Contacts of the helix formed by residues 355 - 369 (chain C) in PDB entry 1EZF
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 SER 355 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C GLN 4.5 1.4 + - - -
260C ASN* 3.8 5.4 + - - +
261C GLU* 3.5 44.6 + - - +
264C THR* 4.0 10.9 + - - -
353C ASP* 3.2 9.9 + - - -
354C PRO* 1.3 78.2 - - - +
356C SER* 1.3 65.5 + - - +
357C SER 3.2 2.7 - - - -
358C LYS* 2.8 28.2 + - - +
359C THR* 2.8 13.9 + - - -
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Residues in contact with SER 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ILE* 3.5 20.5 - - - +
350C PRO 3.9 9.6 + - - -
351C ASP* 5.8 0.2 - - - -
352C SER 5.3 0.9 + - - -
353C ASP* 2.7 34.9 + - - +
355C SER* 1.3 75.2 - - - +
357C SER* 1.3 64.5 + - - +
358C LYS* 4.8 0.7 + - - -
359C THR* 3.1 8.7 + - - -
360C ARG* 3.0 48.7 + - - +
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Residues in contact with SER 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C SER 3.2 0.8 - - - -
356C SER* 1.3 81.8 + - - +
358C LYS* 1.3 78.4 + - - +
360C ARG* 3.4 20.3 + - - +
361C GLN* 3.1 27.4 + - - +
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Residues in contact with LYS 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C THR* 3.7 14.1 - - + +
268C HIS* 4.9 6.1 + - + +
353C ASP 4.8 0.4 + - - -
354C PRO 2.8 24.8 + - - +
355C SER* 2.8 23.1 + - - +
356C SER* 4.8 0.8 + - - -
357C SER* 1.3 104.9 - - - +
359C THR* 1.3 66.0 + - - +
361C GLN* 3.2 11.4 + - - +
362C ILE* 3.1 26.0 + - - +
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Residues in contact with THR 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASN 5.5 0.2 - - - -
264C THR* 2.9 30.6 + - - +
267C LEU* 4.4 8.1 - - + -
304C TYR* 4.4 11.8 + - + -
345C ILE* 4.1 22.7 - - + -
349C ILE* 3.8 22.7 - - + -
353C ASP* 4.9 0.3 + - - -
355C SER* 2.8 17.5 + - - -
356C SER* 3.4 9.5 - - - -
358C LYS* 1.3 76.3 - - - +
360C ARG* 1.3 61.8 + - - +
362C ILE* 3.3 3.4 - - - +
363C ILE* 3.1 32.8 + - + +
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Residues in contact with ARG 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C TYR* 3.7 29.0 - - + -
349C ILE* 3.5 29.8 - - + +
350C PRO 5.4 0.8 + - - -
351C ASP* 5.8 2.4 + - - +
356C SER* 3.0 38.9 + - - +
357C SER* 3.4 30.9 + - - +
359C THR* 1.3 78.5 - - - +
361C GLN* 1.3 51.9 + - - +
363C ILE* 3.4 5.3 + - - +
364C SER* 2.7 37.1 + - - -
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Residues in contact with GLN 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 4.8 14.5 + - - +
357C SER 3.1 19.0 + - - +
358C LYS* 3.2 11.3 + - - +
360C ARG* 1.3 76.9 - - - +
362C ILE* 1.3 58.2 + - - +
364C SER* 3.3 7.8 + - - -
365C THR* 3.0 32.7 + - - -
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Residues in contact with ILE 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C THR* 4.2 2.7 - - + -
267C LEU* 3.8 40.2 - - + +
268C HIS* 3.7 51.3 + - + +
271C PRO* 4.5 6.5 - - + -
358C LYS 3.1 12.8 + - - +
359C THR* 3.3 20.4 - - - +
361C GLN* 1.3 72.5 - - - +
363C ILE* 1.3 59.5 + - - +
365C THR* 2.9 16.8 + - + +
366C ILE* 2.8 45.5 + - + +
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Residues in contact with ILE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.4 12.1 - - + -
342C MET* 3.8 36.8 - - + +
343C GLU* 4.1 9.0 - - - +
345C ILE* 4.0 22.4 - - + -
346C TYR* 3.9 27.1 - - + +
349C ILE* 4.5 0.2 - - + -
359C THR* 3.1 26.4 + - + +
360C ARG 3.8 3.4 - - - +
362C ILE* 1.3 75.0 - - - +
364C SER* 1.3 59.7 + - - +
366C ILE* 3.0 9.7 + - + +
367C ARG* 2.8 49.9 + - + +
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Residues in contact with SER 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.5 34.6 + - - +
45B LYS* 5.9 1.2 - - - +
360C ARG 2.7 22.5 + - - -
361C GLN* 3.5 8.7 - - - -
363C ILE* 1.3 73.2 - - - +
365C THR* 1.3 60.1 + - - +
367C ARG* 3.4 19.1 + - - +
368C THR* 2.8 33.3 + - - +
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Residues in contact with THR 365 (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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36B LEU* 4.0 6.3 - - + +
41B LYS* 3.7 23.0 + - - +
271C PRO* 5.0 9.0 - - + -
361C GLN* 3.0 17.6 + - - -
362C ILE* 2.9 23.9 + - + -
364C SER* 1.3 78.1 - - - +
366C ILE* 1.3 56.7 + - - +
368C THR 3.8 0.3 - - - -
369C GLN* 2.9 51.7 + - + +
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Residues in contact with ILE 366 (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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66B ARG* 4.1 0.2 + - - -
267C LEU* 4.1 2.2 - - + +
270C ILE* 3.9 24.9 - - + -
271C PRO* 3.4 41.3 - - + -
274C ILE* 4.3 5.1 - - + +
338C ILE* 5.2 0.2 - - + -
339C TYR* 3.4 36.5 + - + -
342C MET* 4.4 20.9 - - + -
362C ILE* 2.8 36.8 + - + +
363C ILE* 3.0 9.6 + - - +
365C THR* 1.3 76.3 - - - +
367C ARG* 1.3 63.6 + - - +
369C GLN* 3.8 11.7 + - - +
370C ASN 4.6 0.2 + - - -
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Residues in contact with ARG 367 (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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41B LYS 5.8 0.4 - - - -
44B TYR* 3.6 21.4 - - + -
45B LYS* 3.4 35.6 + - - +
48B ASN* 3.4 27.1 - - - +
59B GLN* 3.6 20.9 - - - +
66B ARG* 2.9 24.4 + - - -
339C TYR* 5.0 1.1 - - + -
342C MET* 6.0 1.3 - - + -
343C GLU* 2.9 42.0 + - - +
346C TYR* 3.4 44.5 - - - -
363C ILE* 2.8 23.4 + - + +
364C SER* 3.7 16.2 - - - +
365C THR 3.3 0.2 - - - -
366C ILE* 1.3 78.9 - - + +
368C THR* 1.3 57.8 + - - +
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Residues in contact with THR 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.5 25.0 - - + +
40B LEU* 4.0 15.6 - - - +
41B LYS* 3.4 35.9 + - + +
44B TYR* 3.2 32.2 - - + -
66B ARG* 3.5 7.5 + - - +
67B ASN* 5.2 0.5 - - - +
364C SER* 2.8 21.9 + - - +
365C THR 4.5 0.9 - - - +
367C ARG* 1.3 76.5 - - + +
369C GLN* 1.3 68.0 + - - +
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Residues in contact with GLN 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASN* 4.9 9.9 + - - -
36B LEU* 3.2 33.7 - - - +
66B ARG* 4.1 2.5 - - - -
271C PRO* 5.4 13.9 - - + +
365C THR* 2.9 28.9 + - + +
366C ILE* 3.8 7.4 + - - +
367C ARG 3.5 1.0 - - - -
368C THR* 1.3 83.2 - - - +
370C ASN* 1.3 100.0 + - + +
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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
------------------------------------------------------------
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