Contacts of the helix formed by residues 344 - 358 (chain C) in PDB entry 3CB4
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 344 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C ASP* 3.1 17.3 + - - -
294C GLN* 3.8 11.9 - - - -
295C VAL* 4.3 14.1 - - - -
342C PHE* 3.1 4.5 - - - +
343C LEU* 1.3 81.6 - - - +
345C LEU* 1.3 59.8 + - - -
347C HIS* 3.4 0.9 + - - +
348C MET* 2.9 30.7 + - - +
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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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83C ASP* 3.3 1.8 + - - -
294C GLN* 4.8 0.4 - - - +
295C VAL* 4.8 2.7 - - + +
344C GLY* 1.3 70.2 - - - -
346C LEU* 1.3 64.9 + - + +
348C MET* 3.3 23.0 - - + +
349C GLU* 2.9 54.2 + - - +
368C PRO* 5.0 1.6 - - + -
450C VAL* 4.3 12.1 - - + +
451C VAL* 3.6 40.8 - - + +
453C ASP* 5.1 10.8 - - - +
455C PHE* 4.7 20.4 - - + -
470C TYR* 3.9 20.1 + - + +
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Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C HIS* 2.8 61.0 - - + +
83C ASP* 3.4 12.6 - - + +
84C PHE* 4.3 10.8 - - + -
345C LEU* 1.3 80.3 - - + +
347C HIS* 1.3 64.3 + - - +
349C GLU* 3.7 16.8 - - + +
350C ILE* 3.2 34.8 + - + +
455C PHE* 6.6 0.4 - - + -
470C TYR* 5.0 2.0 - - + +
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Residues in contact with HIS 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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83C ASP* 2.9 13.3 + - - +
84C PHE* 3.7 30.0 - + + -
321C ASP* 2.9 39.4 + - - -
323C SER 4.2 7.7 + - - -
324C LEU* 4.3 2.8 - - - -
342C PHE* 3.6 15.3 - + + -
343C LEU* 3.0 43.4 - - + +
344C GLY 3.5 12.6 - - - +
346C LEU* 1.3 75.6 - - - +
348C MET* 1.3 65.1 + - - +
350C ILE* 3.2 15.4 + - + +
351C ILE* 3.3 27.3 + - + +
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Residues in contact with MET 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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295C VAL* 4.5 9.4 - - + -
297C ALA* 4.0 17.9 - - - -
299C LEU* 6.1 0.4 - - + -
342C PHE* 3.5 47.3 - - + -
344C GLY 2.9 14.0 + - - +
345C LEU* 3.3 33.7 - - + +
347C HIS* 1.3 77.2 - - - +
349C GLU* 1.3 62.1 + - - +
351C ILE* 3.3 4.0 + - - +
352C GLN* 2.9 53.7 + - - +
365C THR* 5.2 2.0 - - - +
366C THR 6.0 0.4 - - - +
368C PRO* 4.7 16.6 - - + -
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Residues in contact with GLU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LEU* 2.9 48.5 + - - +
346C LEU* 3.9 15.7 - - + +
347C HIS 3.2 0.6 - - - -
348C MET* 1.3 78.7 - - + +
350C ILE* 1.3 60.8 + - - +
352C GLN* 3.9 17.3 - - - +
353C GLU* 3.0 29.5 + - - +
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Residues in contact with ILE 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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84C PHE* 4.5 21.8 - - + -
346C LEU* 3.2 28.8 + - + +
347C HIS* 3.2 9.9 + - + +
349C GLU* 1.3 77.8 - - + +
351C ILE* 1.3 64.0 + - + +
353C GLU* 3.6 7.1 + - - +
354C ARG* 3.1 37.9 + - - +
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Residues in contact with ILE 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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299C LEU* 5.7 0.9 - - + -
314C LEU* 5.2 4.3 - - + -
317C LEU* 4.4 18.6 - - + -
321C ASP* 3.5 11.7 - - - +
324C LEU* 3.6 26.2 - - + -
342C PHE* 4.0 22.7 - - + -
347C HIS* 3.3 42.5 + - + +
348C MET 3.8 5.6 - - - +
350C ILE* 1.3 81.5 - - + +
352C GLN* 1.3 60.7 + - + +
354C ARG* 3.2 10.0 + - + +
355C LEU* 2.8 45.0 + - + +
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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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299C LEU* 4.3 16.6 - - + +
342C PHE* 5.6 0.2 - - + -
348C MET* 2.9 42.3 + - + +
349C GLU* 3.9 24.8 - - - +
351C ILE* 1.3 75.6 - - + +
353C GLU* 1.3 56.2 + - - +
355C LEU* 3.2 8.7 + - - +
356C GLU* 2.9 35.2 + - - +
363C LEU* 6.1 0.9 - - + -
365C THR* 3.2 42.4 + - - +
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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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349C GLU 3.0 20.7 + - - +
350C ILE* 3.6 7.6 - - - +
352C GLN* 1.3 76.1 - - - +
354C ARG* 1.3 56.9 + - - +
356C GLU* 4.5 9.0 - - - +
357C ARG* 2.7 69.4 + - + +
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Residues in contact with ARG 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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317C LEU* 3.3 37.1 + - + +
320C ASN* 6.0 5.9 - - - +
350C ILE* 3.1 28.1 + - - +
351C ILE* 3.4 12.4 - - - +
352C GLN 3.0 0.4 - - - -
353C GLU* 1.3 77.3 - - - +
355C LEU* 1.3 64.6 + - - +
356C GLU 3.2 1.1 - - - -
358C GLU* 3.0 73.2 + - + +
359C TYR* 3.3 11.2 + - + -
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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
----------------------------------------------------------
299C LEU* 4.8 9.9 - - + -
310C PHE* 4.2 12.3 - - + -
313C ALA* 3.9 22.7 - - + -
314C LEU* 4.7 8.1 - - + -
317C LEU* 3.6 28.5 - - + -
351C ILE* 2.8 34.4 + - + +
352C GLN* 3.7 7.4 - - - +
354C ARG* 1.3 75.6 - - - +
356C GLU* 1.3 59.5 + - - +
359C TYR* 3.5 6.9 - - + -
360C ASP 3.2 8.0 + - - -
361C LEU* 2.9 33.0 + - + +
363C LEU* 3.8 32.3 - - + -
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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
----------------------------------------------------------
352C GLN* 2.9 19.6 + - - +
353C GLU* 3.9 9.8 - - - +
355C LEU* 1.3 77.8 - - - +
357C ARG* 1.3 67.1 + - + +
360C ASP* 3.1 24.3 - - - +
361C LEU 3.6 16.1 + - - +
362C ASP* 5.7 1.8 - - - +
554F TYR* 3.5 24.9 + - - +
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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* 2.7 49.5 + - - +
356C GLU* 1.3 92.9 - - + +
358C GLU* 1.3 66.6 + - + +
359C TYR 3.4 0.2 - - - -
360C ASP* 3.8 8.7 + - - +
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Residues in contact with GLU 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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354C ARG* 3.0 61.3 + - + +
357C ARG* 1.3 80.0 - - + +
359C TYR* 1.3 82.3 + - + +
360C ASP* 3.9 1.0 + - - +
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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