Contacts of the helix formed by residues 428 - 438 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B GLN* 3.7 31.4 - - + +
424B TYR* 2.7 72.2 + + + +
425B ALA 3.2 10.6 - - - +
426B LYS 3.5 1.8 + - - -
427B THR* 1.3 106.8 + - + +
429B LYS* 1.3 69.4 + - - +
430B GLU 3.8 0.2 - - - -
431B LEU* 3.7 3.9 + - + +
432B ALA 3.2 11.1 + - - -
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Residues in contact with LYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B THR 4.2 0.4 - - - -
428B HIS* 1.3 67.1 - - - +
430B GLU* 1.3 69.0 + - - +
432B ALA* 2.2 44.5 + - - +
433B ARG* 3.0 6.0 + - - -
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B HIS* 3.3 15.0 + - - +
399B ASP* 5.0 3.8 + - - +
403B ALA* 3.9 18.8 - - + +
406B ARG* 3.4 35.0 + - + +
407B ALA* 3.8 18.2 - - + +
410B GLN* 3.3 24.8 + - - +
429B LYS* 1.3 80.8 + - - +
431B LEU* 1.3 63.0 + - - +
433B ARG* 2.9 16.2 + - - -
434B ALA 3.0 10.4 + - - -
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Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO* 3.9 14.4 - - + +
407B ALA* 3.3 24.9 - - - +
410B GLN* 2.8 25.7 + - + +
411B ALA* 3.6 30.7 - - + +
414B ALA* 4.8 2.2 - - + -
421B LEU* 5.2 9.4 - - + +
424B TYR* 3.6 33.0 - - + -
425B ALA* 4.2 18.2 - - + +
428B HIS* 3.8 6.5 - - + +
429B LYS 2.7 3.0 + - - -
430B GLU* 1.3 71.3 - - - +
432B ALA* 1.3 58.2 + - - +
434B ALA* 3.5 2.5 + - - +
435B LEU* 3.0 36.4 + - + +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ALA* 3.4 32.9 - - + +
428B HIS 3.2 2.8 + - - +
429B LYS* 2.2 30.7 + - - +
431B LEU* 1.3 69.8 - - - +
433B ARG* 1.3 61.7 + - - +
435B LEU* 3.3 8.6 + - - +
436B GLU* 3.3 19.8 + - - +
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Residues in contact with ARG 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B HIS* 3.6 19.5 - - + -
398B PRO* 3.9 14.6 - - + +
399B ASP* 3.7 15.5 - - - +
429B LYS* 3.0 6.4 + - + +
430B GLU* 2.9 12.8 + - - +
432B ALA* 1.3 77.8 - - - +
434B ALA* 1.3 61.5 + - - +
436B GLU* 3.1 22.4 + - - +
437B LYS 3.3 5.0 + - - -
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B HIS* 6.2 0.4 - - - -
372B PRO* 3.7 34.8 - - + -
373B GLY 6.1 0.9 - - - -
397B HIS* 3.9 17.8 + - + -
398B PRO* 4.7 3.4 - - - -
407B ALA* 4.5 1.8 - - + -
430B GLU 3.0 10.5 + - - +
431B LEU 3.7 9.4 - - - +
432B ALA 3.2 0.2 - - - -
433B ARG* 1.3 72.9 - - - +
435B LEU* 1.3 63.6 + - - +
436B GLU 2.9 6.3 + - - -
437B LYS* 3.0 12.4 + - - +
438B TRP* 3.0 24.6 + - + -
439B GLY 3.6 1.3 + - - -
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Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B PRO* 4.6 4.5 - - + +
373B GLY* 3.9 30.3 - - - +
421B LEU* 3.1 32.5 - - + +
422B ASP* 4.4 6.3 - - - +
425B ALA* 3.5 20.0 - - + -
431B LEU* 3.0 20.9 - - + +
432B ALA* 3.3 9.1 + - - +
434B ALA* 1.3 74.9 - - - +
436B GLU* 1.3 58.6 + - - +
439B GLY* 2.9 32.5 + - - +
440B HIS* 4.6 11.9 - - + +
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B PRO* 6.0 0.2 - - + -
432B ALA 3.3 9.9 + - - +
433B ARG* 3.1 15.0 + - - +
434B ALA 2.9 0.6 - - - -
435B LEU* 1.3 78.2 - - - +
437B LYS* 1.3 64.9 + - - +
438B TRP 4.8 0.7 - - - -
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Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B GLY 5.6 1.1 - - - +
398B PRO* 3.6 32.5 - - + +
433B ARG 3.3 1.6 + - - -
434B ALA 3.0 5.7 + - - +
436B GLU* 1.3 81.8 - - - +
438B TRP* 1.3 79.1 + - + +
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Residues in contact with TRP 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B HIS* 3.8 32.3 - + + +
372B PRO* 4.2 9.6 - - + -
392B GLY 3.5 23.1 - - - -
393B GLY* 3.7 21.5 - - - -
396B GLY 3.6 11.4 - - - -
397B HIS* 3.4 31.6 - + + -
398B PRO* 5.1 0.4 - - + -
434B ALA* 3.0 25.6 + - + +
435B LEU 3.9 0.7 - - - -
436B GLU 4.8 0.7 - - - -
437B LYS* 1.3 92.4 - - + +
439B GLY* 1.3 58.9 + - - +
440B HIS 3.2 7.5 + - - -
441B VAL* 3.6 23.9 + - + +
55G TRP* 3.5 29.0 - + - -
56G THR* 3.4 23.6 + - - -
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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