Contacts of the helix formed by residues 867 - 876 (chain A) in PDB entry 3SQ1
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 ASP 867 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834A PRO* 2.9 29.2 + - + +
835A LEU 3.8 5.2 - - - +
836A ARG* 3.7 38.1 - - - +
837A GLU* 5.0 1.2 + - - +
865A TRP 3.3 0.6 + - - -
866A MET* 1.3 70.7 - - - +
868A TYR* 1.3 55.3 + - - +
869A THR* 3.3 12.3 + - - -
870A VAL* 3.1 35.5 + - - +
871A LEU* 3.0 29.6 + - - +
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Residues in contact with TYR 868 (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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771A PHE* 3.4 20.8 - + + -
772A ARG* 3.4 62.8 + - + +
774A LEU 4.8 3.9 + - - -
779A ILE* 3.6 31.2 - - + -
836A ARG* 5.6 0.6 - - - +
863A LEU* 4.6 11.8 + - - +
866A MET* 3.2 42.6 + - + +
867A ASP* 1.3 70.7 + - - +
869A THR* 1.3 60.8 + - - +
871A LEU* 4.0 5.2 - - + -
872A LEU 3.0 24.1 + - - -
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Residues in contact with THR 869 (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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771A PHE* 5.1 2.0 - - - -
772A ARG* 5.0 8.2 + - - +
867A ASP* 3.3 9.0 + - - -
868A TYR* 1.3 79.1 - - - +
870A VAL* 1.3 63.2 + - + +
872A LEU* 3.8 4.9 - - - +
873A GLU* 3.1 29.9 + - + +
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Residues in contact with VAL 870 (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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834A PRO* 3.8 19.3 - - + -
867A ASP* 3.1 33.3 + - + +
869A THR* 1.3 75.1 - - + +
871A LEU* 1.3 68.0 + - - +
873A GLU* 3.3 5.6 + - - +
874A LYS* 2.9 53.0 + - + +
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Residues in contact with LEU 871 (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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741A VAL* 5.2 3.6 - - + -
771A PHE* 4.2 17.5 - - + -
779A ILE* 3.8 58.6 - - + +
833A LEU* 3.9 17.0 - - + -
834A PRO* 3.9 13.2 - - + +
866A MET* 4.1 7.6 - - + -
867A ASP 3.0 19.6 + - - +
868A TYR* 3.4 9.0 - - - +
870A VAL* 1.3 77.0 - - - +
872A LEU* 1.3 64.5 + - + +
874A LYS* 5.0 1.6 - - - +
875A THR* 2.8 44.2 + - + +
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Residues in contact with LEU 872 (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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741A VAL* 6.4 0.2 - - + -
764A PHE* 6.1 0.2 - - + -
767A PHE* 3.9 17.9 - - + -
768A GLU* 4.2 20.6 - - + +
771A PHE* 3.6 34.5 - - + -
772A ARG* 5.9 0.2 - - - +
868A TYR 3.0 18.5 + - - +
869A THR* 3.8 4.5 - - - +
871A LEU* 1.3 80.4 - - + +
873A GLU* 1.3 64.6 + - - +
875A THR* 4.5 1.3 - - - -
876A PHE* 3.0 36.1 + - + +
877A ILE* 2.9 45.4 + - + -
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Residues in contact with GLU 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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869A THR* 3.1 20.2 + - + +
870A VAL* 3.8 5.8 - - - +
872A LEU* 1.3 79.1 - - - +
874A LYS* 1.3 61.5 + - + +
877A ILE* 3.4 38.3 - - - +
878A LYS* 2.9 57.1 + - - +
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Residues in contact with LYS 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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803A PHE* 3.5 30.3 - - - -
834A PRO* 5.0 3.9 - - - +
870A VAL* 2.9 40.1 + - + +
871A LEU* 4.3 1.8 - - - +
873A GLU* 1.3 81.6 - - + +
875A THR* 1.3 67.0 + - + +
878A LYS* 3.9 11.5 - - + +
879A PRO* 3.6 14.6 - - - +
11T A 4.4 10.4 + - - +
12T G 2.7 42.4 + - - +
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Residues in contact with THR 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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731A GLU* 5.2 0.5 - - - +
737A THR* 4.8 3.3 - - - +
738A PRO* 3.8 25.4 - - + +
741A VAL* 3.2 31.4 - - - +
745A LEU* 3.7 4.2 - - - +
779A ILE 5.3 2.2 - - - +
781A SER* 3.7 22.9 - - - +
871A LEU* 2.8 28.6 + - + +
874A LYS* 1.3 84.7 - - + +
876A PHE* 1.3 60.6 + - - +
879A PRO* 3.3 17.5 - - - +
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Residues in contact with PHE 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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741A VAL* 4.2 9.2 - - + -
744A ALA* 3.7 25.8 - - + -
745A LEU* 3.6 32.7 - - + +
748A CYS* 3.8 21.1 - - - -
764A PHE* 3.6 29.6 - + - -
767A PHE* 3.6 32.5 - + + -
768A GLU* 5.5 1.1 - - - -
872A LEU* 3.0 31.8 + - + +
874A LYS 3.6 0.2 - - - -
875A THR* 1.3 82.8 + - - +
877A ILE* 1.3 74.6 + - + +
878A LYS 3.4 0.9 - - - -
879A PRO* 3.3 2.3 - - - +
880A LEU* 3.0 32.2 + - + +
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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