Contacts of the helix formed by residues 428 - 439 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D GLN* 3.2 34.3 - - + +
424D TYR* 2.7 69.2 + + + +
425D ALA 3.0 13.1 + - - +
426D LYS 3.4 0.8 + - - -
427D THR* 1.3 102.9 + - - +
429D LYS* 1.3 65.8 + - - +
430D GLU* 3.4 1.8 - - - -
431D LEU* 3.4 7.1 + - + +
432D ALA 3.0 17.3 + - - -
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Residues in contact with LYS 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D THR 4.2 0.6 - - - -
428D HIS* 1.3 71.2 - - - +
430D GLU* 1.3 61.9 + - - +
432D ALA* 3.0 7.2 + - - +
433D ARG* 2.7 45.1 + - + +
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Residues in contact with GLU 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D HIS* 2.7 29.8 + - + +
399D ASP* 4.9 1.8 - - - +
403D ALA* 3.7 31.6 - - + +
406D ARG* 3.2 37.1 + - + +
407D ALA* 3.4 12.7 - - - +
410D GLN* 2.9 25.2 + - - +
428D HIS* 4.8 0.3 - - - -
429D LYS* 1.3 84.0 + - - +
431D LEU* 1.3 62.4 + - - +
433D ARG* 4.4 0.7 - - - -
434D ALA 3.0 6.8 + - - -
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Residues in contact with LEU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D PRO* 3.8 13.9 - - + -
407D ALA* 3.6 24.2 - - - +
410D GLN* 3.1 17.3 + - + +
411D ALA* 3.7 20.0 - - + +
421D LEU* 4.0 32.8 - - + +
424D TYR* 3.9 28.0 - - + -
425D ALA* 4.1 9.9 - - + -
428D HIS* 3.7 6.5 - - + +
429D LYS 3.3 0.2 - - - -
430D GLU* 1.3 77.7 - - - +
432D ALA* 1.3 58.0 + - - +
434D ALA* 3.1 5.4 + - - +
435D LEU* 2.9 41.8 + - + +
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D ALA* 3.7 24.0 - - + +
428D HIS 3.0 13.6 + - - +
429D LYS* 3.0 12.0 + - - +
431D LEU* 1.3 77.1 - - - +
433D ARG* 1.3 58.3 + - + +
435D LEU* 3.2 5.9 + - - +
436D GLU* 2.9 29.0 + - - +
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Residues in contact with ARG 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D HIS* 3.4 13.9 - - + -
398D PRO* 3.4 40.0 + - + +
399D ASP* 2.8 45.5 + - - +
429D LYS* 2.7 29.7 + - + +
432D ALA* 1.3 73.6 - - + +
434D ALA* 1.3 60.7 + - - +
436D GLU* 3.2 44.1 + - - +
437D LYS 3.4 5.5 + - - -
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Residues in contact with ALA 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D HIS* 6.1 0.4 - - - -
372D PRO* 3.8 31.6 - - + -
373D GLY 6.2 0.4 - - - -
397D HIS* 3.6 17.5 + - + -
398D PRO* 4.9 1.3 - - - -
407D ALA* 4.2 1.6 - - + -
430D GLU 3.0 13.1 + - - +
431D LEU 3.1 8.9 + - - +
433D ARG* 1.3 73.6 - - - +
435D LEU* 1.3 61.2 + - - +
436D GLU 3.1 1.6 - - - -
437D LYS* 3.1 2.4 + - - -
438D TRP* 3.0 44.4 + - + +
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Residues in contact with LEU 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D PRO* 5.2 0.7 - - + -
373D GLY* 3.7 21.5 - - - +
421D LEU* 3.9 13.9 - - + +
422D ASP* 3.8 21.1 - - - +
425D ALA* 3.8 28.9 - - + -
431D LEU* 2.9 26.6 + - + +
432D ALA* 3.2 7.4 + - - +
434D ALA* 1.3 75.2 - - - +
436D GLU* 1.3 59.3 + - - +
439D GLY* 2.8 48.3 + - - +
440D HIS* 4.2 10.1 - - + +
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Residues in contact with GLU 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D PRO* 6.2 0.4 - - - -
432D ALA 2.9 12.4 + - - +
433D ARG* 3.2 47.0 + - - +
434D ALA 3.1 0.2 - - - -
435D LEU* 1.3 79.5 - - - +
437D LYS* 1.3 60.8 + - + +
439D GLY 4.7 0.3 + - - -
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Residues in contact with LYS 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D GLY 2.7 29.5 + - - +
398D PRO* 4.0 20.8 - - + +
433D ARG 3.4 7.7 + - - +
434D ALA 3.1 6.7 + - - +
436D GLU* 1.3 84.2 - - - +
438D TRP* 1.3 86.3 + - + +
56J THR* 3.9 3.1 - - - -
57J THR* 2.8 38.2 + - - -
58J LEU 5.9 0.2 - - - -
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Residues in contact with TRP 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D HIS* 3.4 33.9 - - + +
372D PRO* 3.9 12.1 - - + -
392D GLY 3.7 12.1 - - - -
393D GLY* 3.4 26.9 - - - -
396D GLY* 3.3 23.8 - - - -
397D HIS* 3.4 28.5 - + - -
398D PRO* 5.2 0.4 - - + -
434D ALA* 3.0 33.1 + - + +
437D LYS* 1.3 96.4 - - + +
439D GLY* 1.3 65.6 + - - +
441D VAL* 3.0 32.8 + - + +
55J TRP* 3.5 27.0 - + - -
56J THR* 3.3 19.8 + - - -
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Residues in contact with GLY 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D HIS* 3.3 11.1 + - - -
373D GLY* 3.5 12.5 - - - -
435D LEU* 2.8 35.5 + - - +
436D GLU 4.5 0.4 + - - -
437D LYS 3.7 0.8 - - - -
438D TRP* 1.3 76.7 - - - +
440D HIS* 1.3 66.5 + - - -
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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