Contacts of the helix formed by residues 400 - 418 (chain H) in PDB entry 3KDO
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 400 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 5.1 3.8 - - - -
395H LEU 4.4 0.4 - - - -
397H HIS* 3.7 12.8 + - - +
398H PRO 3.2 5.3 + - - -
399H ASP* 1.3 77.8 - - - +
401H PRO* 1.3 67.6 - - - +
402H ALA* 3.4 2.5 - - - -
403H ALA* 2.4 37.9 + - - +
404H GLY 3.0 3.4 + - - -
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Residues in contact with PRO 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.9 18.8 - - + -
61A TRP* 5.6 6.5 - - + -
176H LEU* 3.8 24.7 - - + -
179H ASP* 5.7 2.9 - - + +
180H LEU* 4.0 10.7 - - + +
394H THR 3.8 14.0 - - - +
395H LEU* 3.8 32.0 - - + +
400H GLY* 1.3 79.7 - - - -
402H ALA* 1.3 56.9 + - - +
403H ALA 2.6 12.3 + - - -
404H GLY* 2.6 14.2 + - - -
405H ALA* 2.9 11.1 + - - +
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Residues in contact with ALA 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179H ASP* 4.5 17.8 - - + +
180H LEU* 4.3 4.1 - - - +
183H ASN* 3.7 28.0 - - - +
399H ASP 6.0 0.4 - - - +
400H GLY 3.4 1.0 - - - -
401H PRO* 1.3 78.6 - - - +
403H ALA* 1.3 55.5 + - - +
405H ALA* 4.1 3.1 - - - -
406H ARG* 2.5 43.3 + - - +
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Residues in contact with ALA 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397H HIS* 3.3 18.4 + - + +
399H ASP* 3.2 38.5 + - + +
400H GLY 2.4 28.9 + - - +
401H PRO 2.6 0.2 + - - -
402H ALA* 1.3 71.7 - - - +
404H GLY* 1.3 62.3 + - - +
406H ARG* 3.2 22.7 + - - +
407H ALA* 3.0 18.9 + - - +
430H GLU* 4.0 2.8 - - + +
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Residues in contact with GLY 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372H PRO* 4.8 1.1 - - - +
393H GLY 5.0 1.6 - - - -
394H THR* 3.3 18.6 - - - -
397H HIS* 3.1 28.8 - - - -
400H GLY 3.0 6.5 + - - -
401H PRO 2.6 9.7 + - - -
403H ALA* 1.3 71.2 - - - +
405H ALA* 1.3 59.0 + - - -
407H ALA* 3.2 3.5 + - - +
408H VAL* 3.1 27.6 + - - +
438H TRP* 5.7 0.2 - - - -
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Residues in contact with ALA 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H TYR* 3.6 22.3 - - + +
180H LEU* 4.0 22.9 - - + +
183H ASN* 2.9 27.6 - - + +
185H ALA* 4.5 0.9 - - + +
394H THR* 3.6 2.2 - - - +
401H PRO 2.9 11.8 + - - +
402H ALA 4.0 3.8 - - - +
404H GLY* 1.3 76.9 - - - +
406H ARG* 1.3 60.9 + - - +
407H ALA 3.1 0.9 + - - -
408H VAL* 3.2 4.5 + - - +
409H ARG* 3.1 23.4 + - - +
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Residues in contact with ARG 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H ASN* 3.3 32.5 + - + +
399H ASP* 5.0 4.4 + - - +
402H ALA* 2.5 45.2 + - - +
403H ALA* 3.2 26.3 + - - +
405H ALA* 1.3 77.9 - - - +
407H ALA* 1.3 54.3 + - - +
409H ARG* 3.7 5.7 + - - +
410H GLN* 2.7 41.5 + - + +
430H GLU* 3.0 37.1 + - + +
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Residues in contact with ALA 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372H PRO* 4.2 8.1 - - + -
397H HIS* 4.0 2.9 - - + -
403H ALA 3.0 12.6 + - - +
404H GLY 3.3 11.2 - - - +
405H ALA 3.1 0.2 - - - -
406H ARG* 1.3 73.9 - - - +
408H VAL* 1.3 61.2 + - - +
410H GLN* 2.8 6.0 + - - +
411H ALA* 2.8 27.9 + - - +
430H GLU* 3.7 30.2 - - - +
431H LEU* 3.9 8.1 - - - +
434H ALA* 4.0 15.9 - - + -
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Residues in contact with VAL 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H TYR* 3.5 43.5 - - + +
372H PRO* 4.0 13.7 - - + -
375H ILE* 4.6 6.3 - - + -
388H LEU* 5.9 0.4 - - + -
390H LEU* 3.7 28.9 - - + -
393H GLY 4.6 1.8 - - - +
394H THR* 4.2 3.6 - - - +
404H GLY 3.1 15.6 + - - +
405H ALA 3.7 5.2 - - - +
407H ALA* 1.3 75.0 - - - +
409H ARG* 1.3 58.6 + - - +
411H ALA* 3.2 6.5 + - - +
412H ILE* 2.8 49.1 + - + +
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Residues in contact with ARG 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ARG* 3.5 49.3 - - - +
158H TYR* 4.1 12.8 - - + -
184H GLY* 2.7 67.7 + - - -
186H ASP* 4.1 0.8 + - - -
222H GLU* 4.2 19.4 + - - -
405H ALA 3.1 10.3 + - - +
406H ARG* 4.0 6.5 - - - +
408H VAL* 1.3 78.8 - - - +
410H GLN* 1.3 58.1 + - + +
412H ILE* 4.0 10.2 - - - +
413H ASP* 3.0 46.7 + - - +
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Residues in contact with GLN 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H ARG* 2.7 25.6 + - + +
407H ALA* 2.8 6.0 + - - +
409H ARG* 1.3 75.6 - - + +
411H ALA* 1.3 53.3 + - - +
413H ASP* 3.0 10.3 + - - +
414H ALA 2.7 30.3 + - - -
424H TYR* 3.5 19.0 - - + -
428H HIS* 3.2 27.8 - - + +
430H GLU* 2.8 30.7 - - - +
431H LEU* 2.7 43.9 - - + +
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Residues in contact with ALA 411 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372H PRO* 3.6 26.9 - - + +
375H ILE* 4.2 12.3 - - + -
407H ALA 2.8 14.9 + - - +
408H VAL 3.5 7.4 - - - +
410H GLN* 1.3 71.6 - - - +
412H ILE* 1.3 51.0 + - - +
414H ALA* 2.5 30.8 + - - +
415H ILE* 2.7 24.6 + - + +
421H LEU* 6.4 1.3 - - + +
431H LEU* 4.0 16.6 - - + +
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Residues in contact with ILE 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ARG* 4.3 15.3 - - + +
156H PRO* 4.2 28.5 - - + +
158H TYR* 4.0 20.2 - - + -
375H ILE* 4.1 15.0 - - + +
379H ILE* 5.0 4.5 - - + -
388H LEU* 4.3 17.3 - - + -
408H VAL* 2.8 41.1 + - + +
409H ARG* 4.0 12.6 - - - +
411H ALA* 1.3 71.9 - - - +
413H ASP* 1.3 60.1 + - - +
415H ILE* 3.2 9.7 + - - +
416H MET* 2.9 42.2 + - + +
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Residues in contact with ASP 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ARG* 5.1 5.4 - - - -
409H ARG* 3.0 40.9 + - - +
410H GLN* 3.0 8.0 + - - +
412H ILE* 1.3 79.7 - - - +
414H ALA* 1.3 61.3 + - - +
416H MET* 3.9 7.8 - - - +
417H GLN* 3.2 24.1 + - - +
424H TYR* 4.0 18.0 + - - +
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Residues in contact with ALA 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410H GLN 2.7 12.0 + - - +
411H ALA* 2.5 23.3 + - - +
413H ASP* 1.3 69.8 - - - +
415H ILE* 1.3 53.3 + - + +
417H GLN* 3.2 2.1 + - - -
418H GLY* 2.7 31.9 + - - -
419H ILE* 3.1 29.4 + - - +
420H PRO 4.9 0.7 - - - +
421H LEU* 5.1 4.9 - - - +
424H TYR* 3.7 30.3 - - + -
431H LEU* 4.7 2.2 - - + -
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Residues in contact with ILE 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375H ILE* 3.8 14.8 - - + -
376H GLN* 3.2 47.1 - - + +
379H ILE* 3.5 43.1 - - + -
380H GLU 5.8 0.2 - - - +
411H ALA* 2.7 21.2 + - + +
412H ILE* 3.8 5.6 - - - +
414H ALA* 1.3 72.5 - - + +
416H MET* 1.3 67.4 + - + +
418H GLY* 3.2 12.8 + - - -
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Residues in contact with MET 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H ASP* 4.0 15.9 - - + +
155H ARG* 3.9 38.6 - - + +
156H PRO* 4.2 8.1 - - - -
379H ILE* 6.1 1.6 - - - -
384H THR* 4.3 18.4 - - + -
412H ILE* 2.9 32.2 + - + +
413H ASP* 3.9 9.4 - - - +
415H ILE* 1.3 81.2 - - + +
417H GLN* 1.3 63.1 + - - +
418H GLY* 3.2 0.7 + - - -
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Residues in contact with GLN 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413H ASP 3.2 16.5 + - - +
416H MET* 1.3 79.2 - - - +
418H GLY* 1.3 56.5 + - - +
419H ILE* 2.8 31.9 - - + +
424H TYR* 5.7 2.7 - - + -
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Residues in contact with GLY 418 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414H ALA 2.7 11.4 + - - -
415H ILE* 3.6 10.5 - - - -
416H MET 3.1 3.6 - - - -
417H GLN* 1.3 74.3 - - - +
419H ILE* 1.3 53.5 + - - +
420H PRO* 2.8 25.0 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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