Contacts of the helix formed by residues 361 - 378 (chain C) in PDB entry 5D0A
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 ASP 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C PRO* 3.6 26.3 - - + +
333C ARG* 3.5 12.8 - - - +
359C GLU* 2.9 15.5 + - - +
360C LYS* 1.3 76.2 - - - +
362C GLU* 1.3 60.2 + - - +
363C GLU* 3.0 16.5 + - - +
364C ALA* 2.8 29.3 + - + +
365C LYS* 2.9 29.2 + - - +
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Residues in contact with GLU 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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51A GLU* 5.4 0.2 - - - -
52A PRO* 3.7 31.6 - - + +
53A ASP* 3.3 48.1 + - - +
360C LYS 3.5 8.2 + - - +
361C ASP* 1.3 75.0 + - - +
363C GLU* 1.3 60.3 + - + +
365C LYS* 3.4 20.2 + - - +
366C LEU* 3.0 27.9 + - - +
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Residues in contact with GLU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PHE* 3.7 34.6 - - + -
330C PRO* 6.1 0.5 - - - +
361C ASP* 3.0 11.4 + - - +
362C GLU* 1.3 74.9 - - + +
364C ALA* 1.3 66.1 + - - +
366C LEU* 3.3 14.5 + - + +
367C GLU* 3.0 25.8 + - - +
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Residues in contact with ALA 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PHE* 4.3 1.9 - - - -
330C PRO* 4.2 16.4 - - + +
333C ARG* 4.5 4.0 - - + +
334C GLY* 4.3 15.5 - - - +
359C GLU* 3.5 32.5 - - + +
361C ASP* 2.8 17.6 + - + +
363C GLU* 1.3 76.8 - - - +
365C LYS* 1.3 62.3 + - - +
367C GLU* 2.9 13.7 + - - +
368C ILE* 2.9 16.6 + - + +
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Residues in contact with LYS 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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53A ASP* 3.4 32.5 + - - -
55A GLU* 4.6 10.2 - - - +
356C LEU* 3.7 30.7 + - + +
357C GLU* 5.8 2.6 + - - +
359C GLU* 3.2 32.6 + - + +
360C LYS 4.7 2.7 - - - +
361C ASP 2.9 19.1 + - - +
362C GLU* 3.6 28.7 + - - +
363C GLU 3.3 0.2 - - - -
364C ALA* 1.3 72.6 - - - +
366C LEU* 1.3 58.3 + - - +
368C ILE* 3.1 13.1 + - - +
369C GLU* 2.9 33.1 + - + +
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Residues in contact with LEU 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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38A ILE* 5.2 3.4 - - + -
41A GLU* 3.2 52.5 - - + +
52A PRO 5.7 4.3 - - - +
54A ILE* 3.9 28.0 - - + -
362C GLU 3.0 17.5 + - - +
363C GLU* 3.5 15.9 - - + +
364C ALA 3.1 0.2 - - - -
365C LYS* 1.3 77.9 - - - +
367C GLU* 1.3 63.2 + - - +
369C GLU* 3.2 12.0 - - + +
370C LYS* 3.0 36.0 + - + +
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Residues in contact with GLU 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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224C PHE* 3.4 34.4 - - + +
230C ARG* 2.7 37.9 + - - -
334C GLY* 3.2 24.2 - - - +
335C THR 5.1 0.2 - - - -
337C ALA* 4.5 0.2 - - - -
338C TRP* 3.5 14.7 + - - +
363C GLU 3.0 12.2 + - - +
364C ALA 2.9 9.2 + - - +
366C LEU* 1.3 78.4 - - + +
368C ILE* 1.3 57.3 + - - +
370C LYS* 2.7 35.9 + - - +
371C GLY* 2.9 24.8 + - - -
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Residues in contact with ILE 368 (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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324C MET* 4.5 7.2 - - + -
333C ARG 5.6 0.4 - - - +
334C GLY* 5.6 1.1 - - - -
337C ALA* 3.6 23.6 - - + -
352C LEU* 3.3 36.9 - - + +
355C ALA* 4.0 9.2 - - + -
356C LEU* 3.9 24.9 - - + +
359C GLU* 3.7 34.5 - - + +
364C ALA* 2.9 18.6 + - + +
365C LYS* 3.1 8.0 + - - +
367C GLU* 1.3 74.1 - - - +
369C GLU* 1.3 53.4 + - - +
371C GLY* 3.0 2.6 + - - -
372C ILE* 2.8 37.6 + - + +
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Residues in contact with GLU 369 (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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34A LYS* 3.5 21.9 + - - -
38A ILE* 4.1 20.3 - - + +
54A ILE* 3.8 24.6 + - + +
55A GLU* 2.7 32.3 + - - +
356C LEU* 3.9 19.9 - - + +
365C LYS* 2.9 23.6 + - + +
366C LEU* 3.2 13.5 - - + +
368C ILE* 1.3 76.0 - - - +
370C LYS* 1.3 62.5 + - - +
372C ILE* 3.2 12.6 + - - +
373C GLU* 3.0 23.2 + - - +
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Residues in contact with LYS 370 (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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38A ILE* 4.2 19.5 - - + +
41A GLU* 3.1 28.9 + - - -
42A SER* 4.5 5.6 - - - +
227C ASP* 2.8 40.2 + - - +
230C ARG* 3.8 1.2 - - - +
338C TRP* 3.9 12.8 - - + +
366C LEU* 3.0 26.7 + - + +
367C GLU* 2.7 42.4 + - - +
369C GLU* 1.3 75.5 - - - +
371C GLY* 1.3 57.1 + - - +
373C GLU* 3.2 8.5 + - - +
374C LEU* 2.9 33.8 + - + +
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Residues in contact with GLY 371 (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 ALA 3.9 19.1 - - - -
338C TRP* 4.3 6.2 - - - +
341C GLY* 3.4 17.0 - - - -
352C LEU* 3.7 9.2 - - - +
367C GLU 2.9 14.0 + - - -
368C ILE 3.0 5.1 + - - -
370C LYS* 1.3 77.4 - - - +
372C ILE* 1.3 61.1 + - - +
374C LEU* 3.2 4.3 + - - -
375C LEU* 3.2 16.8 + - - +
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Residues in contact with ILE 372 (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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34A LYS* 6.3 0.7 - - - +
349C ALA* 4.9 4.3 - - + +
352C LEU* 3.7 28.2 - - + +
353C GLU* 3.6 39.5 - - + +
356C LEU* 4.0 23.1 - - + -
368C ILE* 2.8 31.7 + - + +
369C GLU* 3.6 12.1 - - - +
371C GLY* 1.3 71.4 - - - +
373C GLU* 1.3 60.4 + - - +
375C LEU* 3.1 6.7 + - - +
376C LYS* 2.9 42.7 + - + +
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Residues in contact with GLU 373 (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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34A LYS* 5.5 1.7 - - - +
35A ASP* 2.8 40.5 - - - +
38A ILE* 3.5 30.3 - - + +
369C GLU 3.0 11.2 + - - +
370C LYS* 3.2 13.0 + - - +
372C ILE* 1.3 79.0 - - - +
374C LEU* 1.3 57.7 + - + +
376C LYS* 3.2 11.0 + - - +
377C ALA* 2.9 34.5 + - + +
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Residues in contact with LEU 374 (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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338C TRP* 3.6 39.7 - - + +
341C GLY 3.7 13.6 - - - +
342C LYS* 3.7 39.3 - - + +
370C LYS* 2.9 16.2 + - + +
371C GLY* 3.5 7.9 - - - +
372C ILE 3.2 0.2 - - - -
373C GLU* 1.3 79.1 - - + +
375C LEU* 1.3 57.5 + - - +
377C ALA* 4.0 6.6 - - + +
378C SER* 3.2 31.0 + - - -
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Residues in contact with LEU 375 (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 ILE 4.3 2.5 - - - +
341C GLY* 3.6 17.7 - - - +
344C GLY* 3.5 40.6 - - - +
345C ASP 3.6 17.3 - - - +
346C PRO* 4.0 10.3 - - + +
348C TYR* 4.0 4.0 - - + -
349C ALA* 3.5 44.6 - - + +
352C LEU* 4.0 15.7 - - + -
371C GLY 3.2 4.7 + - - +
372C ILE* 3.1 9.2 + - - +
374C LEU* 1.3 75.3 - - - +
376C LYS* 1.3 68.1 + - + +
378C SER* 4.0 14.0 + - - +
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Residues in contact with LYS 376 (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 ALA* 4.9 15.9 - - - +
353C GLU* 3.9 21.7 + - - -
372C ILE* 2.9 28.6 + - + +
373C GLU* 3.5 13.5 - - + +
375C LEU* 1.3 80.3 - - + +
377C ALA* 1.3 65.3 + - - +
378C SER 4.3 1.9 - - - -
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Residues in contact with ALA 377 (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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373C GLU* 2.9 20.7 + - + +
374C LEU* 4.0 8.7 - - + +
376C LYS* 1.3 80.0 - - - +
378C SER* 1.3 61.4 + - - +
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Residues in contact with SER 378 (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 GLY 4.9 0.2 + - - -
344C GLY* 4.2 21.0 + - - -
374C LEU 3.2 18.2 + - - -
375C LEU* 4.0 16.1 + - - +
376C LYS 4.3 2.0 - - - -
377C ALA* 1.3 84.9 - - - +
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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