Contacts of the helix formed by residues 767 - 776 (chain A) in PDB entry 2YD0
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 VAL 767 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A THR 5.0 0.4 - - - +
716A TRP* 3.6 59.2 - - + -
717A THR 4.3 2.0 - - - +
732A LEU* 3.8 15.9 - - + -
750A TYR* 5.1 2.7 - - + -
763A LEU* 4.8 5.2 - - + -
764A PRO* 3.3 32.3 - - + +
766A ASP* 1.3 78.5 - - + +
768A THR* 1.3 60.3 + - - +
769A LEU 3.3 2.9 - - - -
770A ALA* 3.1 8.4 + - - +
771A VAL* 2.8 41.3 + - + +
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Residues in contact with THR 768 (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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763A LEU* 3.7 14.9 + - + +
764A PRO 2.7 24.6 + - - -
765A VAL* 3.3 15.8 + - - -
767A VAL* 1.3 75.6 - - - +
769A LEU* 1.3 60.4 + - - +
771A VAL* 4.1 6.7 - - - -
772A PHE* 2.8 67.3 + - + +
797A GLU* 6.1 0.2 - - + -
800A GLN* 3.7 18.2 - - - +
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Residues in contact with LEU 769 (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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729A SER* 3.8 24.0 - - - +
730A GLN* 4.4 11.9 - - - +
733A LEU* 3.9 25.5 - - + +
765A VAL 4.5 1.0 + - - -
766A ASP 5.0 0.4 + - - +
767A VAL 3.3 0.6 - - - -
768A THR* 1.3 78.8 - - - +
770A ALA* 1.3 57.3 + - - +
772A PHE* 3.9 3.2 - - - +
773A ALA* 2.9 33.3 + - - +
799A SER 5.6 0.2 - - - -
800A GLN* 4.2 33.1 - - + +
803A PHE* 3.8 39.9 - - + -
804A ALA* 5.3 0.9 - - + +
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Residues in contact with ALA 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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716A TRP* 4.9 7.0 - - + -
729A SER 5.3 0.8 + - - +
732A LEU* 3.8 39.9 - - + +
733A LEU* 3.8 14.0 - - - +
736A CYS* 4.4 11.7 - - - -
747A ALA* 4.6 1.6 - - - -
766A ASP 5.7 0.2 - - - +
767A VAL* 3.1 10.8 + - - +
769A LEU* 1.3 78.5 - - - +
771A VAL* 1.3 57.8 + - - +
773A ALA* 3.5 1.7 + - - +
774A VAL* 3.1 36.6 + - - +
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Residues in contact with VAL 771 (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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716A TRP* 4.0 13.9 - - + -
747A ALA* 4.0 10.3 - - - +
750A TYR* 3.9 18.8 - - + -
751A PHE* 3.7 41.9 - - + +
763A LEU* 4.2 16.4 - - + -
767A VAL* 2.8 38.9 + - + +
768A THR* 3.8 7.2 - - - +
770A ALA* 1.3 73.7 - - - +
772A PHE* 1.3 63.9 + - + +
774A VAL* 3.5 2.8 + - - +
775A GLY 3.1 16.3 + - - -
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Residues in contact with PHE 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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751A PHE* 4.5 5.2 - + - -
754A TRP* 3.9 34.5 - + - -
763A LEU* 3.9 17.5 - - + -
768A THR* 2.8 47.5 + - + +
769A LEU* 4.0 2.2 - - - +
771A VAL* 1.3 77.0 - - + +
773A ALA* 1.3 61.0 + - - +
775A GLY 3.1 0.4 + - - +
776A ALA* 2.9 33.1 + - - +
785A LEU* 3.5 22.6 - - + +
797A GLU* 4.6 12.8 - - + -
800A GLN* 4.0 22.2 - - + +
801A ILE* 4.0 24.0 - - + -
804A ALA* 3.6 15.3 - - + -
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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
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733A LEU* 3.9 19.1 - - + -
736A CYS* 6.2 0.7 - - + -
737A VAL* 4.8 9.2 - - + -
769A LEU 2.9 17.4 + - - +
770A ALA 3.7 4.7 - - - +
772A PHE* 1.3 78.7 - - - +
774A VAL* 1.3 62.5 + - + +
776A ALA* 3.7 5.4 + - - +
777A GLN* 3.5 22.7 + - - +
803A PHE* 4.7 10.3 - - + -
804A ALA* 3.7 14.4 - - + +
807A ARG* 5.0 6.8 - - + +
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Residues in contact with VAL 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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736A CYS* 3.8 25.6 - - + +
744A VAL* 4.2 13.2 - - + +
747A ALA* 3.7 17.7 - - + -
748A GLU* 3.8 43.3 - - + +
751A PHE* 5.9 0.2 - - + -
770A ALA 3.1 19.3 + - - +
771A VAL 4.0 2.0 - - - +
773A ALA* 1.3 78.2 - - + +
775A GLY* 1.3 64.5 + - - +
777A GLN* 3.3 22.3 + - - +
778A SER 4.7 0.7 + - - -
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Residues in contact with GLY 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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751A PHE* 3.5 40.6 - - - -
771A VAL 3.1 6.5 + - - -
772A PHE 3.1 6.3 + - - -
774A VAL* 1.3 78.8 - - - +
776A ALA* 1.3 59.5 + - - +
777A GLN 3.2 1.7 + - - -
778A SER* 3.5 9.9 + - - -
781A GLY* 3.2 22.0 - - - -
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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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772A PHE 2.9 17.2 + - - +
773A ALA 4.1 4.0 - - - +
774A VAL 3.2 0.4 - - - -
775A GLY* 1.3 73.6 - - - +
777A GLN* 1.3 63.3 + - - +
778A SER 3.2 8.5 + - - +
782A TRP* 3.6 34.7 - - + +
785A LEU* 3.8 13.7 - - + +
804A ALA* 3.4 27.6 - - + +
805A LEU* 4.6 0.2 - - - -
808A THR* 4.2 9.7 + - - -
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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