Contacts of the helix formed by residues 845 - 855 (chain I) 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 ASN 845 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84G GLU* 3.6 29.9 + - + +
175G ARG* 3.8 18.5 - - - +
843I PHE* 4.0 4.7 - - - +
844I ALA* 1.3 84.2 - - + +
846I PRO* 1.3 79.9 - - - +
847I ASP* 3.4 31.2 + - - +
848I GLU* 3.1 30.9 - - + +
849I ALA 3.9 1.6 + - - -
866I VAL* 4.4 0.7 - - - +
867I ARG* 4.1 5.5 + - - +
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Residues in contact with PRO 846 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845I ASN* 1.3 101.7 - - - +
847I ASP* 1.3 65.1 + - - +
849I ALA* 3.2 13.3 + - - +
850I LEU* 3.0 20.1 - - + +
866I VAL* 4.3 11.4 - - + -
867I ARG 4.4 6.5 - - - +
868I TYR* 4.1 34.3 - - + -
880I ILE* 4.8 8.0 - - + +
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Residues in contact with ASP 847 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G ARG* 2.9 35.8 - - + +
176G ARG* 3.8 30.3 + - + +
845I ASN* 3.3 22.8 + - + +
846I PRO* 1.3 79.0 - - - +
848I GLU* 1.3 66.1 + - - +
850I LEU* 2.9 17.2 + - - +
851I LEU* 2.9 32.9 + - + +
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Residues in contact with GLU 848 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G LYS* 3.0 36.1 + - - +
84G GLU* 5.7 0.2 - - - -
150G TYR* 3.7 12.3 + - - -
170G VAL* 2.5 44.8 - - - +
175G ARG* 4.5 10.5 + - - +
843I PHE* 3.6 19.4 - - + -
844I ALA* 4.2 0.9 - - + +
845I ASN* 3.1 39.7 - - + +
847I ASP* 1.3 78.5 - - - +
849I ALA* 1.3 64.3 + - - +
851I LEU* 3.6 12.1 + - - +
852I ALA* 3.5 13.5 + - - +
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Residues in contact with ALA 849 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843I PHE* 3.4 28.8 - - + +
846I PRO 3.2 13.1 + - - +
847I ASP 3.0 0.6 + - - -
848I GLU* 1.3 79.6 - - - +
850I LEU* 1.3 65.0 + - + +
852I ALA* 3.3 13.7 + - - +
853I VAL* 3.0 19.8 + - - +
858I VAL* 4.1 1.9 - - - +
866I VAL* 4.0 19.5 - - + -
877I PRO* 5.3 8.3 - - + -
880I ILE* 5.0 8.5 - - + -
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Residues in contact with LEU 850 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846I PRO* 3.0 32.3 - - + +
847I ASP* 2.9 12.0 + - - +
849I ALA* 1.3 81.0 - - + +
851I LEU* 1.3 68.5 + - + +
853I VAL* 3.0 15.9 - - + +
854I ALA* 2.8 27.0 + - - +
860I LEU* 5.9 2.7 - - + -
877I PRO* 5.4 3.1 - - + +
880I ILE* 4.3 15.7 - - + -
881I LEU* 4.0 28.3 - - + -
884I ARG* 3.7 28.7 - - + +
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Residues in contact with LEU 851 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G LEU* 5.3 11.2 - - + -
150G TYR* 4.8 15.7 - - + -
172G SER* 6.4 0.7 - - - -
174G VAL 4.8 4.7 - - - +
175G ARG* 3.1 36.8 - - - +
176G ARG* 5.1 3.4 - - + -
847I ASP* 2.9 31.8 + - + +
848I GLU* 4.0 9.4 - - - +
849I ALA 3.3 0.2 - - - -
850I LEU* 1.3 77.0 - - + +
852I ALA* 1.3 67.2 + - - +
853I VAL 3.0 1.6 - - - -
854I ALA* 3.0 12.7 + - + +
855I HIS* 2.8 31.4 + - + +
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Residues in contact with ALA 852 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G TYR* 4.2 21.5 - - + -
843I PHE* 3.3 30.7 - - + -
848I GLU 3.5 4.0 + - - +
849I ALA 3.3 11.2 + - - +
851I LEU* 1.3 78.5 - - - +
853I VAL* 1.3 60.9 + - - +
855I HIS* 3.3 3.4 + - - -
856I GLY 3.2 3.6 + - - -
857I ILE* 2.8 43.2 + - + +
858I VAL* 4.0 3.8 - - + -
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Residues in contact with VAL 853 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849I ALA 3.0 19.3 - - - +
850I LEU* 3.0 17.9 - - + +
852I ALA* 1.3 77.9 - - - +
854I ALA* 1.3 56.2 + - - +
856I GLY* 2.7 26.2 + - - -
858I VAL* 3.0 36.6 - - + +
859I ASP* 4.6 0.7 - - - -
860I LEU* 4.2 28.0 - - + +
877I PRO* 4.1 15.9 - - + -
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Residues in contact with ALA 854 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ARG* 5.5 7.0 - - - +
42G ARG* 5.4 6.1 + - - -
45G LEU* 5.0 17.3 - - + -
850I LEU 2.8 13.9 + - - +
851I LEU* 3.0 14.3 + - + +
853I VAL* 1.3 75.7 - - - +
855I HIS* 1.3 63.6 + - + +
856I GLY 3.4 0.2 - - - -
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Residues in contact with HIS 855 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG* 5.8 9.3 + - + +
45G LEU* 3.6 25.9 + - + -
46G SER* 3.4 27.7 + - - -
148G VAL 5.2 0.9 - - - -
149G GLY* 3.7 4.7 - - - -
150G TYR* 3.7 42.5 + - + +
851I LEU* 2.8 22.1 + - + +
852I ALA* 3.9 7.6 - - - +
853I VAL 2.9 0.6 + - - -
854I ALA* 1.3 82.8 - - + +
856I GLY* 1.3 59.4 + - - +
857I ILE* 3.5 8.5 - - + +
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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
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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