Contacts of the helix formed by residues 400 - 418 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C THR 4.8 0.2 - - - -
395C LEU 5.1 0.7 - - - -
397C HIS* 3.3 16.7 + - - +
398C PRO 3.6 0.6 - - - -
399C ASP* 1.3 80.1 - - - +
401C PRO* 1.3 77.4 - - - +
402C ALA 3.3 2.5 - - - -
403C ALA* 3.1 12.7 + - - +
404C GLY 3.2 9.2 + - - -
59F TYR* 3.9 20.3 - - - -
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Residues in contact with PRO 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 3.5 33.7 - - + -
179C ASP* 5.4 4.3 - - + -
180C LEU* 3.7 19.0 - - + +
394C THR* 4.0 12.6 - - - +
395C LEU* 4.5 10.1 - - + -
400C GLY* 1.3 82.0 - - - +
402C ALA* 1.3 63.3 + - - +
404C GLY* 3.0 4.0 + - - -
405C ALA 3.0 19.9 + - - -
59F TYR* 3.6 37.7 - - + -
61F TRP* 5.4 3.6 - - + -
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Residues in contact with ALA 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASP* 4.6 15.9 - - + +
180C LEU* 4.5 0.6 - - - +
183C ASN* 3.5 29.2 - - - +
399C ASP 5.9 0.7 - - - +
400C GLY 3.3 1.7 - - - -
401C PRO* 1.3 79.3 - - - +
403C ALA* 1.3 63.4 + - - +
405C ALA* 3.2 4.5 + - - +
406C ARG* 3.1 36.0 + - - +
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Residues in contact with ALA 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C HIS* 3.1 31.4 - - + +
399C ASP* 3.5 19.4 + - + +
400C GLY 3.1 6.3 + - - +
402C ALA* 1.3 77.3 - - - +
404C GLY* 1.3 51.4 + - - +
406C ARG* 3.2 19.1 + - - +
407C ALA* 2.7 35.4 + - - +
430C GLU* 3.4 14.4 - - + +
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Residues in contact with GLY 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C GLY 5.2 1.1 - - - -
394C THR* 3.9 12.1 - - - -
397C HIS* 3.5 26.4 - - - -
400C GLY 3.2 4.9 + - - -
401C PRO 3.0 7.5 + - - -
403C ALA* 1.3 79.7 - - - +
405C ALA* 1.3 52.1 + - - +
407C ALA* 3.0 2.1 + - - +
408C VAL* 2.7 43.5 + - - +
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Residues in contact with ALA 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C TYR* 3.4 24.4 - - + +
180C LEU* 3.9 27.4 - - + +
183C ASN* 3.6 17.5 - - + +
185C ALA* 4.4 1.1 - - + +
394C THR* 3.9 2.6 - - - +
401C PRO 3.0 12.0 + - - +
402C ALA 3.5 8.5 - - - +
404C GLY* 1.3 74.4 - - - +
406C ARG* 1.3 59.7 + - - +
408C VAL* 3.3 2.4 + - - +
409C ARG* 3.0 31.7 + - - +
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Residues in contact with ARG 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ASN* 2.4 60.2 + - - +
402C ALA* 3.1 15.4 + - - +
403C ALA* 3.6 24.2 - - - +
405C ALA* 1.3 75.3 - - - +
407C ALA* 1.3 55.8 + - - +
409C ARG* 3.7 4.7 - - - +
410C GLN* 2.8 44.7 + - + +
430C GLU* 2.9 31.7 + - + +
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Residues in contact with ALA 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PRO* 4.5 6.3 - - + -
397C HIS* 4.0 7.0 - - + -
403C ALA 2.7 18.1 + - - +
404C GLY* 3.2 13.5 - - - +
406C ARG* 1.3 74.0 - - - +
408C VAL* 1.3 56.4 + - - +
410C GLN* 3.4 7.9 - - - +
411C ALA* 2.9 28.8 + - - +
430C GLU* 3.6 32.9 - - + +
431C LEU* 3.9 7.5 - - - +
434C ALA* 4.1 6.7 - - + -
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Residues in contact with VAL 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C TYR* 3.4 49.8 - - + +
372C PRO* 4.2 14.4 - - + -
375C ILE* 4.9 5.2 - - + -
388C LEU* 6.1 0.7 - - + -
390C LEU* 3.8 22.2 - - + -
393C GLY 4.3 3.6 - - - +
394C THR* 3.8 11.4 - - - +
404C GLY 2.7 24.4 + - - +
405C ALA 3.6 0.4 - - - +
407C ALA* 1.3 70.1 - - - +
409C ARG* 1.3 61.0 + - - +
411C ALA* 3.3 6.8 + - - +
412C ILE* 2.9 41.5 + - + +
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Residues in contact with ARG 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ARG* 3.4 49.6 - - - +
158C TYR* 3.8 12.3 - - + -
183C ASN 4.3 0.4 - - - +
184C GLY* 2.8 49.5 + - - +
186C ASP* 4.2 1.0 + - - -
222C GLU* 4.4 17.8 + - - -
405C ALA 3.0 19.9 + - - +
406C ARG* 3.7 7.0 - - - +
408C VAL* 1.3 76.9 - - - +
410C GLN* 1.3 57.9 + - + +
412C ILE* 3.2 11.0 + - - +
413C ASP* 2.8 47.0 + - - +
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Residues in contact with GLN 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ARG* 2.8 29.4 + - + +
407C ALA* 3.4 3.2 - - - +
409C ARG* 1.3 72.9 - - + +
411C ALA* 1.3 63.7 + - - +
413C ASP* 3.0 13.2 + - - +
414C ALA* 2.9 18.9 + - - +
424C TYR* 3.6 17.0 - - + +
428C HIS* 3.4 31.8 - - + +
430C GLU* 3.0 27.8 + - - +
431C LEU* 2.8 44.7 - - + +
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Residues in contact with ALA 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PRO* 3.8 27.1 - - + +
375C ILE* 4.2 9.2 - - + -
407C ALA 2.9 13.4 + - - +
408C VAL 3.5 8.3 - - - +
410C GLN* 1.3 75.3 - - - +
412C ILE* 1.3 63.9 + - - +
414C ALA* 3.0 9.1 + - - +
415C ILE* 2.9 29.8 + - + +
421C LEU* 6.1 3.1 - - + -
431C LEU* 3.9 18.5 - - + +
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Residues in contact with ILE 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ARG* 4.5 15.9 - - + +
156C PRO* 4.3 21.8 - - + +
158C TYR* 3.9 29.2 - - + -
375C ILE* 4.1 15.7 - - + +
379C ILE* 5.2 3.6 - - + -
388C LEU* 4.3 17.3 - - + -
408C VAL* 2.9 27.3 + - + +
409C ARG* 3.4 15.5 - - - +
411C ALA* 1.3 74.7 - - - +
413C ASP* 1.3 65.5 + - - +
415C ILE* 3.2 10.2 + - - +
416C MET* 2.9 36.0 + - + +
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Residues in contact with ASP 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ARG* 5.4 4.5 - - - -
409C ARG* 2.8 36.4 + - - +
410C GLN* 3.0 12.5 + - - +
412C ILE* 1.3 76.5 - - - +
414C ALA* 1.3 57.1 + - - +
416C MET* 3.4 7.8 + - - +
417C GLN* 3.0 30.9 + - - +
424C TYR* 3.8 18.9 + - - +
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Residues in contact with ALA 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C GLN 2.9 7.5 + - - +
411C ALA* 3.0 12.3 + - - +
413C ASP* 1.3 75.6 - - - +
415C ILE* 1.3 54.2 + - + +
417C GLN* 3.2 1.8 + - - -
418C GLY 2.7 29.6 + - - -
419C ILE 3.0 28.6 + - - +
421C LEU* 4.9 7.2 - - + -
424C TYR* 3.4 39.2 - - + -
431C LEU* 5.1 0.2 - - + -
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Residues in contact with ILE 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PRO 5.5 0.9 - - - +
375C ILE* 3.7 24.5 - - + -
376C GLN* 3.6 42.6 - - + +
379C ILE* 3.8 39.3 - - + -
380C GLU* 5.7 0.9 - - + +
411C ALA* 2.9 16.7 + - + +
412C ILE* 3.7 6.1 - - - +
414C ALA* 1.3 78.7 - - + +
416C MET* 1.3 62.8 + - + +
417C GLN 3.5 0.2 + - - -
418C GLY* 3.6 9.4 + - - -
419C ILE 5.0 0.9 - - - +
421C LEU* 6.4 2.5 - - + -
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Residues in contact with MET 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASP* 4.0 14.4 - - + +
155C ARG* 3.7 36.6 - - + +
156C PRO* 4.1 4.3 - - - -
379C ILE* 5.9 2.9 - - + -
384C THR* 3.8 26.9 - - + +
412C ILE* 2.9 32.1 + - + +
413C ASP* 3.8 7.2 - - - +
415C ILE* 1.3 79.6 - - + +
417C GLN* 1.3 60.3 + - - +
418C GLY 3.4 0.2 - - - -
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Residues in contact with GLN 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ASP 3.0 18.5 + - - +
414C ALA* 3.8 0.9 - - - +
416C MET* 1.3 76.8 - - - +
418C GLY* 1.3 57.5 + - - +
419C ILE* 2.9 34.8 - - + +
424C TYR* 5.3 4.0 - - + -
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Residues in contact with GLY 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ALA 2.7 6.6 + - - -
415C ILE* 3.6 8.8 + - - -
416C MET 3.4 3.2 + - - -
417C GLN* 1.3 77.1 - - - +
419C ILE* 1.3 61.9 + - - +
420C PRO* 3.3 10.0 - - - +
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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