Contacts of the helix formed by residues 431 - 435 (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 HIS 431 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H ASP* 3.5 24.5 + - - +
326H ASP* 3.0 49.2 + - + +
327H HIS* 3.7 4.0 + - - -
429H ASP* 3.2 6.2 + - + +
430H VAL* 1.3 78.6 - - - +
432H ARG* 1.3 89.8 + - + +
433H THR* 2.7 39.4 + - - -
434H HIS* 2.9 43.3 + - + +
1048I PRO* 4.8 11.4 - - + +
1071I PHE* 4.3 1.0 - - - -
1075I HIS* 4.2 1.5 - - - -
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Residues in contact with ARG 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430H VAL 3.9 0.6 + - - -
431H HIS* 1.3 98.8 - - + +
433H THR* 1.3 59.3 + - - +
434H HIS 3.1 3.6 + - - -
435H TYR* 3.5 13.5 + - - +
518H LYS 5.8 0.4 + - - -
519H GLY* 4.1 28.1 + - - -
520H GLU* 3.4 10.9 + - - -
1047I LYS* 2.7 37.0 - - - +
1048I PRO* 3.4 28.0 - - + +
1051I GLU* 5.4 1.0 + - - -
1053I PHE* 3.1 37.5 - - - -
1071I PHE* 3.7 11.2 - - - -
1075I HIS* 4.4 12.8 + - - -
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Residues in contact with THR 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H HIS* 3.4 19.1 + - + +
328H LEU* 2.9 51.2 - - + +
431H HIS* 2.7 21.5 + - - -
432H ARG* 1.3 73.4 - - - +
434H HIS* 1.3 54.9 + - - +
435H TYR* 3.0 12.1 + - - -
437H ARG* 3.3 20.7 + - - +
488H ALA* 3.4 25.1 - - + +
491H GLU* 5.1 0.4 - - - +
492H ASP* 5.3 1.1 - - - +
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Residues in contact with HIS 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H LEU* 3.8 17.9 - - + +
331H ARG* 3.7 23.1 + - - -
427H VAL 5.0 2.7 - - - -
429H ASP 3.5 13.0 - - - -
430H VAL* 3.2 21.1 - - + +
431H HIS* 2.9 50.4 + - + +
433H THR* 1.3 68.9 - - - +
435H TYR* 1.3 61.0 + - - +
436H GLY 3.2 0.7 + - - -
437H ARG 3.0 1.5 + - - -
438H ILE* 2.8 72.4 + - + +
453H THR* 6.3 1.3 - - + -
1071I PHE* 4.2 2.2 - - + -
1078I ARG* 5.2 3.3 + - - -
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Residues in contact with TYR 435 (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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432H ARG 3.5 9.6 + - - +
433H THR* 3.0 3.5 + - - +
434H HIS* 1.3 73.1 - - - +
436H GLY* 1.3 56.8 + - - +
437H ARG* 2.6 33.7 + - - +
469H THR* 3.7 2.4 + - - +
471H TYR* 3.6 25.1 + + - +
491H GLU* 3.7 13.7 - - - +
496H ILE* 5.3 3.6 - - + -
498H GLN* 2.5 31.6 + - - -
516H ARG* 5.3 6.9 - - + +
533H ASP* 2.7 28.5 + - - -
538H GLN* 6.0 0.7 - - + -
539H VAL* 3.5 27.8 - - + +
1067I VAL* 5.5 0.9 - - + -
1068I LEU* 4.2 15.0 - - + -
1071I PHE* 3.5 37.5 - + + -
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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
------------------------------------------------------------
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