Contacts of the helix formed by residues 429 - 440 (chain B) in PDB entry 5UFL
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 ASP 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374B ILE* 4.1 14.0 - - + +
379B CYS* 3.3 34.6 - - - +
426B LEU 3.2 6.8 + - - +
427B CYS 3.2 2.9 - - - -
428B GLY* 1.3 77.4 - - - +
430B ASP* 1.3 65.5 + - - +
431B THR* 3.5 22.1 + - - -
432B LEU* 3.5 28.6 - - + +
433B LYS* 2.9 27.5 + - - +
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Residues in contact with ASP 430 (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 CYS 5.4 0.4 - - - +
428B GLY 4.2 0.6 + - - -
429B ASP* 1.3 74.3 + - - +
431B THR* 1.3 64.6 + - - +
433B LYS* 3.7 28.6 + - - +
434B MET* 3.1 26.7 + - - +
492B LEU* 5.0 0.9 - - - +
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Residues in contact with THR 431 (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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379B CYS* 5.9 0.7 - - - -
383B ASP* 3.4 21.5 - - - +
429B ASP* 3.3 17.4 + - - -
430B ASP* 1.3 79.5 - - - +
432B LEU* 1.3 61.9 + - - +
434B MET* 3.3 14.9 + - - +
435B HIS* 3.4 20.1 + - + -
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Residues in contact with LEU 432 (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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370B PHE* 5.1 4.9 - - + -
373B VAL* 5.6 2.7 - - + -
374B ILE* 4.1 21.8 - - + -
379B CYS* 4.6 11.4 - - + +
382B ALA* 5.6 1.3 - - + -
383B ASP* 3.6 28.9 - - + +
386B VAL* 3.7 38.5 - - + +
390B LEU* 5.1 0.7 - - - +
426B LEU* 3.4 27.2 - - + +
429B ASP* 3.4 26.3 + - + +
431B THR* 1.3 73.6 - - - +
433B LYS* 1.3 63.9 + - - +
434B MET 3.3 0.2 - - - -
435B HIS* 3.4 9.1 + - + +
436B ILE* 3.4 24.6 + - - +
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Residues in contact with LYS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B LEU 3.7 3.3 + - - -
427B CYS* 3.8 33.8 + - + +
429B ASP 2.9 17.2 + - - +
430B ASP* 3.7 27.3 + - - +
431B THR 3.3 0.2 - - - -
432B LEU* 1.3 76.8 - - - +
434B MET* 1.3 57.5 + - - +
436B ILE* 3.2 9.0 + - - +
437B ALA* 2.9 27.0 + - - +
488B LYS* 3.6 27.9 + - + +
489B LEU* 3.7 16.6 - - + +
491B PRO* 5.4 2.6 - - - +
492B LEU* 4.0 23.3 - - + +
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Residues in contact with MET 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASP 3.1 14.5 + - - +
431B THR* 3.3 11.2 + - - +
433B LYS* 1.3 74.3 - - - +
435B HIS* 1.3 64.8 + - - +
437B ALA* 4.2 2.9 - - - -
438B LYS* 3.2 34.1 + - + +
492B LEU* 3.6 35.2 - - + +
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Residues in contact with HIS 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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383B ASP* 3.3 33.4 + - - -
386B VAL* 4.4 16.6 - - + -
387B THR* 3.8 25.6 + - + -
390B LEU* 3.7 17.5 - - + +
431B THR* 3.4 15.1 + - + -
432B LEU* 3.5 13.9 - - + +
433B LYS 3.3 0.4 - - - -
434B MET* 1.3 79.2 - - - +
436B ILE* 1.3 62.7 + - - +
438B LYS* 3.7 5.4 + - - +
439B ILE* 3.6 21.1 + - - +
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Residues in contact with ILE 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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390B LEU* 3.8 22.4 - - + -
394B LEU* 5.5 1.1 - - + -
423B LEU* 3.6 28.7 - - + +
426B LEU* 3.5 32.5 - - + -
427B CYS* 4.1 11.2 - - - +
432B LEU 3.6 10.8 - - - +
433B LYS* 3.2 7.0 + - - +
435B HIS* 1.3 74.1 - - - +
437B ALA* 1.3 57.0 + - - +
439B ILE* 3.1 7.3 + - + -
440B LEU* 2.7 49.5 + - + +
485B LEU* 5.0 2.2 - - + -
489B LEU* 3.9 25.4 - - + -
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Residues in contact with ALA 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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433B LYS 2.9 16.6 + - - +
434B MET* 4.1 6.7 - - - +
435B HIS 3.4 0.2 - - - -
436B ILE* 1.3 76.3 - - - +
438B LYS* 1.3 60.4 + - - +
439B ILE 3.5 0.2 + - - -
440B LEU 3.8 7.6 - - - +
489B LEU* 4.0 9.6 - - + +
492B LEU* 3.5 38.8 - - + +
493B VAL* 3.5 30.4 - - + +
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Residues in contact with LYS 438 (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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434B MET* 3.2 26.6 + - + +
435B HIS* 3.9 6.7 - - - +
436B ILE 3.3 0.2 - - - -
437B ALA* 1.3 76.9 - - - +
439B ILE* 1.3 65.0 + - + +
440B LEU 5.3 0.2 - - - -
441B THR* 5.8 1.6 - - - +
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B LEU* 4.7 15.0 - - + -
391B PRO* 5.9 8.7 - - + -
394B LEU* 3.8 27.3 - - + +
435B HIS 3.6 17.2 + - - +
436B ILE* 3.1 9.0 + - - +
438B LYS* 1.3 87.7 - - + +
440B LEU* 1.3 66.0 + - + +
441B THR* 3.4 12.1 + - - +
444B LYS* 5.9 0.3 - - - +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 4.1 17.3 - - + -
397B LEU* 4.8 7.0 - - + -
423B LEU* 4.5 5.8 - - + -
436B ILE* 2.7 32.0 + - + +
437B ALA 3.8 12.7 - - - +
439B ILE* 1.3 69.7 - - + +
441B THR* 1.3 62.4 + - - +
444B LYS* 3.9 30.7 - - + -
445B CYS* 3.8 25.6 - - - -
485B LEU* 3.7 22.7 - - + -
489B LEU* 3.7 27.1 - - + +
493B VAL* 4.3 11.4 - - - +
496B MET* 4.3 2.3 - - + +
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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