Contacts of the helix formed by residues 872 - 880 (chain A) in PDB entry 6DBU
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 872 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A ILE* 5.1 6.5 - - - -
868A VAL* 5.2 3.4 - - - +
870A ARG* 2.9 30.7 + - + +
871A MET* 1.3 78.3 - - - +
873A GLY* 1.3 63.6 + - - +
874A ASN 3.3 3.3 + - - -
875A TYR* 3.0 29.5 + - - +
876A ALA* 3.2 19.2 + - - +
17G C 2.5 40.1 + - - +
18G A 2.9 29.6 + - - -
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Residues in contact with GLY 873 (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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820A ILE* 5.6 2.6 - - - +
872A ASN* 1.3 77.1 - - - +
874A ASN* 1.3 63.1 + - - +
876A ALA* 3.3 5.9 + - - +
877A ARG* 2.8 46.9 + - - +
18G A 5.3 1.8 - - - -
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Residues in contact with ASN 874 (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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865A LEU* 6.1 1.0 - - - +
872A ASN* 3.3 5.8 + - - +
873A GLY* 1.3 73.7 - - - +
875A TYR* 1.3 64.8 + - - +
877A ARG* 2.9 21.1 + - - +
878A ARG* 3.0 52.3 + - - +
18G A 4.1 19.2 + - - +
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Residues in contact with TYR 875 (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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827A TYR* 3.3 25.9 - + - -
859A LEU* 5.0 3.8 - - - +
865A LEU* 4.1 37.4 - - + +
866A LYS 4.4 3.6 - - - -
867A PRO* 6.0 0.4 - - + -
868A VAL* 3.9 32.3 - - + -
871A MET* 4.0 32.1 - - + -
872A ASN* 3.0 24.5 + - - +
874A ASN* 1.3 79.6 - - - +
876A ALA* 1.3 59.2 + - - +
878A ARG* 4.6 3.4 - - - +
879A LEU* 2.9 72.4 + - + +
18G A 5.6 0.4 - - - +
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Residues in contact with ALA 876 (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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819A ASP* 5.0 10.3 - - + +
820A ILE* 5.2 2.2 - - + +
823A ALA* 4.0 26.2 - - + -
871A MET 4.7 3.4 - - - +
872A ASN 3.2 22.1 + - - +
873A GLY* 3.5 6.1 - - - +
874A ASN 3.2 0.2 - - - -
875A TYR* 1.3 80.6 - - - +
877A ARG* 1.3 64.1 + - + +
879A LEU* 5.0 0.7 - - - -
880A MET* 3.3 38.4 + - + +
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Residues in contact with ARG 877 (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 GLY* 2.8 52.4 + - - +
874A ASN* 2.9 19.1 + - - +
876A ALA* 1.3 78.9 - - + +
878A ARG* 1.3 64.7 + - + +
879A LEU 3.4 0.2 + - - -
880A MET* 3.6 8.8 + - - +
881A THR* 3.6 14.6 - - - +
912A LYS* 5.6 11.7 - - - +
916A ARG* 3.9 31.2 - - - +
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Residues in contact with ARG 878 (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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863A MET* 4.2 21.0 + - - +
864A LYS* 3.5 12.9 + - - +
865A LEU* 3.1 41.6 - - + +
874A ASN* 3.0 44.7 + - - +
875A TYR* 4.3 1.3 - - - +
877A ARG* 1.3 76.9 - - - +
879A LEU* 1.3 57.5 + - - +
881A THR* 2.7 28.6 + - + +
884A ALA* 4.8 1.0 - - - +
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Residues in contact with LEU 879 (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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823A ALA* 5.0 8.3 - - + +
826A PHE* 6.0 2.2 - - + -
827A TYR* 4.2 20.9 - - + +
830A PHE* 5.8 11.3 - - + -
859A LEU* 3.6 31.4 - - + -
865A LEU* 3.9 17.9 - - + +
875A TYR* 2.9 53.9 + - + +
876A ALA* 4.5 1.8 - - - +
878A ARG* 1.3 75.0 - - - +
880A MET* 1.3 56.2 + - + +
881A THR* 2.6 25.2 + - - +
884A ALA* 3.3 23.2 - - + +
885A VAL* 5.5 0.2 - - - +
905A MET* 4.4 2.4 - - - +
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Residues in contact with MET 880 (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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819A ASP* 3.9 20.9 - - + +
823A ALA* 3.9 32.5 - - + +
826A PHE* 4.4 12.1 - - + -
876A ALA* 3.3 25.7 + - + +
877A ARG* 3.6 5.7 + - - +
878A ARG 3.5 0.4 - - - -
879A LEU* 1.3 75.3 - - + +
881A THR* 1.3 64.6 + - - +
905A MET* 3.6 18.2 - - + -
908A TYR* 3.2 45.3 - - + +
909A LEU* 3.2 19.1 - - + +
912A LYS* 4.6 13.2 - - + -
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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