.9 + - + +
353C GLU 3.7 3.6 - - - +
355C ARG* 1.3 72.0 - - - +
357C ARG* 1.3 63.6 + - - +
359C SER* 2.7 30.7 + - - +
361C ILE* 4.0 6.0 - - + +
366C ILE* 5.9 0.2 - - - -
369C MET* 4.3 21.1 - - + -
370C PHE* 3.7 17.0 - - + -
501C 9N7 3.5 70.7 - - + +
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Residues in contact with ARG 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 GLU* 2.9 49.0 + - - +
354C ALA* 3.6 11.7 - - - +
355C ARG 3.4 0.2 - - - -
356C ILE* 1.3 75.9 - - - +
358C ASN* 1.3 56.5 + - + +
359C SER 3.7 1.4 + - - -
360C GLY 5.0 0.5 + - - -
361C ILE* 4.6 3.6 - - - +
363C ASP* 5.7 1.1 - - - +
366C ILE* 3.4 49.8 - - + +
367C THR* 4.6 15.4 + - - +
370C PHE* 3.6 35.8 - - + +
374C LYS* 4.5 6.7 - - - +
459C ARG* 5.1 2.9 + - - -
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Residues in contact with ASN 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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282C PHE 4.9 3.7 + - - +
284C ALA* 5.4 2.6 + - - +
287C ASN* 4.3 5.2 + - - -
354C ALA 3.1 16.5 + - - +
355C ARG* 3.3 7.6 + - - +
356C ILE 3.2 0.4 - - - -
357C ARG* 1.3 76.6 - - - +
359C SER* 1.3 59.4 + - - +
360C GLY 3.4 3.7 + - - -
459C ARG* 4.4 20.0 + - - +
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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