Contacts of the helix formed by residues 898 - 905 (chain C) in PDB entry 3LZB
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 GLU 898 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917B ILE* 2.9 28.0 - - + +
920B TYR* 4.1 6.6 - - - -
921B MET* 2.9 52.0 + - + +
924B ARG* 4.4 11.3 + - - +
894C ILE* 3.9 11.3 - - + +
895C PRO* 2.9 36.2 + - + +
897C SER* 1.3 79.3 + - - +
899C ILE* 1.3 60.3 + - - +
900C SER 3.4 2.0 + - - -
901C SER* 3.5 9.1 + - - -
902C ILE* 2.9 30.5 + - - +
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Residues in contact with ILE 899 (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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854C ILE* 4.0 17.9 - - + +
855C LYS* 3.5 30.5 - - + -
862C ILE* 5.0 0.2 - - + -
891C TYR* 3.6 41.3 - - + -
894C ILE* 3.8 16.8 - - + -
895C PRO 3.4 10.1 - - - +
896C ALA* 2.9 23.4 + - - +
897C SER 3.5 0.2 - - - -
898C GLU* 1.3 76.6 - - - +
900C SER* 1.3 63.1 + - - +
902C ILE* 3.2 9.0 + - + +
903C LEU* 2.9 48.1 + - + +
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Residues in contact with SER 900 (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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859C LEU* 3.7 25.3 - - - +
862C ILE* 4.2 17.7 - - - +
863C LEU* 4.1 17.9 - - - +
896C ALA 4.6 2.0 + - - -
897C SER 4.7 5.3 + - - -
898C GLU 3.4 0.2 - - - -
899C ILE* 1.3 73.4 - - - +
901C SER* 1.3 67.2 + - - +
903C LEU* 3.0 5.6 + - - +
904C GLU* 2.7 47.8 + - - +
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Residues in contact with SER 901 (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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917B ILE* 5.0 4.9 - - - +
921B MET* 3.6 32.3 - - - -
897C SER 4.3 3.5 + - - -
898C GLU* 3.7 11.2 + - - -
900C SER* 1.3 83.0 + - - +
902C ILE* 1.3 56.3 + - - +
904C GLU* 3.1 15.0 + - - +
905C LYS* 2.8 30.0 + - - +
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Residues in contact with ILE 902 (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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921B MET* 3.7 18.2 - - + -
891C TYR* 4.0 22.4 - - + -
894C ILE* 3.9 33.9 - - + -
898C GLU* 2.9 19.5 - - - +
899C ILE* 3.2 13.6 + - + +
901C SER* 1.3 70.6 - - - +
903C LEU* 1.3 67.8 + - + +
905C LYS* 3.4 7.3 + - - -
906C GLY 3.4 4.0 + - - -
907C GLU* 2.8 64.9 + - + +
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Residues in contact with LEU 903 (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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857C MET 5.2 1.6 - - - +
859C LEU* 4.1 16.8 - - + -
862C ILE* 4.4 12.3 - - + -
874C TRP* 3.8 27.8 - - + -
891C TYR* 3.8 20.9 - - + +
899C ILE* 2.9 49.4 + - + +
900C SER* 3.3 9.2 - - - +
902C ILE* 1.3 77.9 - - + +
904C GLU* 1.3 56.0 + - - +
906C GLY* 2.8 15.4 + - - -
907C GLU 3.2 17.7 - - - +
908C ARG* 2.8 37.2 + - - +
929C ILE* 4.3 1.7 - - - +
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Residues in contact with GLU 904 (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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859C LEU* 3.9 17.0 - - + -
863C LEU* 3.7 26.0 - - + +
900C SER* 2.7 38.3 + - - +
901C SER* 3.1 13.5 - - - +
903C LEU* 1.3 77.4 - - - +
905C LYS* 1.3 57.5 + - - +
906C GLY* 2.8 7.6 + - - -
929C ILE* 4.9 5.3 - - - +
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Residues in contact with LYS 905 (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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888A SER* 6.0 1.7 - - - -
889A LYS 5.4 0.2 - - - +
892A ASP* 3.5 30.9 - - - +
901C SER 2.8 16.6 + - - +
902C ILE* 3.9 9.0 - - - +
903C LEU 3.3 0.8 - - - -
904C GLU* 1.3 73.3 - - - +
906C GLY* 1.3 59.0 + - - +
907C GLU* 3.5 3.8 - - + +
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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