Contacts of the helix formed by residues 428 - 439 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410G GLN* 3.2 35.9 - - + +
424G TYR* 2.8 71.4 + + + +
425G ALA 3.1 10.3 + - - +
426G LYS 3.5 0.6 - - - -
427G THR* 1.3 100.7 + - - +
429G LYS* 1.3 66.4 + - - +
430G GLU* 3.4 1.8 - - - -
431G LEU* 3.3 6.6 + - + +
432G ALA 3.0 17.8 + - - -
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Residues in contact with LYS 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425G ALA 4.9 0.2 - - - -
427G THR 4.2 0.6 - - - -
428G HIS* 1.3 70.4 - - - +
430G GLU* 1.3 63.5 + - - +
432G ALA* 3.0 8.8 + - - +
433G ARG* 2.7 44.9 + - + +
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Residues in contact with GLU 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397G HIS* 3.0 16.5 + - - -
399G ASP* 5.6 0.7 - - - -
403G ALA* 3.7 19.3 - - + +
406G ARG* 3.2 39.1 + - + +
407G ALA* 3.7 21.3 - - + +
410G GLN* 2.8 28.9 + - - +
428G HIS* 4.6 0.2 - - - -
429G LYS* 1.3 82.4 + - - +
431G LEU* 1.3 65.0 + - - +
433G ARG* 3.1 2.2 + - - -
434G ALA* 2.9 19.1 + - - +
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Residues in contact with LEU 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G PRO* 3.9 13.7 - - + -
407G ALA* 3.9 11.9 - - - +
410G GLN* 2.9 22.0 + - + +
411G ALA* 3.8 34.8 - - + +
421G LEU* 4.0 20.6 - - + +
424G TYR* 3.7 31.2 - - + -
425G ALA* 3.9 21.1 - - + +
428G HIS* 3.3 6.9 + - + +
430G GLU* 1.3 73.9 - - - +
432G ALA* 1.3 58.6 + - - +
434G ALA* 3.0 4.7 + - - +
435G LEU* 2.9 38.1 + - + +
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Residues in contact with ALA 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425G ALA* 3.3 35.1 - - + +
428G HIS 3.0 5.6 + - - +
429G LYS* 3.4 10.3 - - - +
431G LEU* 1.3 76.6 - - - +
433G ARG* 1.3 60.1 + - + +
435G LEU* 3.4 4.5 + - - +
436G GLU* 2.9 29.2 + - - +
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Residues in contact with ARG 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397G HIS* 3.5 14.8 - - + -
398G PRO* 3.3 45.0 + - + +
399G ASP* 2.6 40.4 + - - +
429G LYS* 2.7 29.3 + - + +
430G GLU 3.5 4.5 - - - +
432G ALA* 1.3 74.3 - - + +
434G ALA* 1.3 61.2 + - - +
436G GLU* 3.5 33.5 + - - +
437G LYS 3.5 11.8 + - - -
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Residues in contact with ALA 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371G HIS* 6.2 0.4 - - - -
372G PRO* 3.7 33.2 - - + -
373G GLY 6.2 0.2 - - - -
397G HIS* 3.8 17.0 + - + -
398G PRO* 4.8 0.9 - - - -
407G ALA* 4.2 1.6 - - + -
430G GLU 2.9 11.7 + - - +
431G LEU 3.0 8.7 + - - +
433G ARG* 1.3 74.9 - - - +
435G LEU* 1.3 65.1 + - - +
436G GLU 3.1 1.3 - - - -
437G LYS* 3.1 2.4 + - - -
438G TRP* 3.0 40.0 + - + +
439G GLY 5.0 0.2 - - - +
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Residues in contact with LEU 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372G PRO* 4.8 1.1 - - + -
373G GLY* 3.6 22.2 - - - +
421G LEU* 3.7 26.9 - - + +
422G ASP* 4.5 4.7 - - - +
425G ALA* 3.7 27.6 - - + -
431G LEU* 2.9 21.0 + - + +
432G ALA* 3.8 4.9 - - - +
434G ALA* 1.3 76.6 - - - +
436G GLU* 1.3 59.4 + - - +
439G GLY* 2.7 49.6 + - - +
440G HIS* 4.0 17.9 - - + +
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Residues in contact with GLU 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398G PRO* 6.2 0.4 - - + -
432G ALA 2.9 16.3 + - - +
433G ARG* 3.5 44.5 + - - +
434G ALA 3.1 0.2 - - - -
435G LEU* 1.3 79.5 - - - +
437G LYS* 1.3 59.3 + - + +
439G GLY 4.8 0.3 + - - -
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Residues in contact with LYS 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR* 3.8 3.6 + - - -
57B THR* 3.0 34.8 + - - -
58B LEU 5.9 0.6 - - - -
396G GLY 2.6 30.0 + - - +
398G PRO* 4.0 22.5 - - + +
433G ARG 3.5 8.0 + - - +
434G ALA 3.1 7.2 + - - +
436G GLU* 1.3 82.4 - - + +
438G TRP* 1.3 87.9 + - + +
439G GLY 3.7 0.4 - - - -
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Residues in contact with TRP 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TRP* 3.5 27.6 - + - -
56B THR* 3.3 20.0 + - + -
371G HIS* 3.6 34.3 - + + +
372G PRO* 3.9 11.4 - - + -
392G GLY 3.7 11.4 - - - -
393G GLY* 3.6 25.4 - - - -
396G GLY* 3.4 22.7 - - - -
397G HIS* 3.3 27.4 - + + -
434G ALA* 3.0 31.9 + - + +
437G LYS* 1.3 95.6 - - + +
439G GLY* 1.3 66.8 + - - +
441G VAL* 3.0 30.7 + - + +
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Residues in contact with GLY 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371G HIS* 3.4 10.6 + - - -
373G GLY* 3.4 0.5 - - - -
435G LEU* 2.7 51.1 + - - +
436G GLU 4.6 0.4 + - - -
437G LYS 3.7 1.0 - - - -
438G TRP* 1.3 72.7 - - - +
440G HIS* 1.3 65.7 + - - -
441G VAL* 5.3 1.3 - - - -
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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