Contacts of the helix formed by residues 428 - 439 (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 HIS 428 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410F GLN* 3.1 34.5 - - + +
424F TYR* 2.7 65.5 + + - +
425F ALA 2.7 22.8 + - - +
427F THR* 1.3 100.5 + - + +
429F LYS* 1.3 66.6 + - - +
430F GLU* 3.5 2.0 - - - -
431F LEU* 3.5 4.7 + - + -
432F ALA* 3.0 14.9 + - - +
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Residues in contact with LYS 429 (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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427F THR 4.2 0.6 - - - -
428F HIS* 1.3 68.2 - - - +
430F GLU* 1.3 78.7 + - - +
432F ALA* 2.8 18.8 + - - +
433F ARG* 2.8 28.9 + - + +
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Residues in contact with GLU 430 (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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397F HIS* 2.9 29.0 + - - -
399F ASP* 5.1 2.4 + - - +
403F ALA* 3.6 32.8 - - + +
406F ARG* 3.1 37.2 + - + +
407F ALA* 3.7 12.8 - - - +
410F GLN* 3.1 21.3 + - - +
428F HIS* 4.4 0.2 - - - -
429F LYS* 1.3 81.6 + - - +
431F LEU* 1.3 62.3 + - - +
433F ARG* 3.3 0.8 + - - -
434F ALA* 2.9 8.8 + - - +
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Residues in contact with LEU 431 (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* 4.1 23.1 - - + -
407F ALA* 3.8 11.9 - - - +
410F GLN* 3.0 20.5 + - + +
411F ALA* 4.3 20.4 - - + +
414F ALA* 5.2 0.2 - - + -
421F LEU* 4.1 15.3 - - + +
424F TYR* 3.8 30.5 - - + -
425F ALA* 3.8 19.3 - - + +
428F HIS* 3.8 5.4 - - + +
429F LYS 3.2 0.4 - - - -
430F GLU* 1.3 79.4 - - - +
432F ALA* 1.3 64.3 + - - +
434F ALA* 3.2 1.0 + - - +
435F LEU* 3.0 37.4 + - + +
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Residues in contact with ALA 432 (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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425F ALA* 3.6 26.6 - - + +
426F LYS* 5.7 0.4 - - - -
428F HIS 3.0 14.6 + - - +
429F LYS* 2.8 17.4 + - - +
431F LEU* 1.3 71.8 - - - +
433F ARG* 1.3 64.9 + - + +
435F LEU* 3.1 7.2 + - - +
436F GLU* 3.0 21.2 + - - +
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Residues in contact with ARG 433 (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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397F HIS* 4.2 4.9 - - + -
398F PRO* 3.7 26.5 + - + +
399F ASP* 2.6 44.7 + - - +
429F LYS* 2.8 30.0 + - + +
430F GLU 4.0 2.9 - - - +
432F ALA* 1.3 74.6 - - + +
434F ALA* 1.3 62.3 + - - +
436F GLU* 3.1 37.0 + - - +
437F LYS* 3.2 21.5 + - - +
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Residues in contact with ALA 434 (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* 4.0 26.9 - - + -
373F GLY 6.3 0.2 - - - -
397F HIS* 3.5 23.6 + - + +
398F PRO* 4.9 1.6 - - - -
407F ALA* 4.1 2.7 - - + -
430F GLU 2.9 14.4 + - - +
431F LEU 3.4 9.9 - - - +
432F ALA 3.2 0.2 - - - -
433F ARG* 1.3 77.6 - - - +
435F LEU* 1.3 63.4 + - - +
437F LYS* 3.1 3.1 + - - -
438F TRP* 3.1 36.5 + - + +
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Residues in contact with LEU 435 (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* 4.8 0.4 - - + -
373F GLY* 3.7 20.6 - - - +
421F LEU* 4.3 4.7 - - + -
422F ASP* 3.5 29.8 - - - +
425F ALA* 4.0 26.0 - - + -
431F LEU* 3.0 27.1 + - + +
432F ALA 3.5 6.1 - - - +
434F ALA* 1.3 76.3 - - - +
436F GLU* 1.3 60.7 + - - +
439F GLY* 2.5 51.9 + - - +
440F HIS* 3.9 13.5 - - + +
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Residues in contact with GLU 436 (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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398F PRO* 6.4 0.4 - - - -
432F ALA 3.0 12.7 + - - +
433F ARG* 3.1 38.6 + - - +
434F ALA 3.1 0.2 - - - -
435F LEU* 1.3 79.5 - - - +
437F LYS* 1.3 61.9 + - - +
439F GLY 4.7 0.3 + - - -
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Residues in contact with LYS 437 (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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5C PHE* 4.3 14.8 + - - +
56C THR* 3.9 3.1 - - - -
57C THR* 2.9 36.0 + - - -
58C LEU 5.9 0.4 - - - -
396F GLY 2.6 30.4 + - - +
398F PRO* 4.0 23.5 - - + +
433F ARG 3.2 7.0 + - - +
434F ALA 3.1 8.0 + - - +
436F GLU* 1.3 82.9 - - + +
438F TRP* 1.3 88.8 + - + +
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Residues in contact with TRP 438 (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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5C PHE 4.5 7.8 - - - +
55C TRP* 3.4 27.8 - + - -
56C THR* 3.2 21.8 + - + -
371F HIS* 3.7 34.1 - - + +
372F PRO* 4.2 8.5 - - + -
392F GLY 3.6 18.6 - - - -
393F GLY* 3.8 18.6 - - - -
396F GLY* 3.4 39.0 - - - -
397F HIS* 3.6 12.6 - + - -
398F PRO* 5.1 0.2 - - + -
434F ALA* 3.1 32.5 + - + +
437F LYS* 1.3 95.3 - - + +
439F GLY* 1.3 65.2 + - - +
440F HIS 3.3 0.9 + - - -
441F VAL* 3.1 31.3 + - + +
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Residues in contact with GLY 439 (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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371F HIS* 3.3 5.0 + - - -
373F GLY* 3.1 22.9 - - - -
435F LEU* 2.5 39.3 + - - +
436F GLU 4.7 0.2 + - - -
437F LYS 3.7 0.2 - - - -
438F TRP* 1.3 69.9 - - - +
440F HIS* 1.3 69.5 + - - -
441F VAL 3.6 0.2 - - - -
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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