Contacts of the helix formed by residues 831 - 843 (chain A) in PDB entry 3M62
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 831 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A SER 3.3 8.4 + - - +
830A PHE* 1.3 87.9 - - - +
832A ARG* 1.3 68.2 + - - +
833A ASN* 3.3 29.8 + - - +
834A LEU* 3.0 40.2 + - + +
835A PHE* 3.9 5.9 - - - -
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Residues in contact with ARG 832 (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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830A PHE* 4.0 13.9 - - + -
831A ASN* 1.3 72.9 + - - +
833A ASN* 1.3 58.5 + - - +
835A PHE* 2.7 32.0 + - + +
836A VAL* 3.5 24.0 + - + +
858A LEU* 4.4 19.7 - - - +
861A ALA* 4.2 16.4 - - + +
862A ASN* 3.0 31.8 + - - +
865A GLU* 4.2 37.1 + - + +
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Residues in contact with ASN 833 (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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831A ASN* 3.1 21.1 + - - +
832A ARG* 1.3 78.1 - - - +
834A LEU* 1.3 63.4 + - - +
836A VAL* 3.0 27.5 + - - +
837A ARG* 3.0 40.2 + - - +
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Residues in contact with LEU 834 (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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773A ASN* 4.2 9.4 - - + +
776A LEU* 3.7 30.3 - - + +
777A GLU* 3.7 27.6 - - + +
780A VAL* 3.8 26.6 - - + +
829A SER 3.5 24.2 - - - +
830A PHE* 5.0 0.9 - - - -
831A ASN* 3.0 33.7 + - + +
832A ARG 3.0 0.4 + - - -
833A ASN* 1.3 77.7 - - - +
835A PHE* 1.3 58.8 + - + +
837A ARG* 3.5 6.8 + - - +
838A ALA* 3.0 27.4 + - - +
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Residues in contact with PHE 835 (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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773A ASN* 4.9 2.2 - - - -
776A LEU* 3.7 24.9 - - + -
807A THR* 5.3 0.4 - - + -
810A TYR* 3.8 35.7 - + - -
830A PHE* 3.9 25.1 - + - -
831A ASN 3.9 9.4 - - - -
832A ARG* 2.7 21.2 + - + +
834A LEU* 1.3 73.4 - - + +
836A VAL* 1.3 60.2 - - - +
838A ALA* 3.5 4.8 + - - +
839A VAL* 3.1 34.0 + - - +
857A LEU* 3.7 28.1 - - + +
858A LEU* 4.9 4.9 - - + -
860A PHE* 3.8 26.5 - + - -
861A ALA* 3.7 26.7 - - + -
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Residues in contact with VAL 836 (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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832A ARG* 3.8 39.5 - - + +
833A ASN* 3.0 25.5 + - - +
835A PHE* 1.3 77.4 - - + +
837A ARG* 1.3 59.2 + - + +
839A VAL* 3.2 9.8 + - + +
840A ASP* 3.0 28.0 + - + +
858A LEU* 4.8 9.6 - - + -
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Residues in contact with ARG 837 (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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780A VAL* 2.8 42.8 + - + -
781A GLY* 4.9 4.4 - - - -
833A ASN* 3.0 36.9 + - - +
834A LEU* 3.9 7.0 - - - +
836A VAL* 1.3 76.1 - - + +
838A ALA* 1.3 64.2 + - - +
840A ASP* 3.3 8.5 + - - +
841A ILE* 3.0 35.3 + - + +
844A ARG* 5.8 4.2 - - - +
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Residues in contact with ALA 838 (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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776A LEU* 4.2 7.0 - - + -
780A VAL* 3.7 18.0 - - + +
803A LEU* 3.9 19.9 - - + +
807A THR* 4.3 11.0 - - + -
834A LEU 3.0 18.6 + - - +
835A PHE* 3.6 9.0 - - - +
836A VAL 3.3 0.2 - - - -
837A ARG* 1.3 76.4 - - - +
839A VAL* 1.3 56.5 + - - +
841A ILE* 3.3 0.9 + - - +
842A LEU* 2.8 36.5 + - - +
857A LEU* 4.6 2.7 - - + -
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Residues in contact with VAL 839 (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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835A PHE 3.1 18.1 + - - +
836A VAL* 3.2 11.4 + - + +
838A ALA* 1.3 76.0 - - - +
840A ASP* 1.3 64.7 + - + +
842A LEU* 3.6 7.6 + - - +
843A GLY* 3.2 18.9 + - - -
854A ILE* 3.8 45.1 - - + +
857A LEU* 4.0 18.4 - - + -
858A LEU* 4.2 23.1 - - + -
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Residues in contact with ASP 840 (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 VAL* 3.0 17.8 + - + +
837A ARG* 3.7 7.7 - - - +
839A VAL* 1.3 82.8 - - + +
841A ILE* 1.3 62.9 + - - +
843A GLY* 3.5 7.8 + - - -
844A ARG* 3.2 40.5 + - - +
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Residues in contact with ILE 841 (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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779A LEU 3.9 8.1 - - - +
780A VAL* 3.8 38.6 - - + +
800A LYS* 3.4 28.9 - - + +
803A LEU* 3.7 15.9 - - + -
837A ARG* 3.0 26.6 + - + +
838A ALA 3.8 2.9 - - - +
840A ASP* 1.3 75.7 - - - +
842A LEU* 1.3 66.8 + - - +
844A ARG* 3.0 51.6 + - - +
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Residues in contact with LEU 842 (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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800A LYS* 4.2 0.9 - - - +
803A LEU* 3.9 14.6 - - + -
804A LYS* 3.8 30.1 - - + +
807A THR* 3.8 20.6 - - + +
838A ALA 2.8 28.3 + - - +
839A VAL* 4.0 5.8 - - - +
841A ILE* 1.3 72.2 - - + +
843A GLY* 1.3 57.5 + - - +
844A ARG 3.2 4.3 + - - -
845A LYS 3.4 11.8 + - - +
848A LEU* 3.5 44.0 - - + +
849A ALA* 4.1 17.2 + - + -
853A PHE* 3.8 20.0 - - + -
854A ILE* 5.4 3.1 - - + -
857A LEU* 4.6 9.6 - - + -
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Residues in contact with GLY 843 (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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839A VAL 3.2 12.2 + - - -
840A ASP* 3.9 7.6 - - - -
841A ILE 3.2 1.6 - - - -
842A LEU* 1.3 75.7 - - - +
844A ARG* 1.3 58.3 + - - +
845A LYS 3.4 5.4 - - - -
846A THR* 4.8 8.5 + - - +
849A ALA* 6.0 1.6 - - - -
854A ILE* 5.2 8.9 - - - +
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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