Contacts of the helix formed by residues 438 - 450 (chain C) in PDB entry 5AO4
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 LEU 438 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392C LYS* 5.7 0.7 - - - -
393C ALA* 3.5 37.0 - - + +
429C GLU* 4.7 3.6 - - + +
430C ILE* 4.4 16.4 - - + +
433C SER* 3.6 33.2 - - - +
435C ASP* 3.3 17.9 + - + +
436C PRO 3.2 0.4 - - - -
437C LYS* 1.3 86.1 - - + +
439C LYS* 1.3 63.0 + - - +
440C ASP 3.4 2.2 - - - -
441C ALA* 3.2 11.9 + - + +
442C ARG* 3.0 26.1 + - + +
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Residues in contact with LYS 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C ASP 4.6 0.2 - - - -
436C PRO* 3.3 21.0 + - + +
437C LYS 3.3 3.8 + - - -
438C LEU* 1.3 77.6 - - - +
440C ASP* 1.3 59.1 + - - +
442C ARG* 3.1 31.9 + - - +
443C GLU* 2.9 27.4 + - - +
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Residues in contact with ASP 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C LYS* 3.5 28.3 - - - +
437C LYS 5.0 1.5 + - - +
438C LEU 3.4 0.4 - - - -
439C LYS* 1.3 75.3 - - - +
441C ALA* 1.3 61.8 + - - +
443C GLU* 3.1 9.2 + - - +
444C ILE* 2.9 34.2 + - + +
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ALA* 4.0 14.7 - - - +
392C LYS* 3.3 28.4 - - + +
393C ALA* 4.6 5.6 - - + -
430C ILE* 3.7 20.9 - - + +
438C LEU* 3.2 18.0 + - + +
439C LYS 3.2 0.2 - - - -
440C ASP* 1.3 78.2 - - - +
442C ARG* 1.3 58.0 + - - +
444C ILE* 3.4 3.9 + - - +
445C LEU* 2.9 31.5 + - - +
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Residues in contact with ARG 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C ILE* 3.1 22.2 - - + +
431C LEU* 4.5 12.4 + - - +
433C SER* 3.0 39.7 + - - +
434C THR* 5.1 3.9 - - - +
435C ASP 4.4 6.0 + - - -
438C LEU* 3.0 13.6 + - + +
439C LYS* 3.2 31.7 + - - +
441C ALA* 1.3 76.6 - - - +
443C GLU* 1.3 52.4 + - - +
445C LEU* 3.2 7.2 + - - +
446C LYS* 2.5 35.6 + - - +
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Residues in contact with GLU 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C LYS 2.9 14.8 + - - +
440C ASP* 3.1 10.5 + - - +
442C ARG* 1.3 77.5 - - - +
444C ILE* 1.3 57.3 + - + +
446C LYS* 3.4 10.3 - - - +
447C GLN* 3.0 23.7 + - - +
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Residues in contact with ILE 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C MET* 4.2 27.4 - - + +
388C ASP* 4.4 22.2 - - + +
389C ALA* 4.5 8.5 - - + +
392C LYS* 3.5 34.8 - - + -
440C ASP* 2.9 14.0 + - + +
441C ALA* 3.7 4.7 - - - +
443C GLU* 1.3 76.3 - - + +
445C LEU* 1.3 61.9 + - + +
447C GLN* 2.9 40.7 + - - +
448C ILE* 3.0 9.5 + - + +
454C PHE* 5.4 5.2 - - + -
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Residues in contact with LEU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C MET 5.0 1.8 - - - +
386C ILE* 5.1 3.6 - - - -
389C ALA* 3.5 27.6 - - + -
390C PHE* 5.9 1.8 - - + -
427C PHE* 3.5 53.8 - - + +
430C ILE* 3.5 28.7 - - + -
431C LEU* 3.6 28.7 - - + +
441C ALA 2.9 11.2 + - - +
442C ARG* 3.2 4.5 + - - +
444C ILE* 1.3 74.7 - - + +
446C LYS* 1.3 65.8 + - - +
448C ILE* 3.2 28.3 + - + +
449C GLU* 3.4 6.8 + - - +
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Residues in contact with LYS 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C LEU* 4.5 4.4 - - + +
442C ARG 2.5 21.7 + - - +
443C GLU* 3.4 13.2 - - - +
445C LEU* 1.3 73.6 - - - +
447C GLN* 1.3 61.3 + - - +
449C GLU* 3.0 15.0 + - - +
450C TYR* 3.0 37.4 + - + -
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Residues in contact with GLN 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C MET* 3.2 21.2 - - + +
443C GLU 3.0 14.3 + - - +
444C ILE* 2.9 23.3 + - - +
446C LYS* 1.3 77.2 - - - +
448C ILE* 1.3 56.3 + - - +
450C TYR* 3.8 4.3 + - - +
451C ARG 3.4 1.9 + - - -
452C ASN* 3.0 66.1 + - + +
453C LEU* 4.9 1.2 - - - +
454C PHE* 4.2 13.2 - - - -
555C LYS* 4.7 13.5 + - - +
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Residues in contact with ILE 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C TYR* 5.1 16.6 - - + -
382C ILE* 4.9 21.3 - - + -
385C MET* 3.4 54.1 - - + -
386C ILE* 4.7 2.0 - - + +
427C PHE* 5.0 15.3 - - + -
444C ILE* 3.0 13.6 + - + +
445C LEU* 3.3 26.2 - - + +
446C LYS 3.1 0.2 - - - -
447C GLN* 1.3 78.2 - - - +
449C GLU* 1.3 61.8 + - - +
451C ARG* 3.2 23.2 + - - +
453C LEU* 4.9 4.0 - - + +
142D GLN* 3.7 6.0 - - - +
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Residues in contact with GLU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 5.7 7.9 - - + -
445C LEU 3.4 7.1 + - - +
446C LYS* 3.0 10.5 + - - +
448C ILE* 1.3 80.4 - - + +
450C TYR* 1.3 61.2 + - + +
451C ARG 3.2 1.5 + - - -
137D ASP* 3.6 18.4 - - - +
138D THR 3.6 4.0 + - - -
139D PRO* 4.5 25.8 - - + -
142D GLN* 2.9 27.0 + - + +
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Residues in contact with TYR 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C LYS* 3.0 40.8 + - + +
447C GLN* 3.8 3.3 + - - +
449C GLU* 1.3 76.9 - - + +
451C ARG* 1.3 70.2 + - - +
452C ASN* 3.6 19.3 - - - +
137D ASP* 3.8 20.0 - - - +
138D THR* 5.0 2.2 - - + -
139D PRO* 3.4 39.9 - - + +
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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