Contacts of the helix formed by residues 535 - 540 (chain H) in PDB entry 3AOI
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 SER 535 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9H ILE* 4.6 3.4 - - - -
11H GLU* 5.2 6.7 - - - -
12H VAL 5.7 0.2 - - - -
13H ILE 6.0 0.2 - - - -
458H TYR* 4.6 7.9 - - - -
499H ALA* 4.5 4.7 - - - -
533H ASP* 3.6 3.1 - - - +
534H VAL* 1.3 84.8 - - - +
536H PRO* 1.3 80.4 - - - +
537H LYS* 2.9 41.1 + - - -
538H GLN* 2.7 35.9 + - - +
539H VAL* 4.7 0.3 - - - +
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Residues in contact with PRO 536 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 3.1 29.2 - - + -
498H GLN* 5.9 2.0 - - - +
499H ALA* 4.4 5.6 - - + -
500H ASN* 4.2 20.9 - - - +
533H ASP* 5.8 0.4 - - - +
535H SER* 1.3 92.3 - - - +
537H LYS* 1.3 66.2 + - + +
539H VAL* 3.1 27.3 + - + +
540H PHE* 4.3 3.8 + - - -
905H ILE* 4.8 3.6 - - + -
906H PHE* 3.6 43.2 - - + +
907H ASP* 5.1 3.1 - - + -
1067I VAL* 4.4 4.7 - - + -
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Residues in contact with LYS 537 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 4.4 5.9 - - - +
11H GLU* 2.7 48.8 + - - +
15H LEU* 4.9 9.9 - - + -
457H ALA* 3.8 1.8 - - + -
458H TYR* 4.1 21.5 - - + -
535H SER* 2.9 29.1 + - - +
536H PRO* 1.3 79.5 - - + +
538H GLN* 1.3 52.1 + - - +
539H VAL 2.7 12.5 + - - -
540H PHE* 2.8 17.5 + - - +
545H ASN* 2.8 45.3 + - - +
583H LEU* 4.6 13.7 - - + -
904H PRO* 5.1 7.2 - - + +
905H ILE* 4.3 17.5 - - + +
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Residues in contact with GLN 538 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435H TYR* 6.0 0.7 - - + -
436H GLY* 2.8 31.6 - - - +
456H ALA* 3.4 10.9 - - - +
457H ALA* 3.4 15.1 - - - +
458H TYR* 3.6 22.3 - - + +
469H THR* 3.0 18.5 - - + +
470H PRO* 2.8 30.7 + - - +
471H TYR* 4.5 3.2 - - - -
533H ASP* 3.7 13.0 + - - +
534H VAL* 2.9 13.3 + - - +
535H SER 2.7 43.5 + - - +
537H LYS* 1.3 76.6 - - - +
539H VAL* 1.3 63.1 - - + +
540H PHE 3.2 1.6 - - - -
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Residues in contact with VAL 539 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435H TYR* 3.5 26.9 - - + +
436H GLY 4.0 12.5 + - - +
438H ILE 4.5 3.1 - - - +
439H CYS* 4.5 0.2 - - - -
440H PRO* 3.5 12.1 - - - +
456H ALA* 5.0 0.9 - - - -
533H ASP* 4.5 2.2 - - - +
536H PRO* 3.4 18.6 - - + +
537H LYS 2.7 5.7 + - - -
538H GLN* 1.3 81.9 - - + +
540H PHE* 1.3 83.1 + - + +
906H PHE* 5.3 0.2 - - + -
1067I VAL* 3.9 21.1 - - + +
1071I PHE* 3.6 30.6 - - + -
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Residues in contact with PHE 540 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439H CYS* 3.8 6.7 - - - -
440H PRO* 3.8 22.0 - - + -
441H VAL* 4.3 3.4 - - + -
456H ALA* 3.5 6.5 - - - +
457H ALA* 2.9 23.5 + - - +
536H PRO 4.8 1.6 - - - -
537H LYS 2.8 15.3 + - - +
539H VAL* 1.3 103.0 - - + +
541H SER* 1.3 64.7 + - - +
544H THR* 3.7 17.7 - - + -
545H ASN* 4.4 1.6 - - - +
550H LEU* 3.4 31.4 - - + -
905H ILE* 3.8 17.9 - - + -
906H PHE* 3.5 29.2 - + - -
1070I TYR* 3.3 34.5 - + + -
1071I PHE* 5.5 3.1 - + - -
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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