Contacts of the helix formed by residues 771 - 779 (chain A) in PDB entry 3T06
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 PRO 771 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A MET* 1.3 90.5 - - + +
772A ARG* 1.3 65.7 + - - +
773A GLU* 3.7 14.1 - - + +
774A GLU* 2.9 45.0 + - + +
775A LEU* 3.1 10.2 + - - +
846A LYS* 4.6 3.1 - - - +
850E GLU* 3.3 42.4 - - + +
852E ARG* 6.1 4.7 - - + -
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Residues in contact with ARG 772 (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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765A LYS* 3.1 46.4 + - - +
766A LYS* 5.1 1.4 - - - +
768A ASN* 3.0 30.7 + - - +
770A MET 3.5 5.2 + - - -
771A PRO* 1.3 70.1 - - - +
773A GLU* 1.3 67.2 + - - +
775A LEU* 3.3 17.0 + - - +
776A ALA* 2.9 29.7 + - - +
851E SER* 5.0 6.5 - - - +
852E ARG* 5.1 20.2 - - + +
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Residues in contact with GLU 773 (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 PRO* 3.7 12.0 - - + +
772A ARG* 1.3 85.7 + - - +
774A GLU* 1.3 61.0 + - + +
776A ALA* 3.6 9.0 + - - +
777A ARG* 3.4 37.9 + - - +
849E LYS 3.8 18.4 - - - +
850E GLU* 3.8 6.5 - - + +
851E SER* 2.9 42.0 + - - -
852E ARG* 5.1 1.2 + - - +
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Residues in contact with GLU 774 (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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770A MET* 3.9 12.1 - - - +
771A PRO* 2.9 34.9 + - + +
773A GLU* 1.3 76.4 - - + +
775A LEU* 1.3 66.5 + - - +
777A ARG* 3.3 28.4 + - - +
778A LEU* 3.4 11.3 + - - +
839A ALA* 5.8 0.9 - - - +
842A LEU* 4.2 18.3 - - + +
846A LYS* 2.5 39.9 + - - -
850E GLU* 4.9 1.4 - - - +
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Residues in contact with LEU 775 (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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761A TYR* 4.1 20.2 - - + -
764A MET* 4.1 17.9 - - + +
765A LYS* 3.9 39.7 - - + +
770A MET* 3.8 33.1 - - + +
771A PRO 3.1 10.7 + - - +
772A ARG* 3.5 18.2 - - - +
774A GLU* 1.3 75.1 - - - +
776A ALA* 1.3 66.6 + - - +
778A LEU* 2.8 15.7 + - + +
779A PHE* 3.0 31.8 + - + -
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Residues in contact with ALA 776 (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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761A TYR* 6.4 0.2 - - - -
772A ARG 2.9 18.2 + - - +
773A GLU* 3.6 10.3 - - - +
775A LEU* 1.3 74.7 - - - +
777A ARG* 1.3 62.9 + - + +
779A PHE 4.5 4.9 - - - -
780A PRO* 3.1 29.6 - - + +
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Residues in contact with ARG 777 (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 GLU* 3.4 33.9 + - - +
774A GLU* 3.3 23.8 + - - +
775A LEU 3.1 1.4 - - - -
776A ALA* 1.3 81.6 - - + +
778A LEU* 1.3 59.3 + - - +
780A PRO* 4.0 10.6 - - - +
832A PHE 5.6 0.3 - - - +
835A TYR* 3.6 61.9 + - + +
836A GLN 5.0 1.0 + - - -
839A ALA* 4.2 5.2 - - + +
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Residues in contact with LEU 778 (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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764A MET* 4.8 2.9 - - + -
770A MET* 4.3 12.6 - - + -
774A GLU 3.4 10.0 + - - +
775A LEU* 2.8 11.2 + - + +
777A ARG* 1.3 79.3 - - - +
779A PHE* 1.3 83.2 + - + +
780A PRO* 3.4 7.5 - - - +
832A PHE* 4.7 6.8 - - - +
836A GLN* 5.4 5.3 - - + +
839A ALA* 4.1 22.0 - - + -
840A LEU* 5.2 4.7 - - + -
843A ILE* 4.1 30.1 - - + -
871A LEU* 4.5 10.8 - - + -
875A ILE* 3.2 33.0 - - + +
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Residues in contact with PHE 779 (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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756A LEU* 4.4 11.2 - - + -
760A PHE* 4.2 19.7 - - + -
761A TYR* 3.4 55.1 + + + -
764A MET* 4.5 7.9 - - + -
775A LEU* 3.0 23.2 + - + +
776A ALA* 3.5 7.2 - - - +
778A LEU* 1.3 100.6 - - + +
780A PRO* 1.3 70.0 - - - +
781A ASN 3.4 2.4 + - - -
782A LEU* 3.9 32.0 + - + -
783A PRO* 5.7 0.2 - - - +
832A PHE* 4.3 13.0 - + - -
871A LEU* 4.8 7.2 - - + -
875A ILE* 4.2 21.3 - - + -
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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