Contacts of the helix formed by residues 361 - 377 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330D PRO* 3.6 26.8 - - + +
333D ARG* 3.6 12.8 - - - +
359D GLU* 2.9 15.2 + - - +
360D LYS* 1.3 77.2 - - - +
362D GLU* 1.3 60.2 + - - +
363D GLU* 2.9 19.0 + - - +
364D ALA* 2.7 30.6 + - + +
365D LYS* 2.9 28.0 + - - +
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Residues in contact with GLU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 5.5 0.2 - - - -
52B PRO* 3.6 26.6 - - + +
53B ASP* 3.2 50.2 + - - +
360D LYS 3.4 7.5 + - - +
361D ASP* 1.3 74.1 + - - +
363D GLU* 1.3 58.7 + - + +
365D LYS* 3.4 22.9 + - - +
366D LEU* 3.1 33.6 + - + +
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Residues in contact with GLU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D PHE* 3.5 37.4 - - + +
330D PRO* 5.8 1.0 - - - +
361D ASP* 2.9 13.5 + - - +
362D GLU* 1.3 76.0 - - + +
364D ALA* 1.3 66.5 + - - +
366D LEU* 3.3 17.2 + - + +
367D GLU* 3.1 24.6 + - - +
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Residues in contact with ALA 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D PHE* 4.3 1.0 - - - -
330D PRO 4.2 15.3 - - - +
333D ARG* 4.5 4.3 - - + +
334D GLY* 4.3 17.1 - - - +
359D GLU* 3.5 32.8 - - + +
361D ASP* 2.7 20.4 + - + +
363D GLU* 1.3 71.2 - - - +
365D LYS* 1.3 66.2 + - - +
367D GLU* 3.0 5.8 + - - +
368D ILE* 3.0 24.4 + - + +
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Residues in contact with LYS 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ASP* 2.6 40.6 + - - -
54B ILE 6.1 0.2 - - - +
55B GLU* 5.1 7.4 - - - +
356D LEU* 3.7 27.7 - - + +
359D GLU* 3.3 37.5 + - + +
360D LYS* 4.6 2.4 - - - +
361D ASP 2.9 16.5 + - - +
362D GLU* 3.6 29.3 + - - +
363D GLU 3.3 0.2 - - - -
364D ALA* 1.3 74.2 - - - +
366D LEU* 1.3 63.1 + - + +
368D ILE* 3.1 6.7 + - - +
369D GLU* 3.0 32.5 + - - +
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 5.7 0.9 - - + +
41B GLU* 4.4 33.0 - - + +
52B PRO* 4.0 16.4 - - + +
54B ILE* 3.5 37.7 - - + +
362D GLU* 3.1 25.7 + - + +
363D GLU* 3.4 19.5 - - + +
365D LYS* 1.3 77.6 - - + +
367D GLU* 1.3 56.2 + - + +
369D GLU* 3.2 12.0 + - - +
370D LYS* 2.9 35.2 + - - +
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Residues in contact with GLU 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D PHE* 3.6 29.8 - - + +
230D ARG* 2.7 46.7 + - - -
334D GLY* 3.2 21.1 - - - +
337D ALA* 4.3 2.0 - - - -
338D TRP* 3.5 16.6 + - - +
363D GLU 3.1 14.0 + - - +
364D ALA 3.0 8.3 + - - +
366D LEU* 1.3 76.2 - - + +
368D ILE* 1.3 59.9 + - - +
370D LYS* 2.8 27.4 + - - +
371D GLY* 3.0 24.1 + - - -
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Residues in contact with ILE 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D MET* 4.5 6.7 - - + -
333D ARG 5.5 1.1 - - - +
334D GLY* 5.7 0.2 - - - -
337D ALA* 3.5 24.5 - - + -
352D LEU* 3.3 37.1 - - + +
355D ALA* 3.9 20.2 - - + +
356D LEU* 3.8 16.2 - - + +
359D GLU* 3.7 34.5 - - + +
364D ALA* 3.0 19.1 + - + +
365D LYS* 3.1 7.4 + - - +
367D GLU* 1.3 74.8 - - - +
369D GLU* 1.3 58.6 + - - +
371D GLY* 3.2 2.1 + - - -
372D ILE* 2.8 35.6 + - + +
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Residues in contact with GLU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LYS* 5.3 4.8 - - - -
38B ILE* 4.0 23.3 - - + +
53B ASP* 5.2 0.3 - - - +
54B ILE* 3.7 26.3 + - - +
55B GLU* 3.5 32.6 + - - +
356D LEU* 3.7 22.4 - - + +
365D LYS* 3.0 18.6 + - - +
366D LEU* 3.5 34.4 + - - +
368D ILE* 1.3 75.9 - - - +
370D LYS* 1.3 56.9 + - - +
372D ILE* 3.5 9.5 + - + +
373D GLU* 3.0 27.7 + - - +
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Residues in contact with LYS 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 4.2 18.6 - - + -
41B GLU* 3.1 29.9 + - - -
42B SER* 4.3 7.6 - - - +
227D ASP* 2.8 39.9 + - - +
230D ARG* 3.9 0.6 - - - +
338D TRP* 3.8 13.7 - - + +
366D LEU* 2.9 21.4 + - - +
367D GLU* 2.8 44.1 + - - +
369D GLU* 1.3 74.2 - - - +
371D GLY* 1.3 64.8 + - - +
373D GLU* 3.3 8.2 + - - +
374D LEU* 3.0 29.6 + - + +
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Residues in contact with GLY 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D ALA 3.9 18.2 - - - -
338D TRP* 4.3 5.1 - - - +
341D GLY* 3.5 14.6 - - - -
352D LEU* 3.7 7.6 - - - -
367D GLU 3.0 14.3 + - - -
368D ILE 3.2 4.0 + - - -
370D LYS* 1.3 77.5 - - - +
372D ILE* 1.3 61.4 + - - +
374D LEU* 3.2 6.8 + - - +
375D LEU* 3.1 20.1 + - - +
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Residues in contact with ILE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LYS* 6.0 4.3 - - - +
349D ALA* 4.9 3.8 - - + +
352D LEU* 3.7 23.5 - - + +
353D GLU* 3.4 41.7 - - - +
356D LEU* 4.1 20.9 - - + -
368D ILE* 2.8 23.6 + - + +
369D GLU* 3.7 7.9 - - - +
370D LYS 3.2 0.2 - - - -
371D GLY* 1.3 75.1 - - - +
373D GLU* 1.3 63.0 + - - +
375D LEU* 3.2 5.9 + - - +
376D LYS* 3.0 51.4 + - + +
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Residues in contact with GLU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASP* 3.1 38.9 - - - +
38B ILE* 3.7 27.8 - - + +
369D GLU 3.0 14.2 + - - +
370D LYS* 3.3 12.5 + - - +
372D ILE* 1.3 77.1 - - - +
374D LEU* 1.3 58.6 + - + +
376D LYS* 3.4 5.4 + - - +
377D ALA* 2.9 38.5 + - + +
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Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D TRP* 3.9 32.1 - - + +
341D GLY* 3.6 14.2 - - - +
342D LYS* 3.8 39.3 - - + +
344D GLY* 5.9 0.7 - - - -
370D LYS* 3.0 19.4 + - + +
371D GLY* 3.2 7.4 + - - +
373D GLU* 1.3 76.2 - - + +
375D LEU* 1.3 63.9 + - - +
377D ALA* 3.1 23.7 - - + -
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D ILE 3.9 3.6 - - - +
341D GLY* 3.4 30.5 - - - +
344D GLY* 3.7 21.3 - - - -
345D ASP 3.7 20.4 - - - +
346D PRO* 4.1 19.5 - - + +
348D TYR* 3.9 6.3 - - + -
349D ALA* 3.5 45.5 - - + +
352D LEU* 3.6 18.4 - - + -
371D GLY 3.1 8.0 + - - +
372D ILE* 3.8 6.5 - - - +
374D LEU* 1.3 78.1 - - - +
376D LYS* 1.3 61.9 + - - +
377D ALA 3.7 2.9 + - - -
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Residues in contact with LYS 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ALA* 5.1 10.9 - - + +
353D GLU* 3.0 28.5 + - - -
372D ILE* 3.0 34.5 + - + +
373D GLU* 4.0 5.4 - - - +
375D LEU* 1.3 77.9 - - + +
377D ALA* 1.3 57.8 + - - +
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Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D GLU* 2.9 25.3 + - + +
374D LEU* 3.1 20.2 - - + +
375D LEU 4.3 3.1 - - - -
376D LYS* 1.3 79.3 - - - +
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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