Contacts of the helix formed by residues 400 - 418 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C TYR* 4.0 16.7 - - - -
394F THR 4.6 0.2 - - - -
397F HIS* 2.9 20.6 + - - +
398F PRO 3.4 1.0 + - - -
399F ASP* 1.3 80.1 - - - +
401F PRO* 1.3 64.9 - - - +
402F ALA* 3.5 2.2 - - - -
403F ALA 3.3 3.3 + - - -
404F GLY 2.8 30.0 + - - -
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Residues in contact with PRO 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TYR* 3.6 26.2 - - + -
61C TRP* 5.1 3.6 - - + -
176F LEU* 3.5 28.3 - - + -
179F ASP* 5.3 4.9 - - + +
180F LEU* 3.5 26.7 - - + +
394F THR 3.9 12.1 - - - +
395F LEU* 3.7 15.5 - - + +
400F GLY* 1.3 79.3 - - - +
402F ALA* 1.3 68.6 + - - +
404F GLY* 2.7 2.9 + - - -
405F ALA 2.7 22.3 + - - -
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Residues in contact with ALA 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F ASP* 4.3 19.1 - - + +
180F LEU* 4.1 0.6 - - - +
183F ASN* 3.6 20.0 - - - +
399F ASP 5.9 0.7 - - - +
400F GLY 3.5 0.4 - - - -
401F PRO* 1.3 79.8 - - - +
403F ALA* 1.3 62.8 + - - +
405F ALA* 3.2 5.3 + - - +
406F ARG* 3.1 42.4 + - - +
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Residues in contact with ALA 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397F HIS* 3.7 10.3 - - + +
399F ASP* 3.6 33.3 + - + +
400F GLY 3.3 8.8 + - - +
401F PRO 3.2 0.6 - - - -
402F ALA* 1.3 78.1 - - - +
404F GLY* 1.3 52.6 + - - +
406F ARG* 3.1 27.1 + - - +
407F ALA* 2.8 35.5 + - - +
430F GLU* 3.6 9.1 - - + +
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Residues in contact with GLY 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F PRO* 5.3 0.3 - - - +
393F GLY 4.8 0.6 - - - +
394F THR* 3.5 16.1 - - - -
397F HIS* 3.4 30.7 - - - -
400F GLY 2.8 7.7 + - - -
401F PRO 2.7 12.6 + - - -
403F ALA* 1.3 73.4 - - - +
405F ALA* 1.3 58.8 + - - -
407F ALA* 3.3 2.8 + - - +
408F VAL* 3.1 28.2 + - - +
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Residues in contact with ALA 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F TYR* 3.5 17.2 - - - +
180F LEU* 4.0 22.9 - - + +
183F ASN* 3.3 25.8 - - + +
185F ALA* 4.6 4.7 - - + +
394F THR* 3.8 1.4 - - - +
401F PRO 2.7 14.5 + - - +
402F ALA 3.4 7.9 - - - +
404F GLY* 1.3 72.6 - - - +
406F ARG* 1.3 62.0 + - - +
408F VAL* 3.1 13.7 + - - +
409F ARG* 3.1 16.5 + - - +
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Residues in contact with ARG 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F ASN* 2.5 51.6 + - + +
402F ALA* 3.1 19.5 + - - +
403F ALA* 3.1 33.2 + - - +
405F ALA* 1.3 77.8 - - - +
407F ALA* 1.3 60.8 + - - +
409F ARG* 3.5 5.5 + - - +
410F GLN* 2.9 36.1 + - + +
430F GLU* 3.1 29.7 + - + +
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Residues in contact with ALA 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F PRO* 4.3 5.2 - - + -
397F HIS* 3.8 13.2 - - + +
403F ALA 2.8 13.6 + - - +
404F GLY 3.4 9.6 - - - +
405F ALA 3.1 0.2 - - - -
406F ARG* 1.3 77.5 - - - +
408F VAL* 1.3 63.1 + - - +
410F GLN* 3.4 4.6 + - - +
411F ALA* 3.0 22.5 + - - +
430F GLU* 3.7 31.4 - - + +
431F LEU* 3.8 12.3 - - - +
434F ALA* 4.1 6.5 - - + -
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Residues in contact with VAL 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F TYR* 3.5 45.5 - - + +
372F PRO* 4.0 15.0 - - + -
375F ILE* 4.8 4.7 - - + -
388F LEU* 6.0 0.7 - - + -
390F LEU* 3.6 30.7 - - + -
393F GLY 4.2 3.6 - - - +
394F THR* 3.9 5.6 - - - +
404F GLY 3.1 14.1 + - - +
405F ALA 3.1 7.6 + - - +
407F ALA* 1.3 72.7 - - - +
409F ARG* 1.3 66.5 + - - +
411F ALA* 3.2 5.7 + - - +
412F ILE* 2.9 31.4 + - + +
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Residues in contact with ARG 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ARG* 3.3 45.7 - - - +
158F TYR* 3.9 14.1 - - + -
183F ASN 4.4 0.2 - - - +
184F GLY* 2.6 62.3 + - - +
186F ASP* 4.1 1.2 + - - -
222F GLU* 4.4 19.6 + - - -
405F ALA 3.1 8.1 + - - +
406F ARG* 3.9 9.0 - - - +
408F VAL* 1.3 77.2 - - - +
410F GLN* 1.3 56.6 + - + +
412F ILE* 3.3 13.9 + - - +
413F ASP* 2.8 46.1 + - - +
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Residues in contact with GLN 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F ARG* 2.9 26.7 + - + +
407F ALA 3.5 3.6 - - - +
408F VAL 3.2 0.2 - - - -
409F ARG* 1.3 74.9 - - + +
411F ALA* 1.3 67.9 + - - +
413F ASP* 3.0 12.0 + - - +
414F ALA* 2.8 23.7 + - - +
424F TYR* 3.9 13.5 - - + -
428F HIS* 3.1 28.4 - - + +
430F GLU* 3.1 31.6 + - - +
431F LEU* 3.0 37.8 + - + +
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Residues in contact with ALA 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F PRO* 3.9 23.8 - - + +
375F ILE* 3.9 18.6 - - + -
407F ALA 3.0 11.0 + - - +
408F VAL 3.4 8.1 - - - +
410F GLN* 1.3 77.2 - - - +
412F ILE* 1.3 58.1 + - - +
414F ALA* 3.1 8.9 + - - +
415F ILE* 2.9 34.7 + - - +
421F LEU* 4.2 10.0 - - + +
431F LEU* 4.3 9.5 - - + +
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Residues in contact with ILE 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ARG* 4.3 16.8 - - - +
156F PRO* 4.3 24.2 - - + +
158F TYR* 3.9 28.5 - - + -
375F ILE* 4.3 14.1 - - + -
379F ILE* 5.1 2.9 - - + -
388F LEU* 4.3 16.2 - - + -
408F VAL* 2.9 24.8 + - + +
409F ARG* 3.4 18.4 - - - +
411F ALA* 1.3 72.5 - - - +
413F ASP* 1.3 69.1 + - - +
415F ILE* 3.1 10.3 + - - +
416F MET* 2.9 40.2 + - + +
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Residues in contact with ASP 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ARG* 5.4 4.7 - - - -
409F ARG* 2.8 34.7 + - - +
410F GLN* 3.3 11.5 - - - +
412F ILE* 1.3 76.0 - - - +
414F ALA* 1.3 63.0 + - - +
416F MET* 3.4 6.9 + - - +
417F GLN* 3.0 39.2 + - - +
424F TYR* 4.2 15.5 + - - +
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Residues in contact with ALA 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410F GLN 2.8 11.8 + - - +
411F ALA* 3.2 12.1 - - - +
413F ASP* 1.3 73.4 - - - +
415F ILE* 1.3 59.7 + - - +
417F GLN* 2.8 23.7 + - - -
418F GLY 2.9 10.7 + - - -
419F ILE* 3.2 25.8 + - - +
421F LEU* 4.5 8.5 - - + -
424F TYR* 3.8 33.5 - - + -
431F LEU* 5.2 0.2 - - + -
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Residues in contact with ILE 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375F ILE* 3.8 14.6 - - + -
376F GLN* 3.5 50.5 - - + +
379F ILE* 3.6 46.7 - - + -
380F GLU* 5.7 0.4 - - - +
411F ALA 2.9 23.7 + - - +
412F ILE* 3.6 6.1 - - - +
414F ALA* 1.3 73.3 - - - +
416F MET* 1.3 63.2 + - + +
418F GLY* 3.4 10.7 + - - +
419F ILE 4.3 2.4 + - - -
421F LEU* 4.1 14.4 - - + -
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Residues in contact with MET 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F ASP* 4.2 13.5 - - + -
155F ARG* 3.8 34.1 - - + +
156F PRO* 4.2 5.2 - - - -
379F ILE* 5.8 1.6 - - + -
384F THR* 3.9 27.4 - - + -
412F ILE* 2.9 31.8 + - + +
413F ASP* 3.6 9.4 - - - +
415F ILE* 1.3 81.6 - - + +
417F GLN* 1.3 63.5 + - + +
418F GLY 3.2 1.0 + - - -
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Residues in contact with GLN 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413F ASP* 3.0 21.9 + - - +
414F ALA 2.8 7.2 + - - +
416F MET* 1.3 74.8 - - + +
418F GLY* 1.3 59.6 + - - +
419F ILE* 3.1 24.3 + - + +
424F TYR* 3.6 30.2 + - - -
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Residues in contact with GLY 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414F ALA 2.9 4.1 + - - -
415F ILE* 3.4 9.5 + - - -
416F MET 3.2 5.2 + - - -
417F GLN* 1.3 76.9 - - - +
419F ILE* 1.3 62.1 + - - +
420F PRO* 3.4 9.0 - - - +
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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
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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