Contacts of the helix formed by residues 769 - 781 (chain A) in PDB entry 2YIC
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 GLY 769 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A GLU* 4.3 12.1 - - - -
510A GLY* 6.1 0.9 - - - -
512A GLU* 5.5 2.9 - - - -
712A ASP* 5.6 0.7 - - - -
742A TYR* 3.8 8.5 - - - -
744A ARG* 4.3 4.8 - - - +
767A LYS 4.3 0.2 + - - -
768A ARG* 1.3 76.6 - - - +
770A SER* 1.4 59.7 + - - -
771A ARG 3.2 4.2 + - - -
772A LYS* 3.3 7.3 + - - +
773A ALA* 3.0 26.6 + - - +
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Residues in contact with SER 770 (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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486A LEU* 4.0 13.6 - - - +
490A GLU* 4.5 1.6 + - - -
510A GLY* 5.9 4.7 - - - -
512A GLU* 4.8 14.5 + - - -
513A THR* 2.8 30.1 + - - -
711A GLY 3.4 10.4 + - - -
712A ASP* 4.1 21.3 + - - +
714A PRO* 4.4 1.7 - - - +
742A TYR* 4.5 4.8 + - - -
769A GLY* 1.4 70.4 - - - -
771A ARG* 1.4 55.1 - - - +
773A ALA* 3.8 6.3 - - - +
774A TYR* 2.9 31.4 + - - +
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Residues in contact with ARG 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 4.0 11.0 - - + +
486A LEU* 4.0 25.4 - - + +
487A ASN* 3.0 39.2 + - - +
490A GLU* 3.1 35.8 + - + +
512A GLU* 6.0 1.3 - - + +
769A GLY 3.2 0.6 - - - -
770A SER* 1.4 76.0 - - - +
772A LYS* 1.4 67.8 + - - +
774A TYR 3.6 0.5 + - - -
775A THR* 2.7 41.1 + - - -
792A ALA 4.9 0.6 + - - -
793A LEU* 3.6 29.9 - - - +
796A TYR* 3.5 47.0 - - - +
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Residues in contact with LYS 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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490A GLU* 4.7 3.4 + - - +
768A ARG* 4.5 14.8 - - + -
769A GLY* 3.3 11.1 + - - +
771A ARG* 1.4 89.2 - - - +
773A ALA* 1.3 58.8 + - - +
775A THR* 3.6 5.4 + - - -
776A GLU* 3.1 46.9 + - - +
793A LEU* 6.4 1.6 - - - -
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Residues in contact with ALA 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ASP* 5.1 16.4 - - + +
768A ARG* 4.8 9.1 - - + +
769A GLY 3.0 17.4 + - - +
770A SER* 3.8 8.7 - - - +
772A LYS* 1.3 73.5 - - - +
774A TYR* 1.4 58.9 + - - +
776A GLU* 3.4 8.5 + - - +
777A ALA* 2.9 31.2 + - - +
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Residues in contact with TYR 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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479A GLN* 3.3 38.6 - - - +
482A ILE* 3.8 15.6 - - + +
483A LEU* 3.9 17.0 - - + -
486A LEU* 4.1 8.5 - - + -
712A ASP 5.3 2.4 + - - +
713A ASP* 5.7 0.7 - - - -
714A PRO* 3.6 30.7 - - + -
715A GLU* 2.7 45.6 + - + +
770A SER 2.9 20.7 + - - +
771A ARG 4.1 1.3 - - - +
773A ALA* 1.4 71.9 - - - +
775A THR* 1.4 64.4 + - - +
777A ALA* 3.5 4.3 + - + +
778A LEU* 3.1 52.2 + - + +
781A ARG* 4.4 10.1 - - - -
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Residues in contact with THR 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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483A LEU* 3.2 25.7 - - + +
771A ARG* 2.7 31.2 + - - +
772A LYS* 4.0 6.0 - - - -
774A TYR* 1.4 76.7 - - - +
776A GLU* 1.3 62.6 + - + +
778A LEU* 3.4 12.2 + - - +
779A ILE* 3.2 21.0 + - - +
784A ILE* 4.1 3.0 - - + +
789A ALA* 4.2 32.3 - - + +
792A ALA* 4.6 2.3 - - + +
793A LEU* 4.7 14.1 - - + +
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Residues in contact with GLU 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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768A ARG* 5.3 5.8 - - - +
772A LYS* 3.1 33.0 + - - +
773A ALA* 3.8 7.3 - - - +
775A THR* 1.3 73.0 - - + +
777A ALA* 1.3 60.3 + - - +
779A ILE* 3.4 8.9 + - - +
780A GLY* 3.1 23.9 + - - -
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Residues in contact with ALA 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 ALA 2.9 18.8 + - - +
774A TYR* 3.7 9.0 - - + +
775A THR 3.3 0.2 - - - -
776A GLU* 1.3 72.6 - - - +
778A LEU* 1.4 55.3 + - - +
780A GLY* 3.1 2.8 + - - -
781A ARG* 2.8 59.6 + - - +
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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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479A GLN* 3.6 43.7 - - + +
480A LYS* 5.7 0.7 - - - +
483A LEU* 4.0 21.3 - - + -
715A GLU* 3.9 1.3 - - - +
774A TYR* 3.1 62.8 + - + +
775A THR* 3.7 4.7 - - - +
776A GLU 3.4 0.2 - - - -
777A ALA* 1.4 75.2 - - - +
779A ILE* 1.4 58.8 + - - +
781A ARG* 4.7 3.6 - - - +
782A GLY 3.5 1.7 + - - -
783A ASP* 3.0 40.5 + - + +
784A ILE* 3.1 29.9 + - + -
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Residues in contact with ILE 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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775A THR 3.2 12.8 + - - +
776A GLU* 3.5 12.3 - - - +
777A ALA 3.2 0.2 - - - -
778A LEU* 1.4 76.6 - - - +
780A GLY* 1.3 62.1 + - - +
782A GLY* 3.4 12.8 + - - -
784A ILE* 3.8 19.9 - - + +
785A SER 5.7 2.0 - - - +
786A MET* 6.2 1.1 - - - -
789A ALA* 5.2 9.0 - - + -
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Residues in contact with GLY 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A GLU 3.1 13.5 + - - -
777A ALA* 3.1 4.6 + - - -
779A ILE* 1.3 73.4 - - - +
781A ARG* 1.3 55.2 + - - +
782A GLY* 3.1 8.8 + - - -
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Residues in contact with ARG 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO* 5.6 0.4 - - - +
479A GLN* 3.3 10.9 - - - +
713A ASP* 5.8 3.2 + - - -
715A GLU* 2.9 39.5 + - - -
774A TYR* 4.4 10.1 - - - -
777A ALA* 2.8 41.9 + - - +
778A LEU* 4.7 3.7 - - - +
780A GLY* 1.3 70.9 - - - +
782A GLY* 1.3 58.8 + - - +
783A ASP* 3.2 29.6 + - - +
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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