Contacts of the helix formed by residues 400 - 418 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 3.8 17.7 - - - -
394G THR 4.7 0.4 - - - -
395G LEU 5.0 1.1 - - - -
397G HIS* 2.9 18.7 + - - +
398G PRO 3.5 1.0 + - - -
399G ASP* 1.3 80.2 - - - +
401G PRO* 1.3 71.0 - - - +
402G ALA* 3.4 2.7 - - - -
403G ALA* 3.2 4.0 + - - +
404G GLY 2.9 24.1 + - - -
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Residues in contact with PRO 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.5 37.0 - - + -
61B TRP* 5.4 3.8 - - + -
176G LEU* 3.6 33.9 - - + -
179G ASP* 5.6 3.4 - - + -
180G LEU* 3.6 18.9 - - + +
394G THR* 4.0 12.2 - - - +
395G LEU* 4.6 11.2 - - + +
400G GLY* 1.3 80.2 - - - +
402G ALA* 1.3 67.4 + - - +
404G GLY* 2.9 2.8 + - - -
405G ALA 2.8 20.6 + - - -
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Residues in contact with ALA 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ASP* 4.5 20.9 - - + +
180G LEU* 4.4 1.1 - - - +
183G ASN* 3.7 17.2 - - - +
400G GLY 3.4 0.8 - - - -
401G PRO* 1.3 81.1 - - - +
403G ALA* 1.3 64.1 + - - +
405G ALA* 3.3 4.6 + - - +
406G ARG* 3.3 40.5 + - - +
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Residues in contact with ALA 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397G HIS* 3.8 11.0 - - + +
399G ASP* 3.6 32.7 + - + +
400G GLY 3.2 9.9 + - - +
402G ALA* 1.3 78.3 - - - +
404G GLY* 1.3 57.8 + - - +
406G ARG* 3.2 28.5 + - - +
407G ALA* 2.9 28.6 + - - +
430G GLU* 3.7 7.6 - - + +
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Residues in contact with GLY 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G GLY 4.9 1.2 - - - +
394G THR* 3.5 15.3 - - - -
397G HIS* 3.5 29.7 - - - -
400G GLY 2.9 11.1 + - - -
401G PRO 2.9 4.4 + - - -
403G ALA* 1.3 76.3 - - - +
405G ALA* 1.3 60.7 + - - +
407G ALA* 3.2 3.3 + - - +
408G VAL* 3.0 27.5 + - - +
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Residues in contact with ALA 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G TYR* 3.4 23.1 - - + +
180G LEU* 3.9 26.9 - - + +
183G ASN* 3.4 18.8 - - + +
185G ALA* 4.5 0.9 - - + +
394G THR* 3.9 1.4 - - - +
401G PRO 2.8 14.7 + - - +
402G ALA 3.6 7.4 - - - +
403G ALA 3.3 0.2 - - - -
404G GLY* 1.3 73.6 - - - +
406G ARG* 1.3 63.3 + - - +
408G VAL* 3.3 4.0 + - - +
409G ARG* 3.1 26.2 + - - +
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Residues in contact with ARG 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G ASN* 2.5 52.2 + - + +
402G ALA* 3.3 21.6 + - - +
403G ALA* 3.2 30.1 + - - +
405G ALA* 1.3 76.7 - - - +
407G ALA* 1.3 57.7 + - - +
409G ARG* 3.3 6.2 + - - +
410G GLN* 2.9 40.3 + - + +
430G GLU* 3.2 30.2 + - + +
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Residues in contact with ALA 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G PRO* 4.2 4.8 - - + +
397G HIS* 3.7 20.4 - - + -
403G ALA 2.9 14.1 + - - +
404G GLY 3.4 9.4 - - - +
405G ALA 3.2 0.2 - - - -
406G ARG* 1.3 77.2 - - - +
408G VAL* 1.3 60.4 + - - +
410G GLN* 3.4 7.2 + - - +
411G ALA* 3.1 22.5 + - - +
430G GLU* 3.7 24.8 - - - +
431G LEU* 3.9 9.7 - - - +
434G ALA* 4.2 7.0 - - + -
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Residues in contact with VAL 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G TYR* 3.3 49.4 - - + +
372G PRO* 4.2 15.0 - - + -
375G ILE* 5.0 4.5 - - + -
388G LEU* 6.0 0.7 - - + -
390G LEU* 3.8 30.5 - - + -
393G GLY 4.3 3.4 - - - +
394G THR* 4.0 6.1 - - - +
404G GLY 3.0 15.0 + - - +
405G ALA 3.6 1.6 - - - +
406G ARG 3.2 0.2 - - - -
407G ALA* 1.3 73.8 - - - +
409G ARG* 1.3 64.6 + - - +
411G ALA* 3.2 6.2 + - - +
412G ILE* 3.1 31.7 + - + +
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Residues in contact with ARG 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ARG* 3.4 47.9 - - - +
158G TYR* 3.9 15.3 - - + -
183G ASN 4.4 0.4 - - - +
184G GLY* 2.6 62.4 + - - +
186G ASP* 4.1 0.2 + - - -
222G GLU* 4.0 15.8 + - - -
405G ALA 3.1 9.6 + - - +
406G ARG* 3.3 9.2 + - - +
408G VAL* 1.3 77.9 - - - +
410G GLN* 1.3 57.6 + - + +
412G ILE* 3.4 10.0 + - - +
413G ASP* 3.0 42.3 + - - +
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Residues in contact with GLN 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406G ARG* 2.9 28.6 + - - +
407G ALA* 3.5 4.7 - - - +
409G ARG* 1.3 74.7 - - + +
411G ALA* 1.3 66.6 + - - +
413G ASP* 3.1 11.7 + - - +
414G ALA 3.0 19.4 + - - -
424G TYR* 3.5 16.5 - - + -
428G HIS* 3.2 36.3 - - + +
430G GLU* 2.8 30.1 + - - +
431G LEU* 2.9 33.7 + - + -
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Residues in contact with ALA 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G PRO* 3.7 30.5 - - + +
375G ILE* 4.1 7.6 - - + -
407G ALA 3.1 13.3 + - - +
408G VAL 3.2 8.3 + - - +
410G GLN* 1.3 75.7 - - - +
412G ILE* 1.3 52.6 + - - +
414G ALA* 3.5 2.6 + - - +
415G ILE* 2.7 40.9 + - + +
421G LEU* 3.9 8.1 - - + -
431G LEU* 3.8 20.6 - - + +
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Residues in contact with ILE 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ARG* 4.3 14.6 - - + +
156G PRO* 4.0 24.2 - - + +
158G TYR* 4.2 23.1 - - + -
375G ILE* 4.1 14.8 - - + -
379G ILE* 5.0 2.9 - - + -
388G LEU* 4.1 21.1 - - + -
408G VAL* 3.1 22.6 + - + +
409G ARG* 3.6 15.3 - - - +
410G GLN 3.1 0.2 - - - -
411G ALA* 1.3 74.6 - - - +
413G ASP* 1.3 58.1 + - - +
415G ILE* 3.3 7.5 + - - +
416G MET* 2.8 53.8 + - + +
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Residues in contact with ASP 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ARG* 5.6 3.6 - - - -
409G ARG* 3.0 31.3 + - - +
410G GLN* 3.3 12.3 - - - +
412G ILE* 1.3 78.6 - - - +
414G ALA* 1.3 56.9 + - - +
416G MET* 3.1 7.8 + - - +
417G GLN* 2.9 44.0 + - - +
424G TYR* 3.6 18.3 + - - +
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Residues in contact with ALA 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410G GLN 3.0 6.0 + - - +
411G ALA* 3.8 9.0 - - - +
413G ASP* 1.3 75.9 - - - +
415G ILE* 1.3 59.1 + - - +
417G GLN* 3.0 2.9 + - - -
418G GLY 2.8 9.7 + - - -
419G ILE* 2.8 46.1 + - + +
421G LEU* 4.6 6.3 - - + -
424G TYR* 3.3 45.0 - - + -
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Residues in contact with ILE 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375G ILE* 3.6 33.0 - - + -
376G GLN* 3.9 31.0 - - + +
379G ILE* 3.7 40.4 - - + -
411G ALA* 2.7 29.0 + - + +
412G ILE* 3.6 6.3 - - - +
414G ALA* 1.3 75.0 - - - +
416G MET* 1.3 63.3 + - + +
418G GLY* 3.4 11.3 + - - +
419G ILE 4.7 2.2 - - - -
421G LEU* 3.9 17.0 - - + -
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Residues in contact with MET 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ASP* 4.2 13.5 - - + -
155G ARG* 3.9 35.4 - - + +
156G PRO* 4.2 4.5 - - - -
379G ILE* 5.8 1.6 - - - -
384G THR* 3.9 26.5 - - + -
412G ILE* 2.8 40.3 + - + +
413G ASP* 3.5 7.9 - - - +
415G ILE* 1.3 77.8 - - + +
417G GLN* 1.3 62.4 + - + +
418G GLY 3.4 0.4 + - - -
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Residues in contact with GLN 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413G ASP* 2.9 27.5 + - - +
414G ALA 3.0 3.5 + - - +
416G MET* 1.3 79.4 - - + +
418G GLY* 1.3 63.7 + - - +
419G ILE* 3.2 31.5 + - + +
424G TYR* 4.1 17.4 + - - -
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Residues in contact with GLY 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G ALA 2.8 3.9 + - - -
415G ILE* 3.4 8.7 + - - -
416G MET 3.4 4.0 + - - -
417G GLN* 1.3 79.1 - - - +
419G ILE* 1.3 60.2 + - - +
420G PRO* 3.7 6.9 - - - +
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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