Contacts of the helix formed by residues 361 - 380 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A PRO* 3.7 25.7 - - + +
333A ARG* 3.6 13.0 - - - +
359A GLU* 2.8 18.0 + - - +
360A LYS* 1.3 78.2 - - - +
362A GLU* 1.3 59.4 + - - +
363A GLU* 2.9 17.7 + - - +
364A ALA* 2.7 30.2 + - + +
365A LYS* 2.8 29.7 + - - +
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Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LYS 3.5 9.0 + - - +
361A ASP* 1.3 73.1 + - - +
363A GLU* 1.3 61.9 + - + +
365A LYS* 3.4 16.3 + - - +
366A LEU* 3.0 34.9 + - + +
52C PRO* 3.6 27.4 - - + +
53C ASP* 3.0 53.6 + - - +
56C LYS* 5.6 1.4 + - - -
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 3.5 35.4 - - + -
330A PRO* 5.8 1.4 - - - +
361A ASP* 2.9 12.0 + - - +
362A GLU* 1.3 76.5 - - + +
364A ALA* 1.3 65.3 + - - +
366A LEU* 3.2 19.4 + - + +
367A GLU* 3.1 24.3 + - - +
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 4.2 1.4 - - - -
330A PRO* 3.9 17.9 - - + +
333A ARG* 4.5 4.5 - - + +
334A GLY* 4.2 17.8 - - - +
359A GLU* 3.7 28.9 - - + +
361A ASP* 2.7 20.3 + - + +
363A GLU* 1.3 70.5 - - - +
365A LYS* 1.3 64.7 + - - +
367A GLU* 2.9 13.4 + - - +
368A ILE* 2.9 18.0 + - + +
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Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.4 39.5 - - + +
357A GLU* 5.4 5.2 + - - +
359A GLU* 3.2 37.4 - - + +
360A LYS* 5.1 2.5 - - - +
361A ASP 2.8 17.2 + - - +
362A GLU* 3.5 22.1 + - - +
363A GLU 3.3 0.2 - - - -
364A ALA* 1.3 74.9 - - - +
366A LEU* 1.3 63.3 + - + +
368A ILE* 3.3 3.8 + - - -
369A GLU* 3.0 27.6 + - - +
53C ASP* 2.8 35.0 + - - +
55C GLU* 4.9 8.8 - - + +
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLU* 3.0 25.8 + - + +
363A GLU* 3.3 21.3 - - + +
364A ALA 3.1 0.2 - - - -
365A LYS* 1.3 77.4 - - + +
367A GLU* 1.3 57.1 + - + +
369A GLU* 3.2 10.5 + - - +
370A LYS* 3.0 37.0 + - - +
38C ILE* 5.4 0.3 - - - +
41C GLU* 3.8 39.9 - - + +
52C PRO* 4.0 16.2 - - + +
54C ILE* 3.6 37.0 - - + +
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Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.5 30.5 - - + +
230A ARG* 2.7 46.6 + - - -
334A GLY* 3.1 22.8 - - - +
337A ALA* 4.2 2.2 - - - -
338A TRP* 3.5 19.4 + - - +
363A GLU 3.1 12.5 + - - +
364A ALA 2.9 8.1 + - - +
366A LEU* 1.3 75.8 - - + +
368A ILE* 1.3 60.0 + - - +
370A LYS* 3.0 23.9 + - - +
371A GLY* 2.9 24.6 + - - -
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Residues in contact with ILE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A MET* 4.4 7.6 - - + -
333A ARG* 5.4 1.8 - - + +
334A GLY* 5.7 0.2 - - - -
337A ALA* 3.5 23.8 - - + -
352A LEU* 3.2 38.4 - - + +
355A ALA* 4.0 17.3 - - + +
356A LEU* 3.7 17.0 - - + +
359A GLU* 3.6 35.2 - - + +
364A ALA* 2.9 17.9 + - + +
365A LYS* 3.3 6.7 + - - +
367A GLU* 1.3 75.0 - - - +
369A GLU* 1.3 58.1 + - - +
371A GLY* 3.2 1.4 + - - -
372A ILE* 2.9 36.0 + - + +
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.8 22.0 - - + -
365A LYS* 3.0 22.7 + - - +
366A LEU* 3.2 18.7 + - - +
368A ILE* 1.3 75.2 - - - +
370A LYS* 1.3 57.6 + - - +
372A ILE* 3.4 8.8 + - + +
373A GLU* 2.9 28.8 + - - +
34C LYS* 4.6 4.6 - - - -
38C ILE* 4.0 22.7 - - + +
54C ILE* 3.5 39.3 + - + +
55C GLU* 2.9 30.0 + - - +
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Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASP* 3.0 41.1 + - - +
230A ARG* 4.0 0.6 - - - +
338A TRP* 3.9 13.9 - - + +
366A LEU* 3.0 22.8 + - - +
367A GLU* 3.0 38.4 + - - +
368A ILE 3.3 0.2 - - - -
369A GLU* 1.3 73.9 - - - +
371A GLY* 1.3 60.1 + - - +
373A GLU* 3.2 3.9 + - - +
374A LEU* 2.8 35.4 + - + +
38C ILE* 3.8 24.2 - - + -
41C GLU* 4.7 16.7 + - - +
42C SER* 4.3 18.5 - - - +
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Residues in contact with GLY 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ALA 3.8 19.3 - - - -
338A TRP* 4.2 7.9 - - - +
341A GLY* 3.4 13.0 - - - -
352A LEU* 3.8 7.9 - - - -
367A GLU 2.9 15.1 + - - -
368A ILE 3.2 3.5 + - - -
370A LYS* 1.3 74.4 - - - +
372A ILE* 1.3 61.7 + - - +
374A LEU* 3.1 6.5 + - - +
375A LEU* 3.1 20.1 + - - +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ALA* 5.0 1.8 - - + +
352A LEU* 3.7 29.7 - - + +
353A GLU* 3.3 51.1 - - - +
356A LEU* 4.1 17.7 - - + -
368A ILE* 2.9 24.8 + - + +
369A GLU* 3.5 9.4 - - + +
371A GLY* 1.3 73.6 - - - +
373A GLU* 1.3 59.7 + - - +
375A LEU* 3.3 6.1 + - - +
376A LYS* 3.0 46.0 + - - +
34C LYS* 6.0 6.5 - - - +
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A GLU 2.9 13.8 + - - +
370A LYS* 3.2 12.8 + - - +
372A ILE* 1.3 78.2 - - - +
374A LEU* 1.3 63.6 + - + +
376A LYS* 3.3 17.4 + - - +
377A ALA* 3.0 25.9 + - + +
34C LYS* 5.6 3.1 - - - +
35C ASP* 2.7 43.4 - - - +
38C ILE* 3.7 28.3 - - + +
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A TRP* 3.6 38.4 - - + +
341A GLY 3.7 11.4 - - - +
342A LYS* 3.8 37.2 - - + +
370A LYS* 2.8 21.3 + - + +
371A GLY 3.1 8.0 + - - +
373A GLU* 1.3 74.8 - - + +
375A LEU* 1.3 57.7 + - - +
377A ALA* 3.6 6.3 + - + +
378A SER* 3.1 31.4 + - - -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ILE 4.5 2.2 - - - +
341A GLY* 3.5 26.0 - - - +
344A GLY* 3.5 29.8 - - - +
345A ASP 3.8 14.6 - - - +
346A PRO* 4.3 6.5 - - + -
348A TYR* 4.1 1.8 - - + -
349A ALA* 3.5 45.8 - - + +
352A LEU* 3.8 17.3 - - + -
371A GLY 3.1 7.6 + - - +
372A ILE* 3.7 7.9 - - - +
374A LEU* 1.3 74.0 - - - +
376A LYS* 1.3 61.6 + - - +
378A SER* 3.3 4.3 + - - +
379A GLY* 2.8 30.8 + - - -
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLU* 4.2 9.1 + - - -
372A ILE* 3.0 38.1 + - - +
373A GLU* 3.6 17.9 - - - +
375A LEU* 1.3 77.9 - - - +
377A ALA* 1.3 61.3 + - - +
379A GLY* 4.2 0.3 - - - -
380A MET* 3.4 50.0 + - + +
34C LYS* 5.7 4.6 - - - +
35C ASP* 5.9 0.9 - - - -
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A GLU* 3.0 18.6 + - + +
374A LEU* 4.0 7.0 - - + +
376A LYS* 1.3 77.1 - - - +
378A SER* 1.3 58.0 + - - +
380A MET* 3.5 12.8 + - - +
381A THR* 3.1 16.6 + - - -
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLY 5.6 0.7 - - - -
344A GLY* 4.3 12.2 + - - -
374A LEU 3.1 20.2 + - - -
375A LEU* 3.3 17.8 + - - +
377A ALA* 1.3 74.0 - - - +
379A GLY* 1.3 65.2 + - - +
380A MET 3.2 2.2 + - - -
381A THR* 3.5 20.3 + - - -
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A PRO* 5.5 12.1 - - - -
375A LEU 2.8 17.1 + - - -
376A LYS 4.2 0.4 - - - -
378A SER* 1.3 78.4 + - - +
380A MET* 1.3 59.5 + - - +
381A THR 3.3 5.3 + - - -
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Residues in contact with MET 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LYS* 3.4 38.5 + - + +
377A ALA* 3.7 5.8 - - - +
378A SER 3.2 0.8 - - - -
379A GLY* 1.3 78.3 - - - +
381A THR* 1.3 62.0 + - - +
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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