Contacts of the helix formed by residues 899 - 905 (chain A) in PDB entry 3F2B
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 899 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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860A GLU* 2.6 18.8 + - - -
873A TYR* 3.0 27.4 + - - -
896A VAL* 3.0 14.6 + - - +
897A GLY 3.1 1.4 - - - -
898A SER* 1.3 78.8 - - - +
900A PHE* 1.3 57.9 + - - +
901A VAL* 3.4 2.6 + - - +
902A ALA* 2.8 31.5 + - - +
903A THR* 3.0 10.2 + - - -
908A THR* 4.6 0.7 - - - +
912A PRO* 3.8 3.1 - - - -
960A PHE* 3.9 11.6 - - - -
963A PHE* 4.9 3.1 - - - -
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Residues in contact with PHE 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A ALA* 4.2 2.2 - - + -
845A TYR* 4.0 10.1 - + - -
853A VAL* 3.7 32.1 - - + -
856A ARG* 3.8 26.9 - - + -
857A LEU* 3.8 24.0 - - + -
860A GLU* 2.7 9.8 + - - +
899A SER* 1.3 71.1 - - - +
901A VAL* 1.3 56.2 + - - +
903A THR* 3.0 6.3 + - - -
904A MET* 2.8 70.1 + - + +
911A ASN* 3.8 11.7 - - - -
912A PRO* 3.3 22.4 - - + +
913A LEU* 3.5 31.9 - - + -
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Residues in contact with VAL 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A ILE* 4.0 13.2 - - + -
837A SER* 4.0 10.8 - - - +
857A LEU* 4.0 14.6 - - + -
860A GLU* 2.5 45.5 + - + +
861A LEU* 3.9 34.1 - - + -
864A ILE* 3.8 19.7 - - + -
873A TYR* 4.1 7.6 - - + -
900A PHE* 1.3 71.8 - - - +
902A ALA* 1.3 56.9 + - - +
904A MET* 3.2 7.2 + - - +
905A THR* 2.8 32.4 + - + +
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Residues in contact with ALA 902 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873A TYR* 3.7 15.8 - - + -
896A VAL* 3.5 21.3 - - + +
899A SER* 2.8 19.1 + - - +
901A VAL* 1.3 74.7 - - - +
903A THR* 1.3 64.3 + - - +
905A THR* 3.3 8.9 + - - -
906A GLU 3.1 15.4 + - - -
907A ILE* 3.1 33.2 + - + -
908A THR* 3.6 6.1 - - + +
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Residues in contact with THR 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A SER 3.0 6.2 + - - -
900A PHE* 3.0 11.1 + - - -
902A ALA* 1.3 75.7 - - - +
904A MET* 1.3 82.1 + - + +
906A GLU* 3.0 19.6 + - - +
908A THR* 3.5 16.6 - - - +
909A GLU* 5.1 2.5 - - - +
910A VAL 2.7 28.7 + - - +
911A ASN* 3.9 20.6 - - + +
912A PRO* 3.2 16.3 - - - +
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Residues in contact with MET 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A MET* 4.0 6.4 - - - +
837A SER* 3.8 30.1 - - - +
840A ARG* 3.4 35.4 - - + +
841A ALA* 3.5 31.0 - - - -
844A ILE* 4.0 19.1 - - + -
845A TYR* 4.8 2.5 - - + -
900A PHE* 2.8 62.3 + - + +
901A VAL 3.7 4.3 - - - +
903A THR* 1.3 90.1 - - + +
905A THR* 1.3 58.8 + - - +
906A GLU* 3.3 2.0 + - - +
911A ASN* 4.8 1.6 - - - +
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Residues in contact with THR 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A ILE* 4.3 21.8 - - + +
836A MET* 3.6 28.7 - - + -
837A SER* 4.4 5.6 - - - -
873A TYR* 4.0 8.9 + - + -
877A HIS* 2.7 32.8 + - - -
901A VAL* 2.8 37.3 + - + +
902A ALA* 3.3 12.3 + - - -
903A THR 3.2 0.2 - - - -
904A MET* 1.3 73.8 - - - +
906A GLU* 1.3 63.1 + - - +
907A ILE* 3.2 14.8 - - - +
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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