Contacts of the helix formed by residues 435 - 446 (chain F) in PDB entry 3SZ9
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 435 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280F ASP* 3.4 17.5 - - - +
433F THR* 3.2 8.2 + - - +
434F LYS* 1.3 78.1 - - - +
436F LEU* 1.3 66.5 + - - +
437F ASP* 3.1 14.6 + - - +
438F LYS* 2.9 43.5 + - + +
439F ALA* 3.2 23.0 + - - +
434G LYS* 3.6 25.3 - - - +
436G LEU* 4.3 1.1 - - - +
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Residues in contact with LEU 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F LYS 3.7 1.6 + - - -
435F ASP* 1.3 73.0 - - - +
437F ASP* 1.3 64.8 + - - +
439F ALA* 3.4 3.1 + - - +
440F ASN* 3.1 44.5 + - - +
433G THR 4.3 2.7 - - - +
434G LYS* 2.8 22.9 + - - +
435G ASP 4.3 0.2 - - - -
436G LEU* 3.8 32.7 - - + +
439G ALA* 4.1 17.0 - - + -
440G ASN* 5.8 1.8 - - - +
453G VAL* 3.7 21.1 - - + -
454G ASN* 3.6 26.5 - - - +
493H VAL* 4.2 11.7 - - + -
494H LYS 5.1 0.2 - - - +
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Residues in contact with ASP 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435F ASP* 3.1 11.0 + - - +
436F LEU* 1.3 90.2 - - - +
438F LYS* 1.3 59.4 + - - +
440F ASN* 3.9 2.8 + - - +
441F TYR* 2.9 31.2 + - - +
434G LYS* 6.5 1.1 - - - -
454G ASN* 4.8 5.9 + - - -
494H LYS* 4.0 18.1 - - - +
495H VAL 5.7 0.2 - - - -
496H PRO* 3.9 29.4 - - + +
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Residues in contact with LYS 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F MET* 4.0 22.0 - - + +
279F SER* 5.1 6.5 + - - -
280F ASP* 3.1 27.3 + - - +
413F ILE* 3.7 22.9 - - + -
433F THR* 3.8 23.3 - - + +
435F ASP* 2.9 26.9 + - + +
436F LEU 3.4 0.2 - - - -
437F ASP* 1.3 69.7 - - + +
439F ALA* 1.3 67.9 + - - +
441F TYR* 3.3 2.1 + - - +
442F LEU* 3.0 33.6 + - + +
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Residues in contact with ALA 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431F VAL* 4.7 7.2 - - - +
433F THR* 3.8 15.8 - - + +
435F ASP 3.2 16.2 + - - +
436F LEU 3.5 5.4 - - - +
438F LYS* 1.3 78.9 - - - +
440F ASN* 1.3 59.5 + - - +
442F LEU* 4.2 1.0 - - - +
443F SER* 3.0 32.1 + - - -
453F VAL* 4.0 24.7 - - + +
436G LEU* 4.2 15.5 - - + -
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Residues in contact with ASN 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E TYR* 4.3 6.6 + - - -
6901E EDO 4.0 18.8 - - - -
436F LEU* 3.1 39.6 + - - +
437F ASP* 4.1 5.7 + - - +
439F ALA* 1.3 76.6 - - - +
441F TYR* 1.3 65.2 + - - +
443F SER* 3.6 4.1 + - - -
444F GLN* 3.2 24.9 + - - +
436G LEU* 5.9 1.1 - - - +
151H PHE* 4.5 8.3 - - - -
493H VAL* 4.0 12.1 - - - +
494H LYS 4.8 1.2 + - - -
495H VAL* 4.0 32.0 - - + +
496H PRO* 4.8 2.2 - - + -
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Residues in contact with TYR 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LEU* 5.9 5.5 - - + +
413F ILE* 3.7 34.1 - - + -
414F GLU* 3.7 29.6 - - + +
417F VAL* 3.7 26.5 - - + +
437F ASP 2.9 20.0 + - - +
438F LYS* 3.6 4.5 - - - +
440F ASN* 1.3 79.3 - - - +
442F LEU* 1.3 60.7 + - + +
444F GLN* 3.5 8.7 + - - +
445F ALA* 3.1 35.1 + - + +
496H PRO* 4.5 23.5 - - + +
497H GLN* 5.8 5.8 - - + -
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Residues in contact with LEU 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F ILE* 4.4 14.4 - - + -
278F MET* 3.9 17.9 - - + -
413F ILE* 3.7 30.7 - - + -
416F VAL* 4.2 10.5 - - + -
417F VAL* 3.4 30.5 - - + -
431F VAL* 3.5 40.8 - - + -
438F LYS 3.0 15.1 + - - +
439F ALA 4.3 0.2 - - - +
441F TYR* 1.3 75.8 - - - +
443F SER* 1.3 58.8 + - - +
445F ALA* 4.3 1.6 - - - +
446F LEU* 2.9 40.6 + - + +
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Residues in contact with SER 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E TYR* 3.8 3.6 + - - -
489E LYS* 2.9 31.9 + - - +
491E VAL* 4.0 16.3 - - - +
6901E EDO 2.5 31.5 + - - -
431F VAL* 4.8 0.4 - - - +
439F ALA 3.0 21.8 + - - -
440F ASN* 3.6 2.9 + - - -
442F LEU* 1.3 76.7 - - - +
444F GLN* 1.3 57.8 + - - +
446F LEU* 4.1 0.5 - - - +
451F VAL* 3.9 28.2 - - - +
453F VAL* 4.6 4.9 - - - +
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Residues in contact with GLN 444 (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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72E LEU* 4.8 9.8 - - + +
77E ARG* 5.8 1.7 + - - +
155E ARG* 3.5 27.4 + - - +
157E GLU* 3.8 4.2 - - - +
489E LYS* 2.9 17.7 + - - +
6901E EDO 4.3 8.7 - - - -
440F ASN 3.2 20.0 + - - +
441F TYR* 3.8 7.6 + - - +
443F SER* 1.3 78.7 + - - +
445F ALA* 1.3 59.8 + - - +
495H VAL* 5.7 1.8 - - - +
497H GLN 2.6 28.9 + - - -
498H LYS* 3.9 5.7 - - - +
499H ASN* 2.9 46.5 + - + +
500H SER 5.5 0.2 - - - +
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Residues in contact with ALA 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LEU* 3.6 32.8 - - + +
417F VAL* 4.0 26.2 - - + +
421F ASN* 3.0 21.6 + - - -
441F TYR* 3.1 23.8 + - + +
442F LEU 3.1 2.0 + - - +
444F GLN* 1.3 75.0 - - + +
446F LEU* 1.3 64.8 + - - +
447F GLN* 3.4 5.7 + - - +
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Residues in contact with LEU 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489E LYS* 2.6 37.1 + - - -
274F PRO* 4.6 1.3 - - + -
276F ILE* 3.9 14.6 - - + -
417F VAL* 5.1 4.7 - - - +
420F ALA* 3.6 31.0 - - + -
421F ASN* 3.6 7.6 - - - +
429F ALA* 4.0 28.0 - - + -
430F ALA 4.8 0.2 - - - +
431F VAL* 3.6 28.9 - - + -
442F LEU* 2.9 28.6 + - + +
443F SER 4.2 0.2 + - - -
444F GLN 3.5 0.2 - - - -
445F ALA* 1.3 75.2 - - + +
447F GLN* 1.3 58.7 + - - +
448F ALA* 3.3 1.4 + - + -
451F VAL* 4.1 18.8 - - + -
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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